The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells

Life Sci Alliance. 2020 Dec 29;4(3):e202000825. doi: 10.26508/lsa.202000825. Print 2021 Mar.


In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Binding Sites
  • Cell Line
  • Cell Survival / genetics
  • Diabetes Mellitus, Type 1 / genetics
  • Diabetes Mellitus, Type 2 / genetics
  • Exons
  • Gene Expression Regulation*
  • Gene Knockdown Techniques
  • Humans
  • Insulin-Secreting Cells / metabolism*
  • LIM Domain Proteins / genetics
  • Phosphoproteins / chemistry
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Interaction Maps
  • RNA / metabolism*
  • Serine-Arginine Splicing Factors / chemistry
  • Serine-Arginine Splicing Factors / genetics
  • Serine-Arginine Splicing Factors / metabolism*
  • Transcription Factors / genetics
  • Transcriptome
  • Transfection


  • LIM Domain Proteins
  • LMO7 protein, human
  • Phosphoproteins
  • SRSF6 protein, human
  • Transcription Factors
  • Serine-Arginine Splicing Factors
  • RNA