Synergism of open chromatin regions involved in regulating genes in Bombyx mori
Synergism of open chromatin regions involved in regulating genes in Bombyx mori
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参与家蚕基因调控的开放染色质区域的协同作用
DOI：
10.1016/j.ibmb.2019.04.014
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发表时间：
2019
影响因子：
3.8
通讯作者：
He Huawei
中科院分区：
文献类型：
--
作者：
Zhang Quan;Cheng Tingcai;Sun Yueting;Wang Yi;Feng Tieshan;Li Xiaohong;Liu Lihaoyu;Li Zhiqing;Liu Chun;Xia Qingyou;He Huawei
转录因子及其结合位点的动态变化使得全基因组转录调控研究具有挑战性。家蚕是鳞翅目昆虫中最有价值的模式昆虫之一，其主要作用是吐丝。不同产丝品系中染色质的“打开”和“关闭”与产丝量的变化相关，使该昆虫成为研究基因转录调控的良好模型。然而，很少有研究已经检查了家蚕的开放染色质区域（OCR），并且研究OCR协同作用及其在丝绸生产中的功能仍然具有挑战性。在这里，我们进行了甲醛辅助分离的调控元件（FAIRE）分离的OCRs的大早和D872株的5龄幼虫的丝腺。总共确定了128，908个高置信度OCR，约80%的OCR位于非编码区。OCRs上调邻近基因，并表现出单核苷酸多态性的信号依赖性脆弱性。中等和低信号的OCR更可能具有单核苷酸多态性（SNP）。此外，OCR在5kb的距离内相互作用。我们将OCR相互作用复合体命名为“相关区域簇”（CORE）。核心及其所包含的OCR的功能表现出一些差异。此外，CORE富集了许多与丝蛋白合成相关的基因，其中一些基因被上调。这项研究确定了许多高置信度的调控位点和协同调控模式的OCR影响相邻基因。这些结果为深入了解家蚕的转录调控机制提供了依据，也加深了我们对顺式元件协同作用的理解。
The dynamic variability of transcription factors (TFs) and their binding sites makes it challenging to conduct genome-wide transcription regulation research. The silkwormBombyx mori, which produces silk, is one of the most valuable model insects in the order Lepidoptera. The “opening” and “closing” of chromatin in different silk yield strains is associated with changes in silk production, making this insect a good model for studying the transcriptional regulation of genes. However, few studies have examined the open chromatin regions (OCRs) of silkworms, and studying OCR synergism and their function in silk production remains challenging. Here, we performed formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate OCRs from the silk glands of fifth-instar larvae of the DaZao and D872 strains. In total, 128,908 high confidence OCRs were identified and approximately 80% of OCRs were located in non-coding regions. OCRs upregulated adjacent genes and showed signal-dependent vulnerability to single-nucleotide polymorphisms. Mid- and low-signal OCRs were more likely to have single-nucleotide polymorphisms (SNP). Further, OCRs interacted with each other within a distance of 5 kb. We named the OCR interaction complex as the “cluster of related regions” (COREs). The functions of the CORE and its harbored OCRs showed some differences. Additionally, COREs enriched many silk protein synthesis-associated genes, some of which were upregulated. This study identified numerous high confidence regulation sites and synergistic regulatory modes of OCRs that affect adjacent genes. These results provide insight into silkworm transcriptional regulation and improve our understanding ofcis-element cooperation.