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Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice

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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.

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Data availability

ChIP-seq data reported in this study have been submitted in Gene Expression Omnibus database under the series accession number GSE144419.

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Acknowledgements

We acknowledge the financial support from the Science and Engineering Research Board (SERB), Ministry of Science and Technology (F. No. EMR/2016/001311), and Department of Biotechnology, Government of India, New Delhi, under the National Bioscience Award Scheme. We are thankful to Dr. R. Garg for help in designing experiments and analysis. The help of V. K. Singh, R. Shankar and K. Gupta in data analysis is gratefully acknowledged.

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Authors and Affiliations

  1. School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Annapurna Bhattacharjee & Mukesh Jain

  2. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

    Annapurna Bhattacharjee, Prabhakar Lal Srivastava, Onkar Nath & Mukesh Jain

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  1. Annapurna Bhattacharjee
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  2. Prabhakar Lal Srivastava
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  4. Mukesh Jain
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Contributions

MJ conceived and designed the experiments. AB, PLS and ON analyzed the data. AB and MJ wrote the manuscript and all the authors approved it.

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Correspondence to Mukesh Jain.

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Bhattacharjee, A., Srivastava, P.L., Nath, O. et al. Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice. Plant Mol Biol 105, 205–214 (2021). https://doi.org/10.1007/s11103-020-01078-9

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