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PMID: 30503770 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.

Molecular cell ·Vol. 73 ·No. 1 ·2019-00-03 ·Pages 183-194.e8

Cheung R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S

Abstract

Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of SDVs are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate extant, rare genetic variants can have large functional effects on splicing at appreciable rates, even outside the context of disease, and MFASS enables their empirical assessment at scale.

Keywords
exon recognition massively parallel reporter assay population variation rare variation splicing variant classification
MeSH Terms
Cell Separation Computational Biology Exons Flow Cytometry Gene Expression Profiling/methods HEK293 Cells HeLa Cells Hep G2 Cells High-Throughput Nucleotide Sequencing/methods Humans Introns K562 Cells Mutation Oligonucleotide Array Sequence Analysis RNA Splicing Reproducibility of Results Sequence Analysis, DNA/methods
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Cheung Rocky
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Insigne Kimberly D
Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Yao David
Department of Genetics, Stanford University, Stanford, CA 94035, USA.
Burghard Christina P
Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Wang Jeffrey
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Hsiao Yun-Hua E
Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Jones Eric M
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Goodman Daniel B
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Xiao Xinshu
Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kosuri Sriram
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: [email protected].
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Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-4164
DOI
10.1016/j.molcel.2018.10.037
Email
[email protected]
Published
2019-00-03
Epub
2018-00-29
Pages
183-194.e8
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC6599603
Subset
IM
Grants
NIA NIH HHS · R01 AG056476 · United States
NHGRI NIH HHS · U01 HG009417 · United States
NHGRI NIH HHS · U01 HG007912 · United States
NIGMS NIH HHS · DP2 GM114829 · United States
NLM NIH HHS · T32 LM012424 · United States
External Links
PubMed source DOI: 10.1016/j.molcel.2018.10.037 PMC Full Text View journal details
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