RESEARCH

Our research focuses on understanding mechanisms of gene regulation. We aim at elucidating, using bioinofrmatic methods and analysis of various omic datasets, how gene expression is regulated at the layers of transcription, stability and translation, and at discovering how interruptions in these regulatory mechanisms contribute to the development of human pathological conditions. Novel deep-sequencing techniques greatly enhance our ability to systematically study gene regulation and to decipher regulatory layers that were until recently largely unexplored.

Major regulatory mechanisms that our research pursues are:

Regulation of gene transcription

Combination of various deep-sequencing techniques (e.g., RNA-seq, ChIP-seq) allows integrative analysis of the cellular transcriptome, cistrome and epigenome to outline the intricate logic of regulation of gene transcription. We develop bioinformatics methods for integrative analysis of omic datasets, and apply them to (1) discover how the cellular transcriptome is adapted in response to stress conditions and how it is mis-regulated in disease and (2) computationally infer transcriptional regulators that underlie the alterations in the transcriptome. Recently, another novel deep-sequencing method, global nuclear run-on followed by deep-sequencing (GRO-seq), has led to the discovery of a novel class of RNAs that are transcribed at enhancer regions, and are termed ‘enhancer RNAs’ (eRNAs). We analyze eRNA expression to infer enhancer activity and map putative links between enhancers and promoters of the regulated genes.

Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M, Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD, Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W, Hertzano R. RFX transcription factors are essential for hearing in mice. Nat Commun. 2015 Oct 15;6:8549. doi: 10.1038/ncomms9549. [PubMed]

Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, Chobod Y, Paz A, Amstislavskiy V, Sultan M, Safer H, Nietfeld W, Lehrach H, Shamir R, Yaspo ML, Shiloh Y. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Sci Signal. 2014 May 13;7(325):rs3. [PubMed]

Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Leveille N, Kalluri R, de Laat W, Agami R. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell. 2013 Feb7;49(3):524-35. [PubMed]

Hertzano R, Elkon R, Kurima K, Morrisson A, Chan SL, Sallin M, Biedlingmaier A, Darling DS, Griffith AJ, Eisenman DJ, Strome SE. Cell type-specific transcriptome analysis reveals a major role for Zeb1 and miR-200b in mouse inner  ear morphogenesis. PLoS Genet. 2011;7(9):e1002309 [PubMed]

Elkon R, Linhart C, Halperin Y, Shiloh Y, Shamir R. Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics. 2007;8:394. [PubMed]

Elkon R, Zeller KI, Linhart C, Dang CV, Shamir R, Shiloh Y. In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Res. 2005; 32:4955-4961. [PubMed]

Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res. 2003; 13:773-780. [PubMed]

Regulation of protein translation

In contrast to the enormous progress that was achieved over the last decade in our understanding of regulation of gene transcription, our knowledge of mechanisms that control the translation of mRNAs into proteins remains limited. Recently, the ribosome-profiling deep sequencing technique (also known as Ribo-seq) was introduced. We extensively analyze Ribo-seq data to study how translation efficiency is modulated upon various stresses. Similar to “reverse-engineering” approaches that were applied to clusters of transcriptionally co-regulated genes, in the analysis of Ribo-seq datasets we search for enriched RNA sequence and structural motifs in 5’- and 3’-UTRs of translationally co-regulated transcripts. Further, we globally examine coordination between regulation of transcription and translation.

Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AM, Wolf E, Lorenzin F, Eilers M, Agami R. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Rep. 2015 Nov 4. pii: e201540717. [PubMed]

Loayza-Puch F, Drost J, Rooijers K, Lopes R, Elkon R, Agami R. p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 2013 Apr 17;14(4):R32. [PubMed]

Alternative polyadenylation (APA)

The 3′ end of most protein-coding transcripts is cleaved and polyadenylated. Recent discoveries revealed that the majority of human (and other organisms) genes contain more than one polyadenylation site (poly-A site) at their 3′ untranslated region (3’UTR). Cleavage at upstream polyadenylation sites generates transcripts with shorter 3′ UTR compared to cleavage at distal sites, which results in transcripts with longer 3′ UTRs. As target sites for microRNAs and RNA-binding proteins (RBPs) are often embedded within 3′ UTRs, transcript with longer 3′ UTR potentially contain regulatory sites that are absent in the shorter APA isoforms. Regulatory elements in 3’UTRs mainly regulate (through the binding of microRNAs and RBPs) transcript stability and translation efficiency. Therefore, APA is emerging as an important layer of gene regulation. Novel deep-sequencing techniques (e.g., 3’-seq) enables, for the first time on a genomic scale, the mapping and quantification of the usage of all poly-A sites. We use such data to discover how APA is regulated under various physiological and pathological conditions, and decipher how this regulatory layer affects gene expression.

Alternative polyadenylation (APA)

Therefore, APA is emerging as an important layer of gene regulation. Novel deep-sequencing techniques (e.g., 3’-seq) enables, for the first time on a genomic scale, the mapping and quantification of the usage of all poly-A sites. We use such data to discover how APA is regulated under various physiological and pathological conditions, and decipher how this regulatory layer affects gene expression.

Elkon R, Ugalde AP, Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013 Jul;14(7):496-506. [PubMed]

Elkon R, Drost J, van Haaften G, Jenal M, Schrier M, Vrielink JA, Agami R. E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol. 2012;13(7):R59. [PubMed]

Morris AR, Bos A, Diosdado B, Rooijers K, Elkon R, Bolijn AS, Carvalho B, Meijer GA, Agami R. Alternative cleavage and polyadenylation during colorectal cancer development. Clin Cancer Res. 2012;18(19):5256-66. [PubMed]

Jenal M, Elkon R, Loayza-Puch F, van Haaften G, Kahn U, Menzies FM, Oude Vrielink JA, Bos AJ, Drost J, Rooijers K, Rubinsztein DC, Agami R. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell. 2012;149(3):538-53. [PubMed]

Elkon R, Zlotorynski E, Zeller KI, Agami R. Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics. 2010;11(1):259. [PubMed]