Chow CN, Tseng KC, Hou PF, Wu NY, Lee TY, Chang WC. Mysteries of gene regulation: Promoters are not the sole triggers of gene expression.
Comput Struct Biotechnol J 2022;
20:4910-4920. [PMID:
36147678 PMCID:
PMC9474325 DOI:
10.1016/j.csbj.2022.08.058]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022] Open
Abstract
TF binding peaks were widely distributed in nonpromoters, especially downstream regions of transcription termination sites.
Exons of non-coding regions were the prominent regions of TF binding.
TAD boundaries were colocalized with activating histone marks and TF binding.
Genes with distinct functions demonstrated substantially different behaviors in cis-regulation and epigenetic signatures.
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.
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