Carlos F Buen Abad Najar (Aberrant Splicing)

Global impact of aberrant splicing on human gene expression levels

  • Genetic variants are associated with disease.
  • How are the genetic variants causing the disease?
  • Regulation of expression; eQTLs.
  • RNA splicing is a primary link between genetic variants and disease risk.

Mature transcripts \(\rightarrow\) keep exons, remove introns \(\rightarrow\) isoforms: different transcripts with varying combination of exons (and sometimes, retained introns). Normal isoform ratio is a mixture of isoforms under normal circumstances. Sometimes the process produces isoforms which are different from the normal behaviour \(\rightarrow\) alternate splicing.

Genetic control of mRNA expression level is not well understood.

Enhancer/Promoter Histone marks (H3K27AC / H3K4ME3 CHIP-seq) \(\rightarrow\) Transcription (H3K36ME3 CUT&Tag) \(\rightarrow\) Splicing (nascent RNA-seq) \(\rightarrow\) Export and Decay \(\rightarrow\) Steady-state RNA.

Nascent RNA-seq captures RNA associated with chromation. Collected naRNA from LCLs from 86 Yoruba individuals. naRNA is enriched in unproductive splice junctions.

Are the naRNA-seqs reproducible?

Mis-splicing is prevalent across the transcriptome. Long introns produce more unproductive splice junctions.

Estimate – 2.4% of junctions induce NMD.

Example: Unexplained eQTL in TTC38

rs73886792: Variant is not a chromatin eQTL.

na-RNA: strong sQTL, weak eQTL mRNA: strong sQTL, strong eQTL

\(\rightarrow\) sQTLs are associated with non-chromatin eQTL.

  • 65% of eQTLs are explained by hQTLs.
  • Half eQTL that colocalize with molQTLs but not hQTLs are associated with sQTLs.
  • sQTLs of NMD junctions are strongly enriched for eQTL signals.

Effects on expression

  • Chromatin QTLs affect expression.
  • Protein coding sQTLs do not affect expression.
  • Unproductive sQTLs affect expression.

Also, eQTLs driven by u-sQTLs are conserved across tissues.

Unproductive splicing networks - do they have a different hierarchical organization compared with transcriptional networks? Far fewer master regulators and many more regulatory connections among RBPs than between RBPs and other genes. In other words, what is the relationship between the expression of the NMD isoform and the mRNA or protein levels?