2020
DOI: 10.1186/s13059-020-02093-1
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Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes

Abstract: Background: Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results: Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the s… Show more

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Cited by 42 publications
(33 citation statements)
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References 73 publications
(216 reference statements)
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“…With the former, transcription factors may already be bound to DNA but do not initiate transcription until their cognate signal activates them; with the latter, changes in chromatin accessibility may be related to long-distance transcriptional activation or facilitate other process such as DNA recombination or repair (54,55). The lack of direct correlation between DEGs and DARs has been previously noted in comparable analyses (56,57). We acknowledge that associating DARs with the closest transcriptional unit may to some extent bias the analysis, since genes can be regulated by distal regulatory elements (24,28,58), but to date there are no methods to directly associate changes in chromatin accessibility and changes in gene expression.…”
Section: Discussionmentioning
confidence: 91%
“…With the former, transcription factors may already be bound to DNA but do not initiate transcription until their cognate signal activates them; with the latter, changes in chromatin accessibility may be related to long-distance transcriptional activation or facilitate other process such as DNA recombination or repair (54,55). The lack of direct correlation between DEGs and DARs has been previously noted in comparable analyses (56,57). We acknowledge that associating DARs with the closest transcriptional unit may to some extent bias the analysis, since genes can be regulated by distal regulatory elements (24,28,58), but to date there are no methods to directly associate changes in chromatin accessibility and changes in gene expression.…”
Section: Discussionmentioning
confidence: 91%
“…The studies of gene flow in Triticum species at the whole-genome level just got off the ground recently (Cheng et al 2019;Hao et al 2020b;Zhou et al 2020). By combing with massive data from gene expression (Ramírez-González et al 2018), epigenomics, and regulatory elements profiling (Gardiner et al 2015;Jordan et al 2020;Li et al 2019;Wang et al 2021b), answers to these questions will soon be available. The development of chromosome engineering and genome editing makes it possible to introduce target alleles, multi-gene editing, and directed evolution of protein (Cullot et al 2019;Zhu et al 2020).…”
Section: Discussionmentioning
confidence: 99%
“…In the allopolyploid wheat genome, chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes (Jordan et al 2020). In addition, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid wheat chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression (Lu et al 2020).…”
Section: Discussionmentioning
confidence: 99%
“…Thus, chromatin accessibility changes may provide new insight into the intrinsic nature of the regulation of transcription after plant autopolyploidization. Continuous efforts have focused on studying chromatin accessibility in plant allopolyploids (Jordan et al 2020;Lu et al 2020), implying that chromatin accessibility influences differential gene expression induced by allopolyploidization. However, characterization of open chromatin and investigation of their biological effects in autopolyploidization are lacking.…”
mentioning
confidence: 99%