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Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress

文献类型： 外文期刊

作者： Xu, Qijun 1 ; Huang, Shunmou 3 ; Guo, Ganggang 4 ; Yang, Chunbao 1 ; Wang, Mu 1 ; Zeng, Xingquan 1 ; Wang, Yulin 1 ;

作者机构： 1.State Key Lab Hulless Barley & Yak Germplasm Resou, Lhasa 850002, Peoples R China

2.Tibet Acad Agr & Anim Husb Sci, Agr Res Inst, Lhasa 850002, Peoples R China

3.Henan Agr Univ, Coll Forestry, Zhengzhou 450002, Peoples R China

4.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China

关键词： BS-seq; ChIP-seq; RNA-seq; Transcription factor; Hulless barley; Lowly methylated regions; TFBS; abiotic stress

期刊名称：BMC GENOMICS （ 影响因子：4.547； 五年影响因子：4.931 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Background: The cis-regulatory element became increasingly important for resistance breeding. There were many DNA variations identified by resequencing. To investigate the links between the DNA variations and cis-regulatory element was the fundamental work. DNA variations in cis-regulatory elements caused phenotype variations in general. Results: We used WGBS, ChIP-seq and RNA-seq technology to decipher the regulatory element landscape from eight hulless barley varieties under four kinds of abiotic stresses. We discovered 231,440 lowly methylated regions (LMRs) from the methylome data of eight varieties. The LMRs mainly distributed in the intergenic regions. A total of 97,909 enhancer-gene pairs were identified from the correlation analysis between methylation degree and expression level. A lot of enriched motifs were recognized from the tolerant-specific LMRs. The key transcription factors were screened out and the transcription factor regulatory network was inferred from the enhancer-gene pairs data for drought stress. The NAC transcription factor was predicted to target to TCP, bHLH, bZIP transcription factor genes. We concluded that the H3K27me3 modification regions overlapped with the LMRs more than the H3K4me3. The variation of single nucleotide polymorphism was more abundant in LMRs than the remain regions of the genome. Conclusions: Epigenetic regulation is an important mechanism for organisms to adapt to complex environments. Through the study of DNA methylation and histone modification, we found that many changes had taken place in enhancers and transcription factors in the abiotic stress of hulless barley. For example, transcription factors including NAC may play an important role. This enriched the molecular basis of highland barley stress response.

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