Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

By Hagen U. Tilgner, David G. Knowles, Rory Johnson, Carrie A. Davis, S. Chakrabortty, S. Djebali, João Curado, Michael P. Snyder, Thomas R. Gingeras, Roderic Guigó. 2012

483 citations recorded by the source corpus.

Splicing remains an incompletely understood process. Recent findings suggest that chromatin structure participates in its regulation. Here, we analyze the RNA from subcellular fractions obtained through RNA-seq in the cell line K562. We show that in the human genome, splicing occurs predominantly during transcription. We introduce the coSI measure, based on RNA-seq reads mapping to exon junctions and borders, to assess the degree of splicing completion around internal exons. We show that, as expected, splicing is almost fully completed in cytosolic polyA+ RNA. In chromatin-associated RNA (which includes the RNA that is being transcribed), for 5.6% of exons, the removal of the surrounding introns is fully completed, compared with 0.3% of exons for which no intron-removal has occurred. The remaining exons exist as a mixture of spliced and fewer unspliced molecules, with a median coSI of 0.75. Thus, most RNAs undergo splicing while being transcribed: “co-transcriptional splicing.” Consistent with co-transcriptional spliceosome assembly and splicing, we have found significant enrichment of spliceosomal snRNAs in chromatin-associated RNA compared with other cellular RNA fractions and other nonspliceosomal snRNAs. CoSI scores decrease along the gene, pointing to a “first transcribed, first spliced” rule, yet more downstream exons carry other characteristics, favoring rapid, co-transcriptional intron removal. Exons with low coSI values, that is, in the process of being spliced, are enriched with chromatin marks, consistent with a role for chromatin in splicing during transcription. For alternative exons and long noncoding RNAs, splicing tends to occur later, and the latter might remain unspliced in some cases.

Subfields: Cancer Research, Molecular Biology

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, positive): “This observation is consistent with, and offers a quantitative model for, the previously reported predominance of cotranscriptional splicing in this cell line (45).”
Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing (2019, background): “Partial coupling of splicing to transcription (5), too, suggests a role for the transcription holoenzyme.”
Intron-centric estimation of alternative splicing from RNA-seq data (2012, background): “However, the non-uniform read coverage not only between but also within transcripts makes such estimates generally detrimental (Kakaradov et al., 2012).”
Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs (2013, background): “Even long noncoding RNAs which can be spliced are often found in their unprocessed forms [44], a distinct property of long noncoding RNAs that would result in missed lincRNAs if splicing were a required attribute.”
Long noncoding RNAs: Cellular address codes in development and disease (2013, unknown): “chromatin level, lncRNA loci are similar to mRNA loci, but lncRNAs show a bias for having just one intron and a trend for less-efficient cotranscriptional splicing (Derrien et al., 2012; Tilgner et al., 2012).”
Non-coding RNA: what is functional and what is junk? (2015, unknown): “Interestingly, introns in lncRNAs tend to be spliced post-transcriptionally, while those in mRNAs tend to be removed co-transcriptionally (Derrien et al., 2012; Tilgner et al., 2012).”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, unknown): “…chromatinmodification patterns, and splicing signals of lincRNAs are similar to those of protein-coding genes (Ponjavic et al., 2007; Cabili et al., 2011; Derrien et al., 2012; Pauli et al., 2012), although lincRNA transcripts seem somewhat less efficiently spliced (Tilgner et al., 2012).”