Transcriptome-wide RNA interaction profiling reveals physical and functional targets of hnRNP L in human T cells

Mol Cell Biol. 2014 Jan;34(1):71-83. doi: 10.1128/MCB.00740-13. Epub 2013 Oct 28.

Abstract

The RNA processing factor hnRNP L is required for T cell development and function. However, the spectrum of direct targets of hnRNP L activity in T cells has yet to be defined. In this study, we used cross-linking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq) to identify the RNA binding sites of hnRNP L within the transcriptomes of human CD4(+) and cultured Jurkat T cells. We find that hnRNP L binds preferentially to transcripts encoding proteins involved in RNA processing and in Wnt and T cell receptor (TCR) signaling. This binding is largely conserved across both quiescent and activated T cells, in agreement with the critical role of hnRNP L throughout T cell biology. Importantly, based on the binding profile of hnRNP L, we validate numerous instances of hnRNP L-dependent alternative splicing of genes critical to T cell function. We further show that alternative exons with weak 5' splice site sequences specifically show a strong correlation between hnRNP L binding and hnRNP L-dependent splicing regulation. Together, these data provide the first transcriptome-wide analysis of the RNA targets of hnRNP L in lymphoid cells and add to the functional understanding of hnRNP L in human biology.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alternative Splicing
  • Base Sequence
  • Binding Sites / genetics
  • CD4-Positive T-Lymphocytes / metabolism
  • Cells, Cultured
  • Exons / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein L / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein L / metabolism*
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Protein Binding
  • RNA / genetics
  • RNA / metabolism*
  • RNA Splice Sites / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • T-Lymphocytes / metabolism*
  • Transcriptome*

Substances

  • Heterogeneous-Nuclear Ribonucleoprotein L
  • RNA Splice Sites
  • RNA

Associated data

  • GEO/GSE47604