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Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development.

Judith Marsman1, Adam C O'Neill1, Betty Rui-Yun Kao1

  • 1Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand.

Biochimica Et Biophysica Acta
|December 11, 2013
PubMed
Summary

Cohesin and CTCF regulate the essential Runx1 gene in zebrafish embryos. These proteins bind regulatory elements, influencing gene expression and hematopoiesis, with conserved functions in human leukemia.

Keywords:
ALMCCCTC-binding factorCRECTCFCohesinHematopoiesisICMMOPLMRBRNA polymerase IIRNAPIIRad21Rohon–Beard neuronsRunx1TSSZebrafishanterior lateral mesodermcis-regulatory elementintermediate cell massmorpholino oligonucleotideposterior lateral mesodermtranscription start site

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Area of Science:

  • Developmental Biology
  • Gene Regulation
  • Hematopoiesis

Background:

  • Runx1 is a crucial transcription factor for definitive hematopoiesis.
  • Runx1 gene expression is controlled by two promoters (P1 and P2).
  • Previous work linked cohesin to runx1 expression in zebrafish hematopoietic cells.

Purpose of the Study:

  • To investigate the roles of cohesin and CTCF in regulating zebrafish runx1.
  • To identify cis-regulatory elements (CREs) involved in runx1 transcription.
  • To explore the evolutionary conservation of RUNX1 regulation.

Main Methods:

  • ChIP-seq to identify cohesin and CTCF binding sites on the zebrafish runx1 gene.
  • Analysis of histone modifications and enhancer-like properties at binding sites.
  • In vivo insulator assays and RNA polymerase II (RNAPII) recruitment studies.
  • Functional studies in zebrafish embryos and a human leukemia cell line.

Main Results:

  • Cohesin and CTCF directly bind to the P1 and P2 promoters and an intronic region of zebrafish runx1.
  • Cohesin promotes runx1 expression initiation and influences promoter usage, while CTCF represses it.
  • Intronic binding sites exhibit enhancer-like properties and function as insulators, recruiting RNAPII.
  • CTCF depletion specifically reduced RNAPII at intronic CREs.
  • Cohesin depletion, but not CTCF, increased RUNX1 expression in human leukemia cells.

Conclusions:

  • Cohesin and CTCF play distinct, crucial roles in regulating runx1 during zebrafish embryogenesis.
  • Intronic CREs are key regulatory sites for runx1, modulated by cohesin and CTCF.
  • The regulatory mechanisms involving RUNX1 and cohesin show evolutionary conservation.