@article{chanwala_functions_2026,
	title = {The functions of long noncoding {RNAs} in plants},
	volume = {89},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S136952662500144X},
	doi = {10.1016/j.pbi.2025.102830},
	abstract = {Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.},
	urldate = {2025-12-18},
	journal = {Current Opinion in Plant Biology},
	author = {Chanwala, Jeky and Rosenkranz, Isabell and Kindgren, Peter},
	month = feb,
	year = {2026},
	pages = {102830},
}

Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.

@article{rosenkranz_cis-_2025,
	title = {Cis- and trans-action of the cold-induced {lncRNAs}, {SVALKA} and {SVALNA}, regulate {CBF1} and {CBF3} in {Arabidopsis}},
	volume = {26},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-025-00568-5},
	doi = {10.1038/s44319-025-00568-5},
	abstract = {Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.},
	number = {20},
	urldate = {2025-11-07},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Rosenkranz, Isabell and Mermet, Sarah and Zacharaki, Vasiliki and Kindgren, Peter},
	month = oct,
	year = {2025},
	note = {Num Pages: 5087},
	keywords = {Arabidopsis, Cold Response, Epigenetic Regulation, Long Non-coding RNAs},
	pages = {5070--5087},
}

Long noncoding RNAs (lncRNAs) are emerging as key regulatory players of coding gene expression in eukaryotes. Here, we investigate the roles of the lncRNAs SVALKA (SVK) and SVALNA (SVN) in regulating CBF1 and CBF3 gene expression in Arabidopsis under cold stress conditions. We integrated omics approaches, together with genetics and molecular biology, to uncover the transcriptional dynamics and regulatory mechanisms of SVK and SVN. Our results demonstrate that SVK functions as a cis- and trans-acting lncRNA, regulating both CBF1 and CBF3 through RNAPII collision and chromatin remodeling, while SVN serves a cis role by negatively regulating CBF3 via a RNAPII collision mechanism. We identified isoforms of SVK, originating from distinct transcription start sites and undergo alternative splicing which might be important to adapt stability, crucial for the regulatory functions. Furthermore, we show that two positionally conserved lncRNAs, originating from the upstream antisense strand of neighboring genes, can have different molecular mechanisms to regulate their targets. This study elucidates the complex interplay of lncRNAs in gene regulation, highlighting their essential roles in modulating responses to environmental stresses. Our findings contribute to a deeper understanding of the mechanisms underlying lncRNA functionality and their significance in gene regulatory networks in eukaryotes.

@article{zacharaki_convergent_2025,
	title = {Convergent antisense transcription primes hosting genes for stress responsiveness in plants},
	volume = {18},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S167420522500351X},
	doi = {10.1016/j.molp.2025.10.001},
	abstract = {Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.},
	number = {11},
	urldate = {2025-11-07},
	journal = {Molecular Plant},
	author = {Zacharaki, Vasiliki and Quevedo, Marti and Nardeli, Sarah Muniz and Meena, Shiv Kumar and Monte, Elena and Kindgren, Peter},
	month = nov,
	year = {2025},
	keywords = {Antisense transcription, Arabidopsis, Cold acclimation, Transporters, antisense transcription, cold acclimation, transporters},
	pages = {1920--1931},
}

Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. In this study, we characterize the regulation mediated by long non-coding transcription that initiates on the complementary strand in the 5ʹ end of coding genes (convergent antisense transcription, CASt). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes encoding functional transporters in Arabidopsis, such as the AMINO ACID PERMEASE (AAP) transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in rice AAP genes based on the presence of a long first intron and CASt. Collectively, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.

@article{chanwala_tug--war_2025,
	title = {The tug-of-war between growth and cold tolerance in plants: how to create resilient crops with maintained biomass},
	volume = {0},
	issn = {1674-2052},
	shorttitle = {The tug-of-war between growth and cold tolerance in plants},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(25)00396-X},
	doi = {10.1016/j.molp.2025.11.009},
	language = {English},
	number = {0},
	urldate = {2025-11-28},
	journal = {Molecular Plant},
	publisher = {Elsevier},
	author = {Chanwala, Jeky and Kindgren, Peter},
	month = nov,
	year = {2025},
}

@article{meena_antisense_2024,
	title = {Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in {Arabidopsis}},
	volume = {36},
	issn = {1532-298X},
	doi = {10.1093/plcell/koae160},
	abstract = {Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.},
	language = {eng},
	number = {9},
	journal = {The Plant Cell},
	author = {Meena, Shiv Kumar and Quevedo, Marti and Nardeli, Sarah Muniz and Verez, Clément and Bhat, Susheel Sagar and Zacharaki, Vasiliki and Kindgren, Peter},
	month = sep,
	year = {2024},
	keywords = {Arabidopsis, Arabidopsis Proteins, Cold Temperature, Cold-Shock Response, Gene Expression Regulation, Plant, RNA, Antisense, RNA, Messenger, Stress, Physiological, Transcription Factors, Transcription, Genetic},
	pages = {3467--3482},
}

Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the poly(A) signal of genes (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady-state RNA techniques to identify biologically relevant players in stress responses.

@article{bhat_nuclear_2024,
	title = {The nuclear exosome subunit {HEN2} acts independently of the core exosome to assist transcription in {Arabidopsis}},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae503},
	doi = {10.1093/plphys/kiae503},
	abstract = {Regulation of gene expression is at the frontier of plant responses to various external stimuli including stress. RNA polymerase-based transcription and post-transcriptional degradation of RNA play vital roles in this regulation. Here, we show that HUA ENHANCER 2 (HEN2), a co-factor of the nuclear exosome complex, influences RNAPII transcription elongation in Arabidopsis (Arabidopsis thaliana) under cold conditions. Our results demonstrate that a hen2 mutant is cold sensitive and undergoes substantial transcriptional changes compared to wild type when exposed to cold conditions. We found an accumulation of 5’ fragments from a subset of genes (including C-repeat binding factors 1-3 [CBF1-3]) that do not carry over to their 3’ ends. In fact, hen2 mutants have lower levels of full-length mRNA for a subset of genes. This distinct 5’-end accumulation and 3’-end depletion was not observed in other NEXT complex members or core exosome mutants, highlighting HEN2’s distinctive role. We further used RNAPII-associated nascent RNA to confirm the transcriptional phenotype is a result of lower active transcription specifically at the 3’-end of these genes in a hen2 mutant. Taken together, our data point to the unique role of HEN2 in maintaining RNAPII transcription dynamics especially highlighted under cold stress.},
	urldate = {2024-09-27},
	journal = {Plant Physiology},
	author = {Bhat, Susheel Sagar and Asgari, Mishaneh and Mermet, Sarah and Mishra, Priyanka and Kindgren, Peter},
	month = sep,
	year = {2024},
	pages = {kiae503},
}

Regulation of gene expression is at the frontier of plant responses to various external stimuli including stress. RNA polymerase-based transcription and post-transcriptional degradation of RNA play vital roles in this regulation. Here, we show that HUA ENHANCER 2 (HEN2), a co-factor of the nuclear exosome complex, influences RNAPII transcription elongation in Arabidopsis (Arabidopsis thaliana) under cold conditions. Our results demonstrate that a hen2 mutant is cold sensitive and undergoes substantial transcriptional changes compared to wild type when exposed to cold conditions. We found an accumulation of 5’ fragments from a subset of genes (including C-repeat binding factors 1-3 [CBF1-3]) that do not carry over to their 3’ ends. In fact, hen2 mutants have lower levels of full-length mRNA for a subset of genes. This distinct 5’-end accumulation and 3’-end depletion was not observed in other NEXT complex members or core exosome mutants, highlighting HEN2’s distinctive role. We further used RNAPII-associated nascent RNA to confirm the transcriptional phenotype is a result of lower active transcription specifically at the 3’-end of these genes in a hen2 mutant. Taken together, our data point to the unique role of HEN2 in maintaining RNAPII transcription dynamics especially highlighted under cold stress.

@article{zacharaki_non-coding_2023,
	title = {The non-coding {RNA} {SVALKA} locus produces a cis-natural antisense transcript that negatively regulates the expression of {CBF1} and biomass production at normal temperatures},
	volume = {4},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346223000494},
	doi = {10.1016/j.xplc.2023.100551},
	abstract = {Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding transcription. However, we have few molecular insights into this regulation. Here, we show that a long isoform of the long non-coding RNA SVALKA-L (SVK-L) forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action of SVK-L. This pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene’s mRNA.},
	number = {4},
	urldate = {2023-08-21},
	journal = {Plant Communications},
	author = {Zacharaki, Vasiliki and Meena, Shiv Kumar and Kindgren, Peter},
	month = jul,
	year = {2023},
	keywords = {-natural antisense transcript, cis- natural antisense transcript, non-coding transcription},
	pages = {100551},
}

Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding transcription. However, we have few molecular insights into this regulation. Here, we show that a long isoform of the long non-coding RNA SVALKA-L (SVK-L) forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action of SVK-L. This pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene’s mRNA.

@article{kindgren_native_2020,
	title = {Native elongation transcript sequencing reveals temperature dependent dynamics of nascent {RNAPII} transcription in {Arabidopsis}},
	volume = {48},
	issn = {0305-1048, 1362-4962},
	url = {https://academic.oup.com/nar/article/48/5/2332/5682908},
	doi = {10.1093/nar/gkz1189},
	abstract = {Abstract
            Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter–proximal RNAPII stalling in predisposing genes for transcriptional activation during plant–environment interactions. At gene 3′-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Nucleic Acids Research},
	author = {Kindgren, Peter and Ivanov, Maxim and Marquardt, Sebastian},
	month = mar,
	year = {2020},
	pages = {2332--2347},
}

Abstract Temperature profoundly affects the kinetics of biochemical reactions, yet how large molecular complexes such as the transcription machinery accommodate changing temperatures to maintain cellular function is poorly understood. Here, we developed plant native elongating transcripts sequencing (plaNET-seq) to profile genome-wide nascent RNA polymerase II (RNAPII) transcription during the cold-response of Arabidopsis thaliana with single-nucleotide resolution. Combined with temporal resolution, these data revealed transient genome-wide reprogramming of nascent RNAPII transcription during cold, including characteristics of RNAPII elongation and thousands of non-coding transcripts connected to gene expression. Our results suggest a role for promoter–proximal RNAPII stalling in predisposing genes for transcriptional activation during plant–environment interactions. At gene 3′-ends, cold initially facilitated transcriptional termination by limiting the distance of read-through transcription. Within gene bodies, cold reduced the kinetics of co-transcriptional splicing leading to increased intragenic stalling. Our data resolved multiple distinct mechanisms by which temperature transiently altered the dynamics of nascent RNAPII transcription and associated RNA processing, illustrating potential biotechnological solutions and future focus areas to promote food security in the context of a changing climate.

@article{leng_organismal_2020,
	title = {Organismal benefits of transcription speed control at gene boundaries},
	volume = {21},
	issn = {1469-221X, 1469-3178},
	url = {https://onlinelibrary.wiley.com/doi/10.15252/embr.201949315},
	doi = {10.15252/embr.201949315},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {EMBO reports},
	author = {Leng, Xueyuan and Ivanov, Maxim and Kindgren, Peter and Malik, Indranil and Thieffry, Axel and Brodersen, Peter and Sandelin, Albin and Kaplan, Craig D and Marquardt, Sebastian},
	month = apr,
	year = {2020},
}

@article{ruwe_e_2019,
	title = {The {E} domain of {CRR2} participates in sequence‐specific recognition of {RNA} in plastids},
	volume = {222},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15578},
	doi = {10.1111/nph.15578},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Ruwe, Hannes and Gutmann, Bernard and Schmitz‐Linneweber, Christian and Small, Ian and Kindgren, Peter},
	month = apr,
	year = {2019},
	pages = {218--229},
}

@article{nielsen_transcription-driven_2019,
	title = {Transcription-driven chromatin repression of {Intragenic} transcription start sites},
	volume = {15},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1007969},
	doi = {10/gh9djk},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Nielsen, Mathias and Ard, Ryan and Leng, Xueyuan and Ivanov, Maxim and Kindgren, Peter and Pelechano, Vicent and Marquardt, Sebastian},
	editor = {Köhler, Claudia},
	month = feb,
	year = {2019},
	pages = {e1007969},
}

@article{sun_editing_2018,
	title = {Editing of {Chloroplast} rps14 by {PPR} {Editing} {Factor} {EMB2261} {Is} {Essential} for {Arabidopsis} {Development}},
	volume = {9},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2018.00841/full},
	doi = {10/gkf56c},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Sun, Yueming K. and Gutmann, Bernard and Yap, Aaron and Kindgren, Peter and Small, Ian},
	month = jun,
	year = {2018},
	pages = {841},
}

@article{kindgren_transcriptional_2018,
	title = {Transcriptional read-through of the long non-coding {RNA} {SVALKA} governs plant cold acclimation},
	volume = {9},
	copyright = {2018 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-018-07010-6},
	doi = {10.1038/s41467-018-07010-6},
	abstract = {Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Kindgren, Peter and Ard, Ryan and Ivanov, Maxim and Marquardt, Sebastian},
	month = nov,
	year = {2018},
	note = {Number: 1},
	pages = {4561},
}

Most DNA in the genomes of higher organisms does not encode proteins, yet much is transcribed by RNA polymerase II (RNAPII) into long non-coding RNAs (lncRNAs). The biological significance of most lncRNAs is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVALKA-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to challenging environmental conditions.

@article{noren_circadian_2016,
	title = {Circadian and {Plastid} {Signaling} {Pathways} {Are} {Integrated} to {Ensure} {Correct} {Expression} of the {CBF} and {COR} {Genes} during {Photoperiodic} {Growth}},
	volume = {171},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.16.00374},
	doi = {10/f3rvjv},
	abstract = {The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Norén, Louise and Kindgren, Peter and Stachula, Paulina and Rühl, Mark and Eriksson, Maria E. and Hurry, Vaughan and Strand, Åsa},
	month = jun,
	year = {2016},
	pages = {1392--1406},
}

The circadian clock synchronizes a wide range of biological processes with the day/night cycle, and correct circadian regulation is essential for photosynthetic activity and plant growth. We describe here a mechanism where a plastid signal converges with the circadian clock to fine-tune the regulation of nuclear gene expression in Arabidopsis (Arabidopsis thaliana). Diurnal oscillations of tetrapyrrole levels in the chloroplasts contribute to the regulation of the nucleus-encoded transcription factors C-REPEAT BINDING FACTORS (CBFs). The plastid signal triggered by tetrapyrrole accumulation inhibits the activity of cytosolic HEAT SHOCK PROTEIN90 and, as a consequence, the maturation and stability of the clock component ZEITLUPE (ZTL). ZTL negatively regulates the transcription factor LONG HYPOCOTYL5 (HY5) and PSEUDO-RESPONSE REGULATOR5 (PRR5). Thus, low levels of ZTL result in a HY5- and PRR5-mediated repression of CBF3 and PRR5-mediated repression of CBF1 and CBF2 expression. The plastid signal thereby contributes to the rhythm of CBF expression and the downstream COLD RESPONSIVE expression during day/night cycles. These findings provide insight into how plastid signals converge with, and impact upon, the activity of well-defined clock components involved in circadian regulation.

@article{yap_aef1mpr25_2015,
	title = {{AEF1}/{MPR25} is implicated in {RNA} editing of plastid {atpF} and mitochondrial nad5, and also promotes {atpF} splicing in {Arabidopsis} and rice},
	volume = {81},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25585673},
	doi = {10.1111/tpj.12756},
	abstract = {RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Yap, A. and Kindgren, P. and Colas des Francs-Small, C. and Kazama, T. and Tanz, S. K. and Toriyama, K. and Small, I.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/01/15},
	keywords = {ATP synthase, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis thaliana, Arabidopsis/*genetics/metabolism, Chloroplast Proteins/genetics/metabolism, DNA-Binding Proteins/*genetics/metabolism, Mitochondrial Proteins/genetics/metabolism, Mutation, Oryza/*genetics/metabolism, Plant Proteins/*genetics/metabolism, Plastids/genetics/metabolism, RNA Editing, RNA Splicing, RNA, Chloroplast/genetics, RNA, Messenger/genetics, Transcription Factors/*genetics/metabolism, chloroplast, dual targeting, mitochondria, splicing},
	pages = {661--9},
}

RNA editing is an essential mechanism that modifies target cytidines to uridine in both mitochondrial and plastid mRNA. Target sites are recognized by pentatricopeptide repeat (PPR) proteins. Using bioinformatics predictions based on the code describing sequence recognition by PPR proteins, we have identified an Arabidopsis editing factor required for editing of atpF in plastids. A loss-of-function mutation in ATPF EDITING FACTOR 1 (AEF1, AT3G22150) results in severe variegation, presumably due to decreased plastid ATP synthase levels. Loss of editing at the atpF site is coupled with a large decrease in splicing of the atpF transcript, even though the editing site is within an exon and 53 nucleotides distant from the splice site. The rice orthologue of AEF1, MPR25, has been reported to be required for editing of a site in mitochondrial nad5 transcripts, and we confirm that editing of the same site is affected in the Arabidopsis aef1 mutant. We also show that splicing of chloroplast atpF transcripts is affected in the rice mpr25 mutant. AEF1 is thus highly unusual for an RNA editing specificity factor in that it has functions in both organelles.

@article{kindgren_chloroplast_2015,
	title = {Chloroplast transcription, untangling the {Gordian} {Knot}},
	volume = {206},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25865165},
	doi = {10.1111/nph.13388},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Kindgren, P. and Strand, A.},
	month = may,
	year = {2015},
	note = {Edition: 2015/04/14},
	keywords = {DNA-Directed RNA Polymerases/*chemistry, Plant Proteins/*chemistry, Protein Subunits/*chemistry, Zea mays/*genetics, chloroplast, development, pTAC, plastid encoded RNA polymerase (PEP), plastome, polymerase-associated protein (PAP)},
	pages = {889--891},
}

@article{kindgren_predictable_2015,
	title = {Predictable alteration of sequence recognition by {RNA} editing factors from {Arabidopsis}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25649437},
	doi = {10/f64zv2},
	abstract = {RNA editing factors of the pentatricopeptide repeat (PPR) family show a very high degree of sequence specificity in the recognition of their target sites. A molecular basis for target recognition by editing factors has been proposed based on statistical correlations but has not been tested experimentally. To achieve this, we systematically mutated the pentatricopeptide motifs in the Arabidopsis thaliana RNA editing factor CLB19 to investigate their individual contribution to RNA recognition. We find that the motifs contributing significantly to the specificity of binding follow the previously proposed recognition rules, distinguishing primarily between purines and pyrimidines. Our results are consistent with proposals that each motif recognizes one nucleotide in the RNA target with the protein aligned parallel to the RNA and contiguous motifs aligned with contiguous nucleotides such that the final PPR motif aligns four nucleotides upstream of the edited cytidine. By altering S motifs in CLB19 and another editing factor, OTP82, and using the modified proteins to attempt to complement the respective mutants, we demonstrate that we can predictably alter the specificity of these factors in vivo.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Kindgren, P. and Yap, A. and Bond, C. S. and Small, I.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/05},
	keywords = {Amino Acid Motifs, Amino Acid Sequence, Arabidopsis Proteins/chemistry/*metabolism, Arabidopsis/*metabolism, Base Sequence, Molecular Sequence Data, Mutation/genetics, Nucleic Acid Conformation, Protein Binding, RNA Editing/*genetics, RNA, Plant/metabolism, RNA-Binding Proteins/chemistry/*metabolism, Recombinant Proteins/metabolism, Sequence Alignment},
	pages = {403--16},
}

RNA editing factors of the pentatricopeptide repeat (PPR) family show a very high degree of sequence specificity in the recognition of their target sites. A molecular basis for target recognition by editing factors has been proposed based on statistical correlations but has not been tested experimentally. To achieve this, we systematically mutated the pentatricopeptide motifs in the Arabidopsis thaliana RNA editing factor CLB19 to investigate their individual contribution to RNA recognition. We find that the motifs contributing significantly to the specificity of binding follow the previously proposed recognition rules, distinguishing primarily between purines and pyrimidines. Our results are consistent with proposals that each motif recognizes one nucleotide in the RNA target with the protein aligned parallel to the RNA and contiguous motifs aligned with contiguous nucleotides such that the final PPR motif aligns four nucleotides upstream of the edited cytidine. By altering S motifs in CLB19 and another editing factor, OTP82, and using the modified proteins to attempt to complement the respective mutants, we demonstrate that we can predictably alter the specificity of these factors in vivo.

@article{kindgren_recovery_2015,
	title = {The {Recovery} of {Plastid} {Function} {Is} {Required} for {Optimal} {Response} to {Low} {Temperatures} in {Arabidopsis}},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26366569},
	doi = {10.1371/journal.pone.0138010},
	abstract = {Cold acclimation is an essential response in higher plants to survive freezing temperatures. Here, we report that two independent mutant alleles of the H-subunit of Mg-chelatase, CHLH, gun5-1 and cch in Arabidopsis are sensitive to low temperatures. Plants were grown in photoperiodic conditions and exposed to low temperatures for short- and long-term periods. Tetrapyrrole biosynthesis was initially significantly inhibited in response to low temperature but recovered in wild type (Col-0), although the tetrapyrrole levels were lower in cold compared to control conditions. The gun5-1 and cch alleles showed an inability to recover chlorophyll biosynthesis in addition to a significant decrease in freezing tolerance. We found that the impaired plastid function in the CHLH mutant plants resulted in compromised de novo protein synthesis at low temperatures. The expression of the transcription factors CBF1-3 was super-induced in gun5-1 and cch mutant alleles but expression levels of their target genes, COR15a, COR47 and COR78 were similar or even lower compared to Col-0. In addition, the protein levels of COR15a were lower in gun5-1 and cch and a general defect in protein synthesis could be seen in the gun5-1 mutant following a 35S labelling experiment performed at low temperature. Taken together, our results demonstrate the importance of a functional chloroplast for the cold acclimation process and further suggest that impaired plastid function could result in inhibition of protein synthesis at low temperature.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Kindgren, P. and Dubreuil, C. and Strand, A.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/15},
	keywords = {*Mutation, Acclimatization/*physiology, Alleles, Arabidopsis Proteins/*biosynthesis/genetics, Arabidopsis/genetics/*metabolism, Cold Temperature, Cold-Shock Response/*physiology, Plastids/genetics/*metabolism, Protein Biosynthesis/physiology, Transcription, Genetic/physiology},
	pages = {e0138010},
}

Cold acclimation is an essential response in higher plants to survive freezing temperatures. Here, we report that two independent mutant alleles of the H-subunit of Mg-chelatase, CHLH, gun5-1 and cch in Arabidopsis are sensitive to low temperatures. Plants were grown in photoperiodic conditions and exposed to low temperatures for short- and long-term periods. Tetrapyrrole biosynthesis was initially significantly inhibited in response to low temperature but recovered in wild type (Col-0), although the tetrapyrrole levels were lower in cold compared to control conditions. The gun5-1 and cch alleles showed an inability to recover chlorophyll biosynthesis in addition to a significant decrease in freezing tolerance. We found that the impaired plastid function in the CHLH mutant plants resulted in compromised de novo protein synthesis at low temperatures. The expression of the transcription factors CBF1-3 was super-induced in gun5-1 and cch mutant alleles but expression levels of their target genes, COR15a, COR47 and COR78 were similar or even lower compared to Col-0. In addition, the protein levels of COR15a were lower in gun5-1 and cch and a general defect in protein synthesis could be seen in the gun5-1 mutant following a 35S labelling experiment performed at low temperature. Taken together, our results demonstrate the importance of a functional chloroplast for the cold acclimation process and further suggest that impaired plastid function could result in inhibition of protein synthesis at low temperature.

@article{boussardon_cytidine_2014,
	title = {The cytidine deaminase signature {HxE}(x){nCxxC} of {DYW1} binds zinc and is necessary for {RNA} editing of {ndhD}-1},
	volume = {203},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.12928},
	doi = {10/f6cv49},
	abstract = {In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {New Phytologist},
	author = {Boussardon, Clément and Avon, Alexandra and Kindgren, Peter and Bond, Charles S. and Challenor, Michael and Lurin, Claire and Small, Ian},
	year = {2014},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12928},
	keywords = {DYW domain, RNA editing, cytidine deaminase, pentatricopeptide repeat (PPR) proteins, zinc-binding motif},
	pages = {1090--1095},
}

In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants.

@article{schallenberg-rudinger_dyw-protein_2013,
	title = {A {DYW}-protein knockout in {Physcomitrella} affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype},
	volume = {76},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.12304},
	doi = {10/f5fkxs},
	abstract = {RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR\_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR\_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR\_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR\_71 binding by prior binding of PPR\_65; (ii) the resulting upstream C–U conversion; or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR\_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR\_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.},
	language = {en},
	number = {3},
	urldate = {2021-09-02},
	journal = {The Plant Journal},
	author = {Schallenberg-Rüdinger, Mareike and Kindgren, Peter and Zehrmann, Anja and Small, Ian and Knoop, Volker},
	year = {2013},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12304},
	keywords = {Cytidine deaminase, DYW domain, Pentatricopeptide repeat proteins, Physcomitrella patens, Plant mitochondrial RNA editing, RNA-binding code},
	pages = {420--432},
}

RNA-binding pentatricopeptide repeat (PPR) proteins carrying a carboxy-terminal DYW domain similar to cytidine deaminases have been characterized as site-specific factors for C-to-U RNA editing in plant organelles. Here we report that knockout of DYW-PPR_65 in Physcomitrella patens causes a severe developmental phenotype in the moss and specifically affects two editing sites located 18 nucleotides apart on the mitochondrial ccmFC mRNA. Intriguingly, PPR_71, another DYW-type PPR, had been identified previously as an editing factor specifically affecting only the downstream editing site, ccmFCeU122SF. The now characterized PPR_65 binds specifically only to the upstream target site, ccmFCeU103PS, in full agreement with a recent RNA-recognition code for PPR arrays. The functional interference between the two editing events may be caused by a combination of three factors: (i) the destabilization of an RNA secondary structure interfering with PPR_71 binding by prior binding of PPR_65; (ii) the resulting upstream C–U conversion; or (iii) a direct interaction between the two DYW proteins. Indeed, we find the Physcomitrella DYW-PPRs to interact in yeast-two-hybrid assays. The moss DYW-PPRs also interact yet more strongly with MORF (Multiple Organellar RNA editing Factor)/RIP (RNA editing factor interacting proteins) proteins of Arabidopsis known to be general editing factors in flowering plants, although MORF homologues are entirely absent in the moss. Finally, we demonstrate binding of Physcomitrella DYW-PPR_98, for which no KO lines could be raised, to its predicted target sequence upstream of editing site atp9eU92SL. Together with the functional characterization of DYW-PPR_65, this completes the assignment of RNA editing factors to all editing sites in the Physcomitrella mitochondrial transcriptome.

@article{kindgren_interplay_2012,
	title = {Interplay between {HEAT} {SHOCK} {PROTEIN} 90 and {HY5} {Controls} {PhANG} {Expression} in {Response} to the {GUN5} {Plastid} {Signal}},
	volume = {5},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205214602057},
	doi = {10/fxpbcj},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Molecular Plant},
	author = {Kindgren, Peter and Norén, Louise and Barajas López, Juan de Dios and Shaikhali, Jehad and Strand, Åsa},
	month = jul,
	year = {2012},
	keywords = {abiotic/environmental stress, cell signaling, organelle biogenesis/function},
	pages = {901--913},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus or retrograde communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression in plants. Recently, we identified HSP90 proteins as ligands of the putative plastid signal Mg-ProtoIX. In order to investigate whether the interaction between HSP90 and Mg-ProtoIX is biologically relevant, we produced transgenic lines with reduced levels of cytosolic HSP90 in wild-type and gun5 backgrounds. Our work reveals that HSP90 proteins respond to the tetrapyrrole-mediated plastid signal to control expression of photosynthesis-associated nuclear genes (PhANG) during the response to oxidative stress. We also show that the hy5 mutant is insensitive to tetrapyrrole accumulation and that Mg-ProtoIX, cytosolic HSP90, and HY5 are all part of the same signaling pathway. These findings suggest that a regulatory complex controlling gene expression that includes HSP90 proteins and a transcription factor that is modified by tetrapyrroles in response to changes in the environment is evolutionarily conserved between yeast and plants.

@article{kindgren_plastid_2012,
	title = {The plastid redox insensitive 2 mutant of {Arabidopsis} is impaired in {PEP} activity and high light-dependent plastid redox signalling to the nucleus},
	volume = {70},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2011.04865.x},
	doi = {10/fzx2j5},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.},
	language = {en},
	number = {2},
	urldate = {2021-09-02},
	journal = {The Plant Journal},
	author = {Kindgren, Peter and Kremnev, Dmitry and Blanco, Nicolás E. and López, Juan de Dios Barajas and Fernández, Aurora Piñas and Tellgren-Roth, Christian and Small, Ian and Strand, Åsa},
	year = {2012},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2011.04865.x},
	keywords = {LHCB, PEP, chloroplast, photosynthesis, redox, signalling},
	pages = {279--291},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nuclear and the chloroplastic genomes. The activities of the nuclear and chloroplast genomes must therefore be closely coordinated through intracellular signalling. The plastids produce multiple retrograde signals at different times of their development, and in response to changes in the environment. These signals regulate the expression of nuclear-encoded photosynthesis genes to match the current status of the plastids. Using forward genetics we identified PLASTID REDOX INSENSITIVE 2 (PRIN2), a chloroplast component involved in redox-mediated retrograde signalling. The allelic mutants prin2-1 and prin2-2 demonstrated a misregulation of photosynthesis-associated nuclear gene expression in response to excess light, and an inhibition of photosynthetic electron transport. As a consequence of the misregulation of LHCB1.1 and LHCB2.4, the prin2 mutants displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by a reduced variable to maximal fluorescence ratio (Fv/Fm). PRIN2 is localized to the nucleoids, and plastid transcriptome analyses demonstrated that PRIN2 is required for full expression of genes transcribed by the plastid-encoded RNA polymerase (PEP). Similarly to the prin2 mutants, the ys1 mutant with impaired PEP activity also demonstrated a misregulation of LHCB1.1 and LHCB2.4 expression in response to excess light, suggesting a direct role for PEP activity in redox-mediated retrograde signalling. Taken together, our results indicate that PRIN2 is part of the PEP machinery, and that the PEP complex responds to photosynthetic electron transport and generates a retrograde signal, enabling the plant to synchronize the expression of photosynthetic genes from both the nuclear and plastidic genomes.

@article{kindgren_novel_2011,
	title = {A novel proteomic approach reveals a role for {Mg}-protoporphyrin {IX} in response to oxidative stress},
	volume = {141},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2010.01440.x},
	doi = {10/d2cw82},
	abstract = {The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.},
	language = {en},
	number = {4},
	urldate = {2021-09-02},
	journal = {Physiologia Plantarum},
	author = {Kindgren, Peter and Eriksson, Mats-Jerry and Benedict, Catherine and Mohapatra, Anasuya and Gough, Simon P. and Hansson, Mats and Kieselbach, Thomas and Strand, Åsa},
	year = {2011},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2010.01440.x},
	pages = {310--320},
}

The presence of genes encoding organellar proteins in different cellular compartments necessitates a tight coordination of expression by the different genomes of the eukaryotic cell. This coordination of gene expression is achieved by organelle-to-nucleus communication. Stress-induced perturbations of the tetrapyrrole pathway trigger large changes in nuclear gene expression. In order to investigate whether the tetrapyrrole Mg-ProtoIX itself is an important part of plastid-to-nucleus communication, we used an affinity column containing Mg-ProtoIX covalently linked to an Affi-Gel matrix. The proteins that bound to Mg-ProtoIX were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis combined with nano liquid chromatography–mass spectrometry (MS)/MS. Thus, we present a novel proteomic approach to address the mechanisms involved in cellular signaling and we identified interactions between Mg-ProtoIX and a large number of proteins associated with oxidative stress responses. Our approach revealed an interaction between Mg-ProtoIX and the heat shock protein 90-type protein, HSP81-2 suggesting that a regulatory complex including HSP90 proteins and tetrapyrroles controlling gene expression is evolutionarily conserved between yeast and plants. In addition, our list of putative Mg-ProtoIX-binding proteins demonstrated that binding of tetrapyrroles does not depend on a specific amino acid motif but possibly on a specific fold of the protein.

@article{kleine_genome-wide_2007,
	title = {Genome-{Wide} {Gene} {Expression} {Analysis} {Reveals} a {Critical} {Role} for {CRYPTOCHROME1} in the {Response} of {Arabidopsis} to {High} {Irradiance}},
	volume = {144},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.107.098293},
	doi = {10/fh8w86},
	abstract = {Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.},
	number = {3},
	urldate = {2021-09-02},
	journal = {Plant Physiology},
	author = {Kleine, Tatjana and Kindgren, Peter and Benedict, Catherine and Hendrickson, Luke and Strand, Åsa},
	month = jul,
	year = {2007},
	pages = {1391--1406},
}

Exposure to high irradiance results in dramatic changes in nuclear gene expression in plants. However, little is known about the mechanisms by which changes in irradiance are sensed and how the information is transduced to the nucleus to initiate the genetic response. To investigate whether the photoreceptors are involved in the response to high irradiance, we analyzed expression of EARLY  LIGHT-INDUCIBLE PROTEIN1 (ELIP1), ELIP2, ASCORBATE PEROXIDASE2 (APX2), and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN2.4 (LHCB2.4) in the phytochrome A (phyA), phyB, cryptochrome1 (cry1), and cry2 photoreceptor mutants and long hypocotyl5 (hy5) and HY5 homolog (hyh) transcription factor mutants. Following exposure to high intensity white light for 3 h (1,000 μmol quanta m−2 s−1) expression of ELIP1/2 and APX2 was strongly induced and LHCB2.4 expression repressed in wild type. The cry1 and hy5 mutants showed specific misregulation of ELIP1/2, and we show that the induction of ELIP1/2 expression is mediated via CRY1 in a blue light intensity-dependent manner. Furthermore, using the Affymetrix Arabidopsis (Arabidopsis thaliana) 24 K Gene-Chip, we showed that 77 of the high light-responsive genes are regulated via CRY1, and 26 of those genes were also HY5 dependent. As a consequence of the misregulation of these genes, the cry1 mutant displayed a high irradiance-sensitive phenotype with significant photoinactivation of photosystem II, indicated by reduced maximal fluorescence ratio. Thus, we describe a novel function of CRY1 in mediating plant responses to high irradiances that is essential to the induction of photoprotective mechanisms. This indicates that high irradiance can be sensed in a chloroplast-independent manner by a cytosolic/nucleic component.

@article{ankele_vivo_2007,
	title = {In {Vivo} {Visualization} of {Mg}-{ProtoporphyrinIX}, a {Coordinator} of {Photosynthetic} {Gene} {Expression} in the {Nucleus} and the {Chloroplast}},
	volume = {19},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.048744},
	doi = {10/cttnp7},
	abstract = {The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.},
	number = {6},
	urldate = {2021-09-02},
	journal = {The Plant Cell},
	author = {Ankele, Elisabeth and Kindgren, Peter and Pesquet, Edouard and Strand, Åsa},
	month = jun,
	year = {2007},
	pages = {1964--1979},
}

The photosynthetic apparatus is composed of proteins encoded by genes from both the nucleus and the chloroplast. To ensure that the photosynthetic complexes are assembled stoichiometrically and to enable their rapid reorganization in response to a changing environment, the plastids emit signals that regulate nuclear gene expression to match the status of the plastids. One of the plastid signals, the chlorophyll intermediate Mg-ProtoporphyrinIX (Mg-ProtoIX) accumulates under stress conditions and acts as a negative regulator of photosynthetic gene expression. By taking advantage of the photoreactive property of tetrapyrroles, Mg-ProtoIX could be visualized in the cells using confocal laser scanning spectroscopy. Our results demonstrate that Mg-ProtoIX accumulated both in the chloroplast and in the cytosol during stress conditions. Thus, the signaling metabolite is exported from the chloroplast, transmitting the plastid signal to the cytosol. Our results from the Mg-ProtoIX over- and underaccumulating mutants copper response defect and genome uncoupled5, respectively, demonstrate that the expression of both nuclear- and plastid-encoded photosynthesis genes is regulated by the accumulation of Mg-ProtoIX. Thus, stress-induced accumulation of the signaling metabolite Mg-ProtoIX coordinates nuclear and plastidic photosynthetic gene expression.