TY - JOUR

T1 - Genome-wide discovery of OsHOX24-binding sites and regulation of desiccation stress response in rice

AU - Bhattacharjee, Annapurna

AU - Srivastava, Prabhakar Lal

AU - Nath, Onkar

AU - Jain, Mukesh

PY - 2021/1/1

Y1 - 2021/1/1

N2 - 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. 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.

AB - 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. 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.

KW - Binding Sites

KW - Biological Phenomena

KW - Desiccation

KW - Gene Expression Regulation, Plant

KW - Genes, Plant

KW - Genome-Wide Association Study

KW - Oryza/genetics

KW - Plant Proteins/genetics

KW - Plants, Genetically Modified/genetics

KW - Promoter Regions, Genetic

KW - Seedlings

KW - Stress, Physiological/genetics

KW - Transcription Factors/genetics

KW - Transcriptome

U2 - 10.1007/s11103-020-01078-9

DO - 10.1007/s11103-020-01078-9

M3 - Article

C2 - 33025523

VL - 105

SP - 205

EP - 214

JO - Plant Molecular Biology

JF - Plant Molecular Biology

SN - 0167-4412

IS - 1-2

ER -