Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells

Sci Rep. 2017 Mar 20:7:44825. doi: 10.1038/srep44825.

Abstract

Memory T cells exhibit transcriptional memory and "remember" their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFκB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to "remember" their initial environmental encounter.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Binding Sites
  • CD4-Positive T-Lymphocytes / immunology
  • CD4-Positive T-Lymphocytes / metabolism
  • Chromatin / genetics*
  • Chromatin Assembly and Disassembly*
  • GATA Transcription Factors / metabolism
  • Gene Expression Profiling
  • Histones / metabolism
  • Humans
  • Immunologic Memory / genetics*
  • Lymphocyte Activation / genetics
  • Lymphocyte Activation / immunology
  • NFATC Transcription Factors / metabolism
  • Promoter Regions, Genetic
  • Protein Binding
  • T-Lymphocytes / immunology*
  • T-Lymphocytes / metabolism*
  • Transcription, Genetic*

Substances

  • Chromatin
  • GATA Transcription Factors
  • Histones
  • NFATC Transcription Factors