Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

First author: Daniel Bouyer; Affiliations: Ecole Normale Supérieure (巴黎高等师范学校): Paris, France

Corresponding author: Arp Schnittger 

Retinoblastoma (pRb) is a multifunctional regulator, which was likely present in the last common ancestor of all eukaryotes. The Arabidopsis pRb homolog RETINOBLASTOMA RELATED 1 (RBR1), similar to its animal counterparts, controls not only cell proliferation but is also implicated in developmental decisions, stress responses and maintenance of genome integrity. Although most functions of pRb-type proteins involve chromatin association, a genome-wide understanding of RBR1 binding sites in Arabidopsis is still missing. Here, we present a plant chromatin immunoprecipitation protocol optimized for genome-wide studies of indirectly DNA-bound proteins like RBR1. Our analysis revealed binding of Arabidopsis RBR1 to approximately 1000 genes and roughly 500 transposable elements, preferentially MITES. The RBR1-decorated genes broadly overlap with previously identified targets of two major transcription factors controlling the cell cycle, i.e. E2F and MYB3R3 and represent a robust inventory of RBR1-targets in dividing cells. Consistently, enriched motifs in the RBR1-marked domains include sequences related to the E2F consensus site and the MSA-core element bound by MYB3R transcription factors. Following up a key role of RBR1 in DNA damage response, we performed a meta-analysis combining the information about the RBR1-binding sites with genome-wide expression studies under DNA stress. As a result, we present the identification and mutant characterization of three novel genes required for growth upon genotoxic stress.

pRb是一个多功能的调控子，存在于所有真核生物共同的祖先中。拟南芥pRb同源物为RBR1，与其在动物中的同源基因相似，不仅控制细胞的增殖，同时参与发育决定、胁迫响应和基因组完整性维持。尽管pRb蛋白的主要功能是与染色质相关，而拟南芥中RBR1在全基因组的结合位点仍然还不清楚。本文，作者采用优化过的植物染色质免疫沉淀方法对RBR1蛋白在全基因组上的结合位点进行了扫描。研究结果显示拟南芥RBR1大概结合到1000个基因和大约500个转座元件，优先结合在MITES。RBR1结合的基因与先前报道的两个控制细胞周期的转录因子E2F和MYB3R3所结合的靶基因具有极高的重叠，说明了RBR1可能参与了细胞分裂。同时，对于RBR1标记的结构域的基序富集分析鉴定到了E2F一致性位点相关的序列和由MYB3R转录因子结合的MSA核心元件。为了研究RBR1在DNA损伤响应中发挥关键作用，作者进行了元分析，结合了RBR1结合位点和DNA胁迫下基因组范围表达数据。分析结果显示，作者鉴定了三个新的基因作用于基因损害胁迫下的植物正常生长。

doi: https://doi.org/10.1371/journal.pgen.1007797

Journal: PLOS Genetics

Published date: 30 November, 2018