Chromatin looping defines expression of TAL1, its flanking genes, and regulation in T-ALL

Blood. 2013 Dec 19;122(26):4199-209. doi: 10.1182/blood-2013-02-483875. Epub 2013 Nov 7.

Abstract

TAL1 is an important regulator of hematopoiesis and its expression is tightly controlled despite complexities in its genomic organization. It is frequently misregulated in T-cell acute lymphoblastic leukemia (T-ALL), often due to deletions between TAL1 and the neighboring STIL gene. To better understand the events that lead to TAL1 expression in hematopoiesis and in T-ALL, we studied looping interactions at the TAL1 locus. In TAL1-expressing erythroid cells, the locus adopts a looping "hub" which brings into close physical proximity all known TAL1 cis-regulatory elements including CTCF-bound insulators. Loss of GATA1 results in disassembly of the hub and loss of CTCF/RAD21 from one of its insulators. Genes flanking TAL1 are partly dependent on hub integrity for their transcriptional regulation. We identified looping patterns unique to TAL1-expressing T-ALL cells, and, intriguingly, loops occurring between the TAL1 and STIL genes at the common TAL1/STIL breakpoints found in T-ALL. These findings redefine how TAL1 and neighboring genes communicate within the nucleus, and indicate that looping facilitates both normal and aberrant TAL1 expression and may predispose to structural rearrangements in T-ALL. We also propose that GATA1-dependent looping mechanisms may facilitate the conservation of TAL1 regulation despite cis-regulatory remodeling during vertebrate evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Basic Helix-Loop-Helix Transcription Factors / genetics*
  • Chromatin / chemistry
  • Chromatin / genetics*
  • Enhancer Elements, Genetic / genetics
  • GATA1 Transcription Factor / genetics
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics
  • Jurkat Cells
  • K562 Cells
  • Lymphocytes / cytology
  • Membrane Proteins / genetics
  • Mice
  • Mice, Inbred ICR
  • Nucleoside-Phosphate Kinase / genetics
  • Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / genetics*
  • Promoter Regions, Genetic / genetics
  • Protein Conformation
  • Proto-Oncogene Proteins / genetics*
  • T-Cell Acute Lymphocytic Leukemia Protein 1

Substances

  • Basic Helix-Loop-Helix Transcription Factors
  • Chromatin
  • GATA1 Transcription Factor
  • GATA1 protein, human
  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • PDZK1IP1 protein, human
  • Proto-Oncogene Proteins
  • STIL protein, human
  • T-Cell Acute Lymphocytic Leukemia Protein 1
  • TAL1 protein, human
  • cytidylate kinase
  • Nucleoside-Phosphate Kinase