Biological Science Research Center, Southwest University, Chongqing 400715, China; State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
Insect Biochem Mol Biol. 2019 Jul;110:10-18. doi: 10.1016/j.ibmb.2019.04.014. Epub 2019 Apr 18.
The dynamic variability of transcription factors (TFs) and their binding sites makes it challenging to conduct genome-wide transcription regulation research. The silkworm Bombyx 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 of cis-element cooperation.
转录因子（TFs）及其结合位点的动态可变性使得进行全基因组转录调控研究具有挑战性。产丝的家蚕是鳞翅目昆虫中最有价值的模式昆虫之一。不同产丝量品系中染色质的“开启”和“关闭”与丝生产的变化有关，使这种昆虫成为研究基因转录调控的良好模型。然而，很少有研究检查家蚕的开放染色质区域（OCRs），并且研究 OCR 协同作用及其在丝生产中的功能仍然具有挑战性。在这里，我们通过甲醛辅助分离调控元件（FAIRE）从大造和 D872 品系五龄幼虫的丝腺中分离 OCRs。总共鉴定出 128908 个高置信 OCRs，大约 80%的 OCRs 位于非编码区域。OCRs 上调了相邻基因，并表现出对单核苷酸多态性的信号依赖性脆弱性。中信号和低信号 OCRs 更有可能具有单核苷酸多态性（SNP）。此外，OCRs 在 5kb 距离内相互作用。我们将 OCR 相互作用复合物命名为“相关区域簇”（COREs）。CORE 和其包含的 OCR 的功能存在一些差异。此外，COREs 富集了许多与丝蛋白合成相关的基因，其中一些基因上调。这项研究确定了许多高置信度的调控位点和 OCR 的协同调控模式，这些模式影响相邻基因。这些结果为家蚕转录调控提供了深入了解，并提高了我们对顺式元件协同作用的认识。
