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PLoS Genet. 2018 Nov 30;14(11):e1007797. doi: 10.1371/journal.pgen.1007797. eCollection 2018 Nov.

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

Author information

1
Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U1024, Paris, France.
2
University of Hamburg, Department of Developmental Biology, Hamburg, Germany.
3
RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Kanagawa, Japan.

Abstract

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.

PMID:
30500810
PMCID:
PMC6268010
DOI:
10.1371/journal.pgen.1007797
[Indexed for MEDLINE]
Free PMC Article

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