Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress
Abstract 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 e...
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| Format: | Article |
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BMC
2022-12-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-09070-x |
| _version_ | 1828087275292983296 |
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| author | Qijun Xu Shunmou Huang Ganggang Guo Chunbao Yang Mu Wang Xingquan Zeng Yulin Wang |
| author_facet | Qijun Xu Shunmou Huang Ganggang Guo Chunbao Yang Mu Wang Xingquan Zeng Yulin Wang |
| author_sort | Qijun Xu |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-11T05:09:48Z |
| format | Article |
| id | doaj.art-8e5391dcaaab4e758789d46f46b78770 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T05:09:48Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-8e5391dcaaab4e758789d46f46b787702022-12-25T12:06:08ZengBMCBMC Genomics1471-21642022-12-0123111010.1186/s12864-022-09070-xInferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stressQijun Xu0Shunmou Huang1Ganggang Guo2Chunbao Yang3Mu Wang4Xingquan Zeng5Yulin Wang6State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic ImprovementCollege of Forestry, Henan Agricultural UniversityInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic ImprovementState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic ImprovementState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic ImprovementState Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic ImprovementAbstract 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.https://doi.org/10.1186/s12864-022-09070-xBS-seqChIP-seqRNA-seqTranscription factorHulless barleyLowly methylated regions |
| spellingShingle | Qijun Xu Shunmou Huang Ganggang Guo Chunbao Yang Mu Wang Xingquan Zeng Yulin Wang Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress BMC Genomics BS-seq ChIP-seq RNA-seq Transcription factor Hulless barley Lowly methylated regions |
| title | Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| title_full | Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| title_fullStr | Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| title_full_unstemmed | Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| title_short | Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| title_sort | inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress |
| topic | BS-seq ChIP-seq RNA-seq Transcription factor Hulless barley Lowly methylated regions |
| url | https://doi.org/10.1186/s12864-022-09070-x |
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