BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes

Yu, Yaoguang; Liang, Zeyin; Song, Xin; Fu, Wei; Xu, Jianqu; Lei, Yawen; Yuan, Lei; Ruan, Jiuxiao; Chen, Chen; Fu, Wenqun; Cui, Yuhai; Huang, Shangzhi; Li, Chenlong

doi:10.1038/s41477-020-0734-z

Cited by 45 publications

(70 citation statements)

References 81 publications

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“…BRD9 and GLTSCR1/1L physically interact with each other and show a high degree of genome-wide colocalization (Gatchalian et al, 2018;Michel et al, 2018). Here, we found that Arabidopsis BRD1, BRD2, and BRD13 all interacted directly with BRIP1 and BRIP2 (Figure 1F), which were previously shown to be the Arabidopsis homologs of human GLTSCR1/1L (Yu et al, 2020). Moreover, BRD1/2/13 showed extensive genome-wide colocalization with BRIP1/2 (Supplemental Figure 12).…”

Section: Discussionsupporting

confidence: 67%

“…Next, we compared the genome-wide occupancy profiles of the three BRDs with those of BRM, which were also generated using 14-day-old seedlings (Yu et al, 2020). We found that the three BRDs were extremely closely colocalized with BRM peak summits (Figure 4).…”

Section: Brds Colocalize With Brm On Chromatinmentioning

confidence: 99%

“…To identify novel subunits of Arabidopsis SWI/SNF complexes, we previously performed immunoprecipitation followed by mass spectrometry (Li et al, 2016) of a stable transgenic line that expressed green fluorescent protein (GFP)-tagged BRM driven by the BRM promoter in the brm-1 mutant background. We identified three bromodomain-containing proteins, BRD1 (AT1G20670), BRD2 (AT1G76380), and BRD13 (AT5G55040), that were copurified with BRM, as well as multiple core subunits of Arabidopsis SWI/SNF complexes (Yu et al, 2020) (Supplemental Figure 1 and Supplemental Table 1). A phylogenetic analysis using bromodomain amino acid sequences revealed that, among the 29 bromodomaincontaining proteins in Arabidopsis (Supplemental Figure 2A), BRD1, BRD2, and BRD13 were clustered into a branch (Supplemental Figure 2B).…”

Section: Brd1 and Brd2 Interact With Brm In Vitro And In Vivomentioning

confidence: 99%

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Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis

et al. 2021

Molecular Plant

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Section: Discussionsupporting

confidence: 67%

Section: Brds Colocalize With Brm On Chromatinmentioning

confidence: 99%

Section: Brd1 and Brd2 Interact With Brm In Vitro And In Vivomentioning

confidence: 99%

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Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis

et al. 2021

Molecular Plant

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“…Recently, the genome‐wide occupancy of BRM has been profiled (Li et al ., 2016; Archacki et al ., 2017; Yu et al ., 2020), which aids in speeding up the decipherment of BRM’s important roles in plant developmental processes. Although a few direct targets of SYD have already been identified by chromatin immunoprecipitation combined with quantitative PCR (ChIP‐qPCR) during the past decade (Kwon et al ., 2005; Walley et al ., 2008; Wu et al ., 2015), the global occupancy of SYD has yet to be revealed.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide occupancy of Arabidopsis SWI/SNF chromatin remodeler SPLAYED provides insights into its interplay with its close homolog BRAHMA and Polycomb proteins

Chen

Thapa

et al. 2021

The Plant Journal

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SUMMARY SPLAYED (SYD) is a SWItch/Sucrose Non‐Fermentable (SWI/SNF)‐type chromatin remodeler identified in Arabidopsis thaliana (Arabidopsis). It is believed to play both redundant and differential roles with its closest homolog BRAHMA (BRM) in diverse plant growth and development processes. To better understand how SYD functions, we profiled the genome‐wide occupancy of SYD and its impact on the global transcriptome and trimethylation of histone H3 on lysine 27 (H3K27me3). To map the global occupancy of SYD, we generated a GFP‐tagged transgenic line and used it for chromatin immunoprecipitation experiments followed by next‐generation sequencing, by which more than 6000 SYD target genes were identified. Through integrating SYD occupancy and transcriptome profiles, we found that SYD preferentially targets to nucleosome‐free regions of expressed genes. Further analysis revealed that SYD occupancy peaks exhibit five distinct patterns, which were also shared by BRM and BAF60, a conserved SWI/SNF complex component, indicating the common target sites of these SWI/SNF chromatin remodelers and the functional relevance of such distinct patterns. To investigate the interplay between SYD and Polycomb‐group (PcG) proteins, we performed a genome‐wide analysis of H3K27me3 in syd‐5. We observed both increases and decreases in H3K27me3 levels at a few hundred genes in syd‐5 compared to wild type. Our results imply that SYD can act antagonistically or synergistically with PcG at specific genes. Together, our SYD genome‐wide occupancy data and the transcriptome and H3K27me3 profiles provide a much‐needed resource for dissecting SYD’s crucial roles in the regulation of plant growth and development.

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“…Therefore, to dissect the working mechanism of CHRs, it will be of great importance to identify their corresponding ChBPs or RNA‐binding proteins under specific stress conditions in plants. Recently, by Co‐IP and proteomics mass spectrometry analysis, additional subunits of CHR complexes (such as BRAHMA‐INTERACTING PROTEIN1 [BRIP1] and BRIP2 from the SWI2/SNF2 complexes, ARID5 for the ISWI complex) have been identified and their roles described during plant development (Tan et al, 2020; Yu et al, 2020). Thus, a major goal in the field would be to detect stress‐specific interacting proteins or subunits of plant CHR complexes.…”

Section: Discussionmentioning

confidence: 99%

Chromatin remodeling factors regulate environmental stress responses in plants

Song

Liu

Han

2021

JIPB

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Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post‐transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants’ response to environmental stress.

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BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes

Cited by 45 publications

References 81 publications

Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis

Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis

Genome‐wide occupancy of Arabidopsis SWI/SNF chromatin remodeler SPLAYED provides insights into its interplay with its close homolog BRAHMA and Polycomb proteins

Chromatin remodeling factors regulate environmental stress responses in plants

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