TY - JOUR
T1 - Mysteries of gene regulation
T2 - Promoters are not the sole triggers of gene expression
AU - Chow, Chi Nga
AU - Tseng, Kuan Chieh
AU - Hou, Ping Fu
AU - Wu, Nai Yun
AU - Lee, Tzong Yi
AU - Chang, Wen Chi
N1 - Publisher Copyright:
© 2022 The Author(s)
PY - 2022/1
Y1 - 2022/1
N2 - Cis-regulatory elements of promoters are essential for gene regulation by transcription factors (TFs). However, the regulatory roles of nonpromoter regions, TFs, and epigenetic marks remain poorly understood in plants. In this study, we characterized the cis-regulatory regions of 53 TFs and 19 histone marks in 328 chromatin immunoprecipitation (ChIP-seq) datasets from Arabidopsis. The genome-wide maps indicated that both promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs. The maps also revealed a diverse of histone combinations. The analysis suggested that exons play critical roles in the regulation of non-coding genes. Additionally, comparative analysis between heat-stress-responsive and nonresponsive genes indicated that the genes with distinct functions also exhibited substantial differences in cis-regulatory regions, histone regulation, and topologically associating domain (TAD) boundary organization. By integrating multiple high-throughput sequencing datasets, this study generated regulatory models for protein-coding genes, non-coding genes, and TAD boundaries to explain the complexity of transcriptional regulation.
AB - Cis-regulatory elements of promoters are essential for gene regulation by transcription factors (TFs). However, the regulatory roles of nonpromoter regions, TFs, and epigenetic marks remain poorly understood in plants. In this study, we characterized the cis-regulatory regions of 53 TFs and 19 histone marks in 328 chromatin immunoprecipitation (ChIP-seq) datasets from Arabidopsis. The genome-wide maps indicated that both promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs. The maps also revealed a diverse of histone combinations. The analysis suggested that exons play critical roles in the regulation of non-coding genes. Additionally, comparative analysis between heat-stress-responsive and nonresponsive genes indicated that the genes with distinct functions also exhibited substantial differences in cis-regulatory regions, histone regulation, and topologically associating domain (TAD) boundary organization. By integrating multiple high-throughput sequencing datasets, this study generated regulatory models for protein-coding genes, non-coding genes, and TAD boundaries to explain the complexity of transcriptional regulation.
KW - ChIP-seq
KW - Cis-regulatory elements
KW - Hi-seq
KW - Histone modification
KW - Topologically associating domain
KW - Transcription factors
UR - http://www.scopus.com/inward/record.url?scp=85137744227&partnerID=8YFLogxK
U2 - 10.1016/j.csbj.2022.08.058
DO - 10.1016/j.csbj.2022.08.058
M3 - Article
AN - SCOPUS:85137744227
SN - 2001-0370
VL - 20
SP - 4910
EP - 4920
JO - Computational and Structural Biotechnology Journal
JF - Computational and Structural Biotechnology Journal
ER -