Tissue-specific regulation of gene expression via unproductive splicing

Abstract

Eukaryotic gene expression is regulated post-transcriptionally by a mechanism called unproductive splicing, in which mRNA is triggered to degrade by the nonsense-mediated decay (NMD) pathway as a result of regulated alternative splicing (AS). Only a few dozen unproductive splicing events (USEs) are currently documented, and many more remain to be identified. Here, we analyzed RNA-seq experiments from the Genotype-Tissue Expression (GTEx) Consortium to identify USEs, in which an increase in the NMD isoform splicing rate is accompanied by tissue-specific down-regulation of the host gene. To characterize RNA-binding proteins (RBPs) that regulate USEs, we superimposed these results with RBP footprinting data and experiments on the response of the transcriptome to the perturbation of expression of a large panel of RBPs. Concordant tissue-specific changes between the expression of RBP and USE splicing rate revealed a high-confidence regulatory network including 27 tissue-specific USEs with strong evidence of RBP binding. Among them, we found previously unknown PTBP1-controlled events in the DCLK2 and IQGAP1 genes, for which we confirmed the regulatory effect using small interfering RNA (siRNA) knockdown experiments in the A549 cell line. In sum, we present a transcriptomic pipeline that allows the identification of tissue-specific USEs, potentially many more than were reported here using stringent filters.

Multi-omic profiling of pathogen-stimulated primary immune cells

“…Genes that undergo intron retention loss mainly have functions in mRNA splicing and processing and in immunity. Tissue- or cell-type specific unproductive splicing has been widely observed as an autoregulatory process for mRNA splicing factors 74 , which is supported by our data in immune cells. A couple of pertinent examples have been illustrated in greater detail.…”

BRD2 and BRD3 genes independently evolved RNA structures to control unproductive splicing

“…The optimal least squares line is shown in dashed blue. Tissue color codes are as in [32]. (B) The difference in the median exon 3b inclusion rate (ΔΨ, tumor vs. normal tissue) is negatively correlated ( r p = −0.3) with the difference in log 10 -transformed median transcript abundance (Δ log 10 TPM ).…”

“…(B) The difference in the median exon 3b inclusion rate (ΔΨ, tumor vs. normal tissue) is negatively correlated ( r p = −0.3) with the difference in log 10 -transformed median transcript abundance (Δ log 10 TPM ). TCGA project color codes and abbreviations are as in [32]. (C) The response of exon 3b inclusion (Ψ) to α-amanitin treatment.…”

CCAR1 promotes DNA repair via an unanticipated role in alternative splicing

“…The database of rMATS- and Deseq2-processed RNA-binding protein (RBP) perturbations available at the ENCODE portal 43 and SRA archive, was constructed before 55 . The database was queried for the rMATS output for poison exon 15 within the FANCA gene.…”