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The ENCODE Project publishes new genomic insights in special issue of Genome Research
Date:9/5/2012

functions. Splicing can produce different forms of action for that molecule that have varied biological functions but the mechanism and timing by which splicing occurs across the genome has remained poorly understood. Previous studies have shown that splicing can occur while the RNA is still being transcribed from its template.

Now, analyses by The ENCODE Consortium are shedding light on the scale of co-transcriptional splicing genome-wide. In this issue, Tilgner and colleagues analyzed sequencing data from RNA isolated in different regions of the cell, allowing them to define splicing events at different stages and measure which splicing events are occurring during transcription. They found that most RNAs are being spliced while they are transcribed, and interestingly, for lncRNAs, splicing occurs late, and in some cases, not at all.

In previous studies, researchers have found that another well-known class of small regulatory RNAs, called microRNAs (miRNAs), are in some cases generated by splicing (called mirtrons), in addition to the typical miRNA biogenesis pathway. Recently, hundreds of mirtrons were identified in model organisms, but the prevalence of mirtrons in mammals remained unknown. Utilizing the wealth of small RNA datasets produced by The ENCODE Consortium and specialized analysis tools, a study by Ladewig et al. in this issue identified more than 200 mammalian mirtrons, confirming some that had been previously identified and showing evidence for many more that have not been previously characterized, and revealing new insight into the evolution and biology of miRNAs.

References:

  • Tilgner et al., Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res doi: 10.1101/gr.134445.111
  • Ladewig et al., Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res doi
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Contact: Peggy Calicchia
calicchi@cshl.edu
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

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