Numerous recursive sites contribute to accuracy of splicing in long introns in flies

PLoS Genetics
Athma A PaiChristopher B Burge

Abstract

Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates that are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells. These approaches identified hundreds of novel sites of recursive splicing, expanding the catalog of recursively spliced fly introns by 4-fold. A subset of recursive sites were validated by RT-PCR and sequencing. Recursive sites occur in most very long (> 40 kb) fly introns, including many genes involved in morphogenesis and development, and tend to occur near the midpoints of introns. Suggesting a possible function for recursive splicing, we observe that fly introns with recursive sites are spliced more accurately than comparably sized non-recursive introns.

References

Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Nov 30, 2005·Methods : a Companion to Methods in Enzymology·Jamie F ConklinA Javier Lopez
Mar 24, 2009·BMC Bioinformatics·Fatemeh Zare-MirakabadBahram Goliaei
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 25, 2009·Development·Wael Tadros, Howard D Lipshitz
Oct 13, 2009·Nature Structural & Molecular Biology·Jarnail Singh, Richard A Padgett
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
May 3, 2013·F1000prime Reports·Mattia BrugioloKarla M Neugebauer
Sep 17, 2013·Cell Reports·Robert M MartinMaria Carmo-Fonseca
Nov 16, 2013·Nucleic Acids Research·Susan E St PierreUNKNOWN FlyBase Consortium
Jul 30, 2014·Molecular Biology and Evolution·Carlo G Artieri, Hunter B Fraser
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
May 15, 2015·Nature·Michael O DuffBrenton R Graveley
May 15, 2015·Nature·Christopher R SibleyJernej Ule
Aug 10, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter

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Citations

Jun 12, 2020·The Plant Journal : for Cell and Molecular Biology·Qundan LvKejun Cheng
Jan 14, 2021·Molecular Cell·Kirsten A ReimerKarla M Neugebauer
Apr 23, 2021·Wiley Interdisciplinary Reviews. RNA·John G Conboy
Dec 16, 2021·Human Genetics·Anjani KumariMarzena Wojciechowska
Oct 21, 2021·RNA·Pedro PrudêncioMaria Carmo-Fonseca
Jan 29, 2022·PloS One·Sohyun Moon, Ying-Tao Zhao

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Methods Mentioned

BETA
RNA-seq
ChIP-seq
PCR

Software Mentioned

Rachet
RepeatMasker
STAR
custom script
RachetJunctions
RachetPair
bedtools
RachetJunction
RachetScan
samtools view

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