Noam Shomron

I am a Post-Doctorate Associate at Chris Burge’s lab at MIT pursuing better understanding of mechanisms governing microRNA regulation and function.

See my homepage

My interests and goals lie within seeking better understanding of the mechanisms governing regulation of gene expression on the RNA level, in particular, regulation by microRNAs and also alternative splicing. I would like to decipher the role these processes play in molding the transcriptome and proteome and thus affect cellular fate during states of health and disease.

I explore microRNA and splicing regulation using bench work, computational biology and high-throughput techniques. I focus on several aspects that together shed light on these small non-coding RNAs and their roles in molecular biology and evolution. On the miRNA annotation level, I complemented the miRNA registry (miRbase) with hundreds of mammalian high-confidence miRNA homologs and looked into their genomic organization and regulation. Regarding miRNA roles, I proposed a new function for miRNAs in buffering developmental related gene expression and I linked miRNA regulation to oncofetal genes relevant to human cancer. For miRNA targeting, I deciphered determinants of targeting by endogenous (and exogenous) miRNAs (also applicable to siRNAs).

Also see: http://web.mit.edu/nshomron/www http://pag.csail.mit.edu/mirnaminer http://genes.mit.edu/targetrank

Selected Publications:

Alberstein M, Amit M, Vaknin K, O'Donnell A, Farhy C, Lerenthal Y, Shomron N, Shaham O, Sharrocks A, Ashery-Padan R, Ast G. Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA (New York, N.Y.) 13 (11) , 1988-99 (2007) (Epub 05 Sep 2007) PubMed ID:(17804646)

Ibrahim E, Hims M, Shomron N, Burge C, Slaugenhaupt S, Reed R. Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Human mutation 28 (1) , 41-53 (2007) PubMed ID:(16964593)

Nielsen C, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge C. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA (New York, N.Y.) 13 (11) , 1894-910 (2007) (Epub 13 Sep 2007) PubMed ID:(17872505)

Hornstein E, Shomron N. Canalization of development by microRNAs. Nature genetics 38 Suppl , S20-4 (2006) PubMed ID:(16736020)

Stadler M, Shomron N, Yeo G, Schneider A, Xiao X, Burge C. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS genetics 2 (11) , e191 (2006) (Epub 28 Sep 2006) PubMed ID:(17121466)

Ohler U, Shomron N, Burge C. Recognition of unknown conserved alternatively spliced exons. PLoS computational biology 1 (2) , 113-22 (2005) (Epub 08 Jul 2005) PubMed ID:(16110330)

Shomron N, Alberstein M, Reznik M, Ast G. Stress alters the subcellular distribution of hSlu7 and thus modulates alternative splicing. Journal of cell science 118 (Pt 6) , 1151-9 (2005) (Epub 22 Feb 2005) PubMed ID:(15728250)

Pessah N, Reznik M, Shamis M, Yantiri F, Xin H, Bowdish K, Shomron N, Ast G, Shabat D. Bioactivation of carbamate-based 20(S)-camptothecin prodrugs. Bioorganic & medicinal chemistry 12 (8) , 1859-66 (2004) PubMed ID:(15051055)

Shomron N, Reznik M, Ast G. Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus. Molecular biology of the cell 15 (8) , 3782-95 (2004) (Epub 04 Jun 2004) PubMed ID:(15181151)

Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science (New York, N.Y.) 300 (5623) , 1288-91 (2003) PubMed ID:(12764196

Malca H, Shomron N, Ast G. The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex. Molecular and cellular biology 23 (10) , 3442-55 (2003) PubMed ID:(12724403)

Shomron N, Ast G. Boric acid reversibly inhibits the second step of pre-mRNA splicing. FEBS letters 552 (2-3) , 219-24 (2003) PubMed ID:(14527690)

Shomron N, Malca H, Vig I, Ast G. Reversible inhibition of the second step of splicing suggests a possible role of zinc in the second step of splicing. Nucleic acids research 30 (19) , 4127-37 (2002) PubMed ID:(12364591)