Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Cell Rep. 2012 Feb 23;1(2):167-78. doi: 10.1016/j.celrep.2012.02.001.


Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq), and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and autoregulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.

Publication types

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

MeSH terms

  • Alternative Splicing / genetics*
  • Base Sequence
  • Binding Sites / genetics
  • Blotting, Western
  • Exons / genetics
  • Fibroblasts / metabolism
  • Genes, Neoplasm / genetics
  • Genome, Human / genetics*
  • HEK293 Cells
  • Heterogeneous-Nuclear Ribonucleoproteins / metabolism*
  • Humans
  • Molecular Sequence Data
  • Nucleotide Motifs / genetics
  • Oligonucleotide Array Sequence Analysis
  • Organ Specificity / genetics
  • Protein Binding / genetics
  • Protein Interaction Mapping
  • RNA Precursors / metabolism
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction


  • Heterogeneous-Nuclear Ribonucleoproteins
  • RNA Precursors

Associated data

  • GEO/GSE34992