Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

Quan Zhang,Huawei He,Xiaomin Xu,Youbing Guo,Shengkai Jin,Duolian Liu,Qingyou Xia,Zhiqing Li,Yuqian Wu,Tingcai Cheng,Yueting Sun

doi:10.1038/s41598-017-13186-6

Abstract

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.

Highlights

Open chromatin regions (OCRs) are nucleosome-depleted regions that can be bound by protein factors[1] and can play various roles in DNA replication[2], nuclear organization[3], and gene transcription[4]
To further our understanding of silk protein gene regulation and associated regulatory motifs in B. mori, we subjected DNA isolated from the silk glands of this organism to formaldehyde-assisted isolation of regulatory elements (FAIRE)-seq and transcriptomic sequencing (RNA-seq) analyses; a genome-wide map of open chromatin regions (OCRs) was obtained and we identified regulatory motifs for OCRs
DNA molecules isolated from B. mori silk glands and a BmE cell line (Fig. 1a) were analyzed by FAIRE-seq

Summary

Introduction

Open chromatin regions (OCRs) are nucleosome-depleted regions that can be bound by protein factors[1] and can play various roles in DNA replication[2], nuclear organization[3], and gene transcription[4]. The larval silk gland of these insects is a specialized organ that synthesizes, assembles, and secretes silk proteins Silk proteins such as fibroins and sericins are primarily produced in the posterior silk gland (PSG) and middle silk gland (MSG), respectively, and the genes that encode these factors exhibit rhythmic “on” and “off ” transcriptional regulation during development, resulting in distinct and specific temporal and spatial expression[7]. Next-generation sequencing technology can be combined with various genome-wide assays, such as self-transcribing active regulatory region (STARR)[11,12], chromatin immunoprecipitation (ChIP)[13,14], and nucleosome-depleted or “open chromatin” site isolation assays These latter assays exploit DNase[1]. Our results provide valuable data and insights, and will aid in enhancing our understanding of the mechanisms governing the specific and efficient transcription of silk protein genes

Methods

Results

Conclusion