Premium
Genome‐wide occupancy of Arabidopsis SWI/SNF chromatin remodeler SPLAYED provides insights into its interplay with its close homolog BRAHMA and Polycomb proteins
Author(s) -
Shu Jie,
Chen Chen,
Li Chenlong,
Thapa Raj K.,
Song Jingpu,
Xie Xin,
Nguyen Vi,
Bian Shaomin,
Liu Jun,
Kohalmi Susanne E.,
Cui Yuhai
Publication year - 2021
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.15159
Subject(s) - chromatin , biology , arabidopsis , transcriptome , genome , arabidopsis thaliana , chromatin remodeling , genetics , gene , histone , swi/snf , computational biology , chromatin immunoprecipitation , promoter , gene expression , mutant
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.