“Evolutionary changes in anatomy and way of life are more often based on changes in the mechanisms controlling the expression of genes than on sequence changes in proteins” (Mary-Claire King and A. C. Wilson, Science, 1975).

Proper embryo development requires a precise and carefully orchestrated set of programs that depend on gene expression. Gene expression is regulated through the integrated action of many distal-regulatory elements, such as enhancers. While many potential regulatory elements have been systemically identified, their targeted genes and tissue-specific activity have yet to be explored. Furthermore, mutations in these regulatory elements altering spatiotemporal gene expression can lead to morphological differences between species, developmental abnormalities, and human disease. Elucidating gene regulatory elements and their networks are essential to understanding their mechanism of action and the ‘regulatory code’, topics our lab is working to address.

Current Projects

The dual function of DNA sequences: coding exons can also function as transcriptional enhancers:

Protein coding sequences have been shown to contain additional functional information, such as splicing, mRNA stability, microRNA target sites, and transcriptional enhancer activity. Our study analyzing enhancer-associated ChIP-seq datasets (p300, H3K27ac, H3K4me1) found that, on average, 6% of peaks overlap coding exons, suggesting that numerous exonic-enhancers (eExons) are embedded in mammalian genomes. Furthermore, functional characterization of potential eExons in zebrafish and mice found that over half of them are functional developmental enhancers. In addition, it was shown that eExons can regulate the gene in which they reside, as well as nearby genes, suggesting that mutations in these exons could lead to phenotypes that are not due to the function of the encoded protein. However, the functional consequence of point mutations in eExons has yet to be determined. Using massively parallel reporter assays, we are dissecting the enhancer activity of eExons at single nucleotide resolution to elucidate the effect of mutations on protein function, enhancer activity, or both.

Functional genomic characterization of gene regulatory elements associated with epilepsy.

Epilepsy is a complex and heterogeneous disease, making it difficult to precisely diagnose and provide effective treatments. A major and under-explored cause of complex disorders, such as epilepsy, could be mutations in gene regulatory elements, such as enhancers. To test this hypothesis, we are focusing on infantile spasms (IS), a sub-type of epilepsy that begins in infancy and is associated with ventral forebrain development and forebrain synapse function. Using advanced sequencing technologies, the regulatory elements of mouse forebrain at embryonic day 16.5 will be explored in order to understand the regulatory networks that are associated with IS. In this project, not only will the potential regulatory elements be identified but so will their targeted gene promoters. Using chromatin interaction analysis followed by pair end tag sequencing (ChIA-PET) on the mouse E16.5 forebrain, we hope to reveal the chromatin connectivity between candidate enhancers and promoter regions of IS-associated genes, such as FOXG1 and STXBP1. Furthermore, enhancer candidates will be tested for their forebrain activity using zebrafish transgenic assays. We anticipated that these novel datasets of neuronal enhancers that are involved in the spatiotemporal regulation of IS-associated genes will highlight novel genomic regions that could be involved in epilepsy pathogenesis and brain development.

Birnbaum RY, Patwardhan RP, Kim MJ, Findlay G, Smith RP, Zhao J, Ku AA, Shendure J, Ahituv N. (2014) Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genetics 10:e1004592.

Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. (2014) Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry 4:e431.

Yanovsky-Dagan S, Avitzour M, Altarescu G, Renbaum P, Eldar-Geva T, Schonberger O, Mitrani-Rosenbaum S, Levy-Lahad E, Birnbaum RY, Gepstein L, Epsztejn-Litman S, Eiges R. (2015) Uncovering the role of hypermethylation by CTG expansion in Myotonic Dystrophy Type 1 using mutant human embryonic stem cells. Stem Cell Reports 5:221-31.

Hirsh N, Birnbaum RY. (2015) Dual function of DNA sequences: protein-coding sequences function as transcriptional enhancers. Perspectives in Biology and Medicine 58:182-95.

Belinson H, Nakatani J, Babineau BA, Birnbaum RY, Bershteyn M, McEvilly RJ, Long J, Willert K, Klein OD, Ahituv N, Rosenfeld MG, Wynshaw-Boris A (2016) Prenatal β-catenin/Brn2/Tbr2 transcriptional cascade regulates adult social and stereotypic behaviors. Molecular Psychiatry 21(10):1417-33.

Ph.D. Ben Gurion University of the Negev, 2008