At least 15% of all disease-associated point mutations affect pre-mRNA splicing. Mutations at the 5' splice site (5'ss) are associated with a variety of human diseases, and are especially detrimental, due to their interference with initial recognition of the exon-intron boundary by U1 snRNP (a spliceosomal component). While some 5'ss can tolerate point mutations, others cannot, and these result in aberrant splicing that may cause human diseases; yet, the reasons for this difference are poorly understood. The objective of the proposed research is to enhance our understanding of 5'ss recognition and determine the characteristics of 5'ss that are prone to perturbation by mutations. The mechanism of splicing modulation by antisense oligonucleotides will also be examined, so as to facilitate their development as targeted therapeutics.
Aim one will identify general rules that determine 5'ss susceptibility to mutations, focusing on one of the 5'ss in BRCA2 that is mutated in human breast cancers. Mutational analysis within this 5'ss will be performed to map positions critical fo its proper recognition. Other disease-related genes with exactly the same 5'ss motif will be studied to determine the generality of the findings. By establishing the types of 5'ss susceptible to mutations, we can predict individuals at risk of developing certain diseases, and improve targeted therapeutics. Less than 1% of introns are of the GC-AG type, which has long been assumed to be spliced in the same manner as the canonical GT-AG type. Yet, T?C mutations at the +2 position in GT-AG introns abolish recognition, suggesting a different mechanism or snRNP may be necessary for normal GC-AG recognition. Using biochemical and molecular techniques to manipulate the alternative usage of GC and GT 5'ss in NPHP1 (nephoronophthisis 1), aim two will either validate the current assumptions or uncover a new mechanism for GC 5'ss recognition. Finally, antisense oligonucleotides (ASOs) are a promising therapeutic approach to correct splicing in defective genes. Yet, developing effective ASOs is slow and labor-intensive, and the underlying mechanisms are not fully understood.
Aim three will use biochemical and bioinformatics approaches to dissect a potential mechanism of action of ASOs that alter splicing and determine whether the ASOs can structurally stabilize U1 snRNP binding to 5'ss. Altogether, these studies will explore basic mechanisms to contribute to the understanding of disease-causing 5'ss mutations, to improve predictions of disease-causing splicing mutations, and to facilitate targeted-ASO drug development. The technical and conceptual experience gained by completing this proposed research will be critical steps towards achieving my long-term career goal to become an independent biomedical researcher.

Public Health Relevance

Mutations that alter 5'-splice-site recognition can result in aberrant splicing and cause various human diseases. This proposal will elucidate mechanistic aspects of 5'-splice-site recognition and susceptibility to mutation. It will facilitate the predicion of disease-causing splicing mutations and the development of antisense drugs to correct defective splicing.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Reddy, Michael K
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Cold Spring Harbor Laboratory
Cold Spring Harbor
United States
Zip Code
Wong, Mandy S; Kinney, Justin B; Krainer, Adrian R (2018) Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell 71:1012-1026.e3