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Research

Alternative splicing is a mechanism by which more than one mRNA transcript is generated from the same mRNA precursor. Recent findings suggest that almost all human genes undergo alternative splicing, and we demonstrated that humans contain the highest level of alternative splicing.

 

Alternative splicing can be specific to tissue type, environment, or developmental stage. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers.

 

Our group has made seminal contributions to our understanding of the complexity of genomic expression through alternative mRNA splicing and the involvement of this process in genetic disorders and cancer.

Our lab made several breakthroughs in the field of alternative splicing and discovered two out of three demonstrated mechanisms for the origin of alternative exons: (i) Alu exonization, i.e. the birthing process of new exons from intronic Alu sequences, and (ii) exons that changed their mode of splicing from constitutive to alternative during evolution.

We have shown that in humans most new exons have originated from the primate-specific Alu retrotransposon. We determined the molecular mechanism that leads to exonization from Alu elements and demonstrated that this process must advance via alternative splicing so as to enrich the transcriptome without compromising the integrity of the proteome (Genome Res, 2002; Science, 2003; Mol Cell, 2004; Nat Rev Genet, 2004; Genome Biol, 2007a; Genome Biol, 2007b; BMC Mol Biol, 2007; PLos Genet, 2008; Nucleic Acids Res, 2008; Genome Biol, 2008; Mol Cell Biol, 2008; PLoS Comput Biol, 2009; PLoS Genet, 2009; Nucleic Acids Res, 2010; Genome Biol., 2010; PLoS One, 2010). We also identified a large number of the known regulatory elements that determine the splicing outcome of alternative exons and defined some of the characteristics of alternative exons (Genome Res, 2003; Trends Genet, 2004; Mol Cell, 2004; RNA, 2004; Sci Am, 2005; Nucleic Acids Res, 2005; Mol Cell, 2006; Nucleic Acids Res, 2007; PLoS Comput Biol, 2007; Genome Res, 2008; Nucleic Acids Res, 2009; Nucleic Acids Res, 2010; Nat Rev Genet, 2010; Genome Res, 2012).

 

In recent years our lab has focused on the connections between chromatin structure, epigenetic determinants, transcription, and splicing. We demonstrated that nucleosomes are differentially positioned in a manner that marks exons in comparison with introns. We have also revealed that GC content architecture, specific histone modifications, and DNA methylation differ between exons and introns, and have been able to identify several mechanisms by which these affect the splicing process (Nat. Com 2020, 2021; NAR 2019; Nat Struct Mol Biol, 2009; EMBO J, 2010; Cell Rep, 2012; Genome Res, 2013; PLoS One, 2013; Epigenomics, 2013; Genome Res, 2014; Cell Rep, 2015a; Trends Genet, 2015; Cell Rep, 2015b; Annu Rev Biochem, 2015; Trends Genet, 2016).

 

Familial Dysautonomia (FD) is a severe neurodegenerative genetic disorder restricted to the Ashkenazi Jewish population. The disease results from a mutation in the IKBKAP gene, which leads to exon 20 skipping in a tissue-specific manner and the consequent reduction of wildtype IKBKAP protein levels. Thus, any treatment that elevates wild type IKBKAP mRNA levels is a promising therapy. Our group elucidated the molecular mechanism leading to exon 20 skipping and to neurodegeneration in FD, and identified a new therapy for FD, which is currently undergoing the third and final stage of clinical trials following two stages that were completed with extremely positive results (Hum Mol Genet, 2007; PLoS One, 2010; Hum Mol Genet, 2013; Hum Mol Genet, 2016; PLoS Genet, 2016).

The broad focus of our research is on pre-mRNA splicing regulation and the importance of alternative splicing in generating transcriptomic diversity unique to our species.

 

We study mechanisms of alternative splicing regulation using a combination of computational and experimental (mostly molecular biology) methods. We also study the potential link between the 3D genome organization (Hi-C), DNA packaging, and splicing, and are interested in the effects nucleosomal positioning, specific histone modifications and other epigenetic characteristics have on the regulation of alternative splicing in normal development, genetic disorders and cancer. An increasing body of evidence indicates that transcription and splicing are coupled and it is widely acknowledged that chromatin organization and DNA modification regulate transcription.

 

Little is known, however, about the cross-talk between chromatin structure and splicing. We continue to examine how RNA polymerase II and DNA modifications mediate cross-talk between chromatin structure and splicing. We also study the splicing regulation in the 3D nucleus and in evolution.

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