Journal article

Genome-wide discovery of human splicing branchpoints

Tim R Mercer, Michael B Clark, Stacey B Andersen, Marion E Brunck, Wilfried Haerty, Joanna Crawford, Ryan J Taft, Lars K Nielsen, Marcel E Dinger, John S Mattick

GENOME RESEARCH | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2015

Abstract

During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, an..

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University of Melbourne Researchers

Grants

Awarded by Australian National Health and Medical Research Council Fellowships


Awarded by Australian Research Council Discovery Career Research Award


Awarded by Biotechnology and Biological Sciences Research Council


Awarded by Medical Research Council


Funding Acknowledgements

The authors would like to thank the following funding sources: Australian National Health and Medical Research Council Fellowships (631668 to J.S.M., also supporting T.R.M. and M.B.C., 631542 to M.E.D., and APP1072662 to M.B.C.); a Queensland State Government (National and International Research Alliance Program, to L.K.N.); and an Australian Research Council Discovery Career Research Award (DE120101916 to R.J.T.). We would also like to thank Roderic Guigo (Centre for Genomic Regulation, Barcelona), IMB Core sequencing facility, Patrick Danoy, Jeffrey Jeddeloh, Ryan Bannen (Roche/NimbleGen), and Daniel Gerhardt (Mater Research) for technical advice and assistance with capture sequencing. We would also like to thank Claudia Wehrspaun for analysis advice and Professor Stephen Rader and Yang Li for manuscript advice. This work was supported by the NeCTAR Genomics Virtual Lab (GVL). The contents of the published material are solely the responsibility of the administering institution, a participating institution, or individual authors and do not reflect the views of NHMRC.