000			03721nab|a22003857a|4500
999			_c63351 _d63343
001			63351
003			MX-TxCIM
005			20211006085222.0
008			200910s2021||||xxk|||p|op||||00||0|eng|d
022			_a1471-2164
024	8		_ahttps://doi.org/10.1186/s12864-020-07324-0
040			_aMX-TxCIM
041			_aeng
100	1		_aDeschamps, S. _918522
245	1	0	_aChromatin loop anchors contain core structural components of the gene expression machinery in maize
260			_aLondon (United Kingdom) : _bBioMed Central, _c2021.
500			_aPeer review
500			_aOpen Access
520			_aBackground: Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results: Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions: Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.
546			_aText in English
650		7	_aMaize _gAGROVOC _2 _91173
650		7	_2AGROVOC _914145 _aChromatin
650		7	_2AGROVOC _99041 _aRNA Sequence
650		7	_2AGROVOC _98835 _aGene Expression
700	1		_918523 _aCrow, J.A.
700	1		_918524 _aChaidir, N.
700	1		_918525 _aPeterson-Burch, B.
700	1		_918526 _aKumar, S.
700	0		_918527 _aHaining Lin
700	1		_918528 _aZastrow-Hayes, G.
700	1		_917716 _aMay, G.D.
773	0		_tBMC Genomics _gv. 22, art. 23 _dLondon (United Kingdom) : BioMed Central, 2021. _x1471-2164 _wu56896
856	4		_yClick here to access online _uhttps://doi.org/10.1186/s12864-020-07324-0
942			_cJA _n0 _2ddc