Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori.
Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori.
复制标题
家蚕全基因组开放染色质区域及其对丝蛋白基因调控的影响
DOI：
10.1038/s41598-017-13186-6
复制
发表时间：
2017-10-10
影响因子：
4.6
通讯作者：
Xia Q
中科院分区：
文献类型：
--
作者：
Zhang Q;Cheng T;Jin S;Guo Y;Wu Y;Liu D;Xu X;Sun Y;Li Z;He H;Xia Q
核小体缺失的开放染色质区域（OCR）通常含有与活性DNA调控元件相关的转录因子（TF）结合位点。为了研究丝蛋白基因的调控，从3天5龄蚕的丝腺和胚胎衍生（BmE）细胞分离的DNA分子进行甲醛辅助分离的调控元件（FAIRE）和高通量测序。总共鉴定了68，000个OCR，并预测了许多TF结合基序。特别是，位于丝蛋白基因附近的OCRs含有功能性TF的潜在结合位点。此外，许多TF被发现与丝蛋白基因上游的OCRs簇结合，并调节这些基因的表达。丝蛋白基因的表达可能不仅与调节转录因子（如fkh、Bmdimm和Bmsage）有关，而且与发育和胚胎诱导的转录因子（如zen、eve、Br和eip74ef）有关。阐明丝蛋白基因的全基因组OCRs及其调控基序将为研究丝蛋白基因的转录调控机制提供有价值的数据和线索。
Nucleosome-depleted open chromatin regions (OCRs) often harbor transcription factor (TF) binding sites that are associated with active DNA regulatory elements. To investigate the regulation of silk-protein genes, DNA molecules isolated from the silk glands of third-day fifth-instar silkworm larvae and embryo-derived (BmE) cells were subjected to formal dehyde-assisted isolation of regulatory elements (FAIRE) and high-throughput sequencing. In total, 68,000 OCRs were identified, and a number of TF-binding motifs were predicted. In particular, OCRs located near silk-protein genes contained potential binding sites for functional TFs. Moreover, many TFs were found to bind to clusters of OCRs upstream of silk-protein genes, and to regulate the expression of these genes. The expression of silk protein genes may be related not only to regulating TFs (such as fkh, Bmdimm, and Bmsage), but also to developmental and hormone-induced TFs (such as zen, eve, Br, and eip74ef). Elucidation of genome-wide OCRs and their regulatory motifs in silk protein genes will provide valuable data and clues for characterizing the mechanisms of transcriptional control of silk protein genes.
登录
查看更多内容
影响因子：
4.6
作者：
Prasad N;Tarikere S;Khanale D;Habib F;Shashidhara LS
通讯作者：
Shashidhara LS
影响因子：
11.4
作者：
Bartkuhn, Marek;Straub, Tobias;Renkawitz, Rainer
通讯作者：
Renkawitz, Rainer
DOI：
10.1007/978-1-4939-2596-4_11
发表时间：
2015-01-01
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Ostrow, A Zachary;Viggiani, Christopher J;Aparicio, Oscar M
通讯作者：
Aparicio, Oscar M
影响因子：
7
作者：
MacAlpine, Heather K.;Gordan, Raluca;MacAlpine, David M.
通讯作者：
MacAlpine, David M.
人类胰岛中的开放染色质图。
影响因子：
30.8
作者：
Gaulton, Kyle J.;Nammo, Takao;Pasquali, Lorenzo;Simon, Jeremy M.;Giresi, Paul G.;Fogarty, Marie P.;Panhuis, Tami M.;Mieczkowski, Piotr;Secchi, Antonio;Bosco, Domenico;Berney, Thierry;Montanya, Eduard;Mohlke, Karen L.;Lieb, Jason D.;Ferrer, Jorge
通讯作者：
Ferrer, Jorge