Chromatin‐remodeling complexes: Conserved and plant‐specific subunits in <i>Arabidopsis</i>

Shang, Ji‐Yun; He, Xin‐Jian

doi:10.1111/jipb.13208

Cited by 57 publications

(34 citation statements)

References 193 publications

(319 reference statements)

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“…Plants conserve multiple SWI/SNF subunits and their misregulation can cause strong developmental defects and altered responses to the environment ( 36 , 37 ). The model plant Arabidopsis presents multiple paralogs of these subunits e.g.…”

Section: Introductionmentioning

confidence: 99%

“…The model plant Arabidopsis presents multiple paralogs of these subunits e.g. four ATPases (BRAHMA (BRM), SPLAYED (SYD), MINUSCULE1 (MINU1) and MINU2), four SWI3s (A, B, C, and D) and two SWP73s (A and B), which suggest the formation of multiple variants of the SWI/SNF complex ( 36 ). Through a comprehensive evolutionary study of the conservation of SWI/SNF subunits across eukaryotes, we recently reported a model for the evolution of SWI/SNF subclasses that predicts the presence of two major subclasses in plants ( 35 ).…”

Section: Introductionmentioning

confidence: 99%

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The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

Diego-Martin

Pérez-Alemany

Candela-Ferre

et al. 2022

Nucleic Acids Research

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Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of this SWI/SNF complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcription start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and transcription start site determination.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

Diego-Martin

Pérez-Alemany

Candela-Ferre

et al. 2022

Nucleic Acids Research

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show abstract

“…The model plant Arabidopsis presents multiple paralogs of these subunits e.g. four ATPases (BRAHMA 3 (BRM), SPLAYED (SYD), MINUSCULE1 (MINU1), and MINU2), four SWI3s (A, B, C, and D), and two SWP73s (A and B), which suggest the formation of multiple variants of the SWI/SNF complex (36). Through a comprehensive evolutionary study of the conservation of SWI/SNF subunits across eukaryotes, we recently reported a model for the evolution of SWI/SNF subclasses that predicts the presence of two major subclasses in plants (35).…”

Section: Introductionmentioning

confidence: 99%

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and 5’ transcript length determination in Arabidopsis

Diego-Martin

Pérez-Alemany

Candela-Ferre

et al. 2022

Preprint

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Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of the plant BAF-like complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcriptional start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and 5′ transcript length determination.

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“…Chromatin remodeling complexes regulate gene transcription by stabilizing or removing nucleosomes occupying the binding sites for transcription factors [ 95 , 96 ]. The SWI/SNF (switch/sucrose non-fermenting) complex is a well-characterized chromatin-remodeling complex in plants.…”

Section: Chromatin Modifications For Drought-responsive Gene Transcri...mentioning

confidence: 99%

Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants

Nguyen

Cheong

2022

IJMS

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Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.

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Chromatin‐remodeling complexes: Conserved and plant‐specific subunits in Arabidopsis

Cited by 57 publications

References 193 publications

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and 5’ transcript length determination in Arabidopsis

Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants

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