Differential Grainy head binding correlates with variation in chromatin structure and gene expression in Drosophila melanogaster.
Differential Grainy head binding correlates with variation in chromatin structure and gene expression in Drosophila melanogaster.
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DOI：
10.1186/s12864-022-09082-7
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发表时间：
2022-12-27
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
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表型进化通常是由基因调控机制改变引起的基因表达变异引起的。影响染色质重塑的遗传变异已被确定为可变基因表达的潜在来源，然而，特定的染色质重塑因子的作用仍不清楚。在这里，我们通过研究基因表达的变化，染色质结构的变化，和变化的先锋因子颗粒状头的成虫翅盘之间的两个不同的菌株的果蝇和他们的F1杂种之间的结合之间的关系，解决这个知识差距。我们发现，（1）颗粒状头结合的变化主要是由于顺式作用但位于经典颗粒状头结合基序之外的序列变化，（2）颗粒状头结合的变化与染色质可及性的变化相关，（3）染色质可及性的这种变化，加上颗粒状头结合的变化，在某些情况下与基因表达的变化相关，但在其他情况下则不相关。这三个分子层之间的相互作用是复杂的，但这些结果表明，影响先锋因子结合的遗传变异有助于染色质重塑和基因表达的演变。在线版本包含补充材料，可通过10.1186/s12864-022-09082-7获得。
Phenotypic evolution is often caused by variation in gene expression resulting from altered gene regulatory mechanisms. Genetic variation affecting chromatin remodeling has been identified as a potential source of variable gene expression; however, the roles of specific chromatin remodeling factors remain unclear. Here, we address this knowledge gap by examining the relationship between variation in gene expression, variation in chromatin structure, and variation in binding of the pioneer factor Grainy head between imaginal wing discs of two divergent strains of Drosophila melanogaster and their F1 hybrid. We find that (1) variation in Grainy head binding is mostly due to sequence changes that act in cis but are located outside of the canonical Grainy head binding motif, (2) variation in Grainy head binding correlates with changes in chromatin accessibility, and (3) this variation in chromatin accessibility, coupled with variation in Grainy head binding, correlates with variation in gene expression in some cases but not others. Interactions among these three molecular layers is complex, but these results suggest that genetic variation affecting the binding of pioneer factors contributes to variation in chromatin remodeling and the evolution of gene expression. The online version contains supplementary material available at 10.1186/s12864-022-09082-7.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
2.7
作者：
Harrison MM;Botchan MR;Cline TW
通讯作者：
Cline TW
影响因子：
16
作者：
Larson ED;Marsh AJ;Harrison MM
通讯作者：
Harrison MM
影响因子：
8.8
作者：
Coolon, Joseph D.;Stevenson, Kraig R.;Wittkopp, Patricia J.
通讯作者：
Wittkopp, Patricia J.