Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice
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Genome‑wide discovery of OsHOX24‑binding sites and regulation of desiccation stress response in rice Annapurna Bhattacharjee1,2 · Prabhakar Lal Srivastava2 · Onkar Nath2 · Mukesh Jain1,2 Received: 24 August 2020 / Accepted: 25 September 2020 © Springer Nature B.V. 2020
Abstract Key message OsHOX24 mediates regulation of desiccation stress response via complex regulatory network as indicated by its binding to several target genes including transcription factors in rice. Abstract HD-ZIP I subfamily of homeobox transcription factors (TFs) are involved in abiotic stress responses and plant development. Previously, we demonstrated the role of OsHOX24, a member of HD-ZIP I subfamily, in abiotic stress responses. In this study, we identified downstream targets of OsHOX24 under control and desiccation stress conditions via chromatin immunoprecipitation-sequencing (ChIP-seq) approach in wild-type and OsHOX24 over-expression transgenic in rice. OsHOX24-binding sites in each sample and differential binding sites between the samples were detected at various genomic locations, including genic and intergenic regions. Gene ontology enrichment analysis revealed that OsHOX24 direct target genes were involved in several biological processes, including plant development, ABA-mediated signalling pathway, ubiquitin-dependent protein catabolic process, ion transport, abiotic and biotic stress responses besides transcriptional and translational regulation. The enrichment of several cis-regulatory motifs representing binding sites of other TFs, such as ABFs, ERF1, MYB1, LTREs and SORLIP2, suggested the involvement of OsHOX24 in a complex regulatory network. These findings indicate that OsHOX24-mediated desiccation stress regulation involves modulation of a plethora of target genes, which participate in diverse pathways in rice. Keywords Chromatin immunoprecipitation · Desiccation · Homeobox · Rice · Transcription factor
Introduction Abiotic stresses continue to pose perennial challenges to plant’s survival and productivity. The molecular signalling mechanism and gene regulatory networks operative under abiotic stresses in plants are quite complex due to involvement of a plethora of components (Nakashima et al. 2009; Urano et al. 2010). The components which participate in such regulatory networks include various transcription Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11103-020-01078-9) contains supplementary material, which is available to authorized users. * Mukesh Jain [email protected] 1
School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
2
factors (TFs) (Nakashima et al. 2009; Todaka et al. 2015). Over the years, several efforts have been made to understand the role of TFs in regulatory networks operative during abiotic stresses (Golldack et al. 2011; Wang et al. 2016). The knowledge of DNA binding la
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