Identification of a Distal Locus Enhancer Element That Controls Cell Type-Specific TNF and LTA Gene Expression in Human T Cells

J Immunol. 2020 Nov 1;205(9):2479-2488. doi: 10.4049/jimmunol.1901311. Epub 2020 Sep 25.


The human TNF/LT locus genes TNF, LTA, and LTB are expressed in a cell type-specific manner. In this study, we show that a highly conserved NFAT binding site within the distal noncoding element hHS-8 coordinately controls TNF and LTA gene expression in human T cells. Upon activation of primary human CD4+ T cells, hHS-8 and the TNF and LTA promoters display increased H3K27 acetylation and nuclease sensitivity and coordinate induction of TNF, LTA, and hHS-8 enhancer RNA transcription occurs. Functional analyses using CRISPR/dead(d)Cas9 targeting of the hHS-8-NFAT site in the human T cell line CEM demonstrate significant reduction of TNF and LTA mRNA synthesis and of RNA polymerase II recruitment to their promoters. These studies elucidate how a distal element regulates the inducible cell type-specific gene expression program of the human TNF/LT locus and provide an approach for modulation of TNF and LTA transcription in human disease using CRISPR/dCas9.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Binding Sites / genetics
  • CD4-Positive T-Lymphocytes / metabolism*
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Conserved Sequence / genetics
  • Enhancer Elements, Genetic / genetics
  • Gene Expression / genetics*
  • Histones / genetics
  • Humans
  • Leukocytes, Mononuclear / metabolism
  • Lymphotoxin-alpha / genetics*
  • Promoter Regions, Genetic / genetics
  • Protein Binding / genetics
  • RNA Polymerase II / genetics
  • RNA, Messenger / genetics
  • THP-1 Cells / metabolism
  • Transcription, Genetic / genetics
  • Tumor Necrosis Factor-alpha / genetics*


  • Histones
  • Lymphotoxin-alpha
  • RNA, Messenger
  • Tumor Necrosis Factor-alpha
  • RNA Polymerase II