Mysteries of gene regulation: Promoters are not the sole triggers of gene expression

Chi Nga Chow, Kuan Chieh Tseng, Ping Fu Hou, Nai Yun Wu, Tzong Yi Lee, Wen Chi Chang

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)4910-4920
Number of pages11
JournalComputational and Structural Biotechnology Journal
Volume20
DOIs
Publication statusPublished - 2022 Jan

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Computer Science Applications

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