ESEfinder: a web resource to identify exonic splicing enhancers
- L. Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, A. Krainer
- BiologyNucleic Acids Res.
- 1 July 2003
ESEfinder (http://exon.cshl.edu/ESE/) is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.
Listening to silence and understanding nonsense: exonic mutations that affect splicing
- L. Cartegni, S. Chew, A. Krainer
- BiologyNature reviews genetics
- 1 April 2002
As the splicing mechanisms that depend on exonic signals are elucidated, new therapeutic approaches to treating certain genetic diseases can begin to be explored.
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
- Philip J. Smith, Chaolin Zhang, Jinhua Wang, S. Chew, Michael Q. Zhang, A. Krainer
- BiologyHuman Molecular Genetics
- 15 August 2006
A refined functional SELEX screen for motifs that can act as ESEs in response to the human SR protein SF2/ASF is carried out and an increased specificity score matrix is derived that accurately predicts the exon-skipping phenotypes of deleterious point mutations.
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors.
- E. Birney, S. Kumar, A. Krainer
- BiologyNucleic Acids Research
- 25 December 1993
Analysis of sequence motifs found in metazoan protein factors involved in constitutive pre-mRNA splicing and in alternative splicing regulation indicates that the RRM is an ancient conserved region (ACR) that has diversified by duplication of genes and intragenic domains.
The gene encoding the splicing factor SF2/ASF is a proto-oncogene
- R. Karni, E. Stanchina, S. Lowe, Rahul Sinha, D. Mu, A. Krainer
- BiologyNature Structural &Molecular Biology
- 1 March 2007
It is found that the splicing factor SF2/ASF is upregulated in various human tumors, in part due to amplification of its gene, SFRS1, and can act as an oncoprotein and is a potential target for cancer therapy.
Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1
- L. Cartegni, A. Krainer
- BiologyNature Genetics
- 4 March 2002
The abrogation of the SF2/ASF-dependent ESE is the basis for inefficient inclusion of exon 7 in SMN2, resulting in the spinal muscular atrophy phenotype.
The human splicing code reveals new insights into the genetic determinants of disease
- H. Xiong, B. Alipanahi, B. Frey
- BiologyScience
- 9 January 2015
A computational model is developed that scores how strongly genetic variants affect RNA splicing, a critical step in gene expression whose disruption contributes to many diseases, including cancers and neurological disorders, and provides insights into the role of aberrant splicing in disease.
Comprehensive splice-site analysis using comparative genomics
- N. Sheth, X. Roca, M. Hastings, Ted Roeder, A. Krainer, R. Sachidanandam
- BiologyNucleic Acids Research
- 12 August 2006
This study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.
Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model.
- Y. Hua, K. Sahashi, A. Krainer
- BiologyGenes & Development
- 1 August 2010
It is concluded that this MOE ASO is a promising drug candidate for SMA therapy, and, more generally, that ASOs can be used to efficiently redirect alternative splicing of target genes in the CNS.
Role of the Modular Domains of SR Proteins in Subnuclear Localization and Alternative Splicing Specificity
- J. Cáceres, T. Misteli, G. Screaton, D. Spector, A. Krainer
- BiologyJournal of Cell Biology
- 28 July 1997
It is found that the RS domain of SF2/ASF is neither necessary nor sufficient for targeting to the nuclear speckles, and RRM2 ofSF2/asF plays an important role in alternative splicing specificity: deletion of this domain results in a protein that has altered specificity in 5′ splice site selection.
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