Ramin Shiekhattar, Ph.D.

Herbert Kean, M.D., Family Professor
Professor, Gene Expression and Regulation Program 
215-898-3896, Office

Introduction

The laboratory of Ramin Shiekhattar, Ph.D., is interested in the biochemical events that contribute to the development of cancer. The focus of the laboratory's research is the biochemical isolation of proteins encoded by genes known to be involved in human cancer. The Shiekhattar laboratory also studies the role of these proteins on normal cellular growth and uses cells derived from tumors to study the function of these genes in cell culture models.

Research Summary

The Shiekhattar laboratory is pursuing research in two major areas. The first is the molecular mechanism of cancer. A number of human familial cancer syndromes are caused by the inheritance of a mutant allele of a tumor suppressor gene. These genes are involved in regulating cell growth, and they contribute to carcinogenesis when mutated or lost. Thus, individuals who carry only one functional copy of a given tumor suppressor gene are predisposed to cancer, since a second mutation in the same gene will render them lacking an important negative growth regulator.

The second major research area of the Shiekhattar laboratory is the epigenetic regulation of gene expression. The laboratory's goal is to understand the epigenetic regulation of gene expression in mammalian development and genetic disease. Histone modifying enzymes are a crucial component of the epigenetic control of gene activity through the regulation of chromatin state. Shiekhattar's laboratory has identified a number of factors such as chromatin remodeling complexes and histone-deacetylases that are involved in this process.

Recent Scientific Advances

BRCA1/BRCA2-containing complexes: Over the past several years, the Shiekhattar laboratory has used biochemical procedures to isolate multiprotein complexes containing proteins encoded by several tumor suppressor genes, including BRCA1, BRCA2, Nf1 and Nf2. The laboratory has begun to decipher the biochemical role of these complexes in regulation of transcription and DNA repair. Moreover, through mass spectrometric microsequencing of the constituents of these complexes, Shiekhattar's laboratory has also identified novel genes whose mutations may contribute to cancer. The laboratory is analyzing the function of these novel genes and their pattern of expression in normal as well as malignant tissues.

Chromatin remodeling: Recent genetic and biochemical studies have identified a host of multisubunit complexes that, in an ATP-dependent manner, are able to alter the structure of the nucleosome. To gain further insight into the biochemical activity and polypeptide composition of chromatin remodeling complexes in human cells, the Shiekhattar laboratory has initiated a systematic analysis of novel chromatin remodeling activities from human cells. This analysis has revealed a novel two subunit (135 kDa and 180 kDa) chromatin remodeling complex displaying a unique mononucleosome DNaseI cleavage pattern. Mass spectrometric analysis of the two subunits identified the 135 kDa subunit h. The 180 kDa subunit was identified through the analysis of expressed sequence tags as a protein closely related to Williams syndrome transcription factor (WSTF). The gene for WSTF is deleted in Williams syndrome, a complex developmental disorder marked by mental retardation, growth defects, cardiovascular disease, dysmorphic facial features, and a unique cognitive profile. This disorder is due to a contiguous gene deletion (< 1Mb) at 7q11.23. The Shiekhattar laboratory has therefore named the chromatin remodeling complex, WCRF for Williams syndrome transcription factor-related chromatin remodeling factor. Analysis of the nonredundant GeneBank database using the BLAST algorithm revealed the presence of another closely related protein to the WCRF180 subunit, indicating the presence of a family of WCRF180-related proteins.

Chromatin remodeling meets chromosome segregation: Nucleosomal DNA is arranged in a higher-order structure that presents a barrier to most cellular processes involving protein DNA interactions. The cellular machinery involved in sister chromatid cohesion, the cohesin complex, also requires access to the nucleosomal DNA to perform its function in chromosome segregation. The machineries that provide this accessibility are termed chromatin remodelling factors. The Shiekhattar laboratory has isolated a human ISWI (SNF2h)-containing chromatin remodelling complex that encompasses components of the cohesin and NuRD complexes. The laboratory has shown that the hRAD21 subunit of the cohesin complex directly interacts with the ATPase subunit SNF2h. Mapping of hRAD21, SNF2h and Mi2 binding sites by chromatin immunoprecipitation experiments reveals the specific association of these three proteins with human DNA elements containing Alu sequences. The laboratory has found a correlation between modification of histone tails and association of the SNF2h/cohesin complex with chromatin. Moreover, the laboratory has shown that the association of the cohesin complex with chromatin can be regulated by the state of DNA methylation. Finally, the Shiekhattar laboratory has presented evidence pointing to a role for the ATPase activity of SNF2h in the loading of hRAD21 on chromatin.

Histone deacetylases: The Shiekhattar laboratory has identified a family of histone deacetylase complexes that function through modifying chromatin structure to keep genes silent. The polypeptide composition of these complexes has in common a core of two subunits, HDAC1,2 and BHC110, an FAD-binding protein. The laboratory has isolated two members of this family, the BHC and XFIM complexes, and shown that the BHC complex is involved in regulation of neuronal specific genes. A candidate X-linked mental retardation gene and the transcription initiation factor II-I (TFII-I) are components of a second member of this family of complexes. Other subunits of these complexes include polypeptides associated with cancer causing chromosomal translocations. These findings not only delineate a novel class of multiprotein complexes involved in transcriptional repression but also identified a novel enzyme BHC110 whose activity remains to be determined.

Selected Publications

1 - Fortschegger K, de Graaf P, Outchkourov NS, van Schaik FM, Timmers HT, Shiekhattar R., PHF8 targets histone methylation and RNA polymerase II to activate transcription., Molecular and Cellular Biology. 2010 Jul;30(13):3286-98. [Epub 2010 Apr 26] , 20421419

2 - Baillat D, Shiekhattar R., Functional dissection of the human TNRC6 (GW182-related) family of proteins., Molecular and Cellular Biology. 2009 Aug;29(15):4144-55. [Epub 2009 May 26], 19470757

3 - Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A., An operational definition of epigenetics., Genes and Development. 2009 Apr 1;23(7):781-3., 19339683

4 - Melo SA, Ropero S, Moutinho C, et al., Liu CG, Villanueva A, Capella G, Schwartz S Jr, Shiekhattar R, Esteller M., A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function., Nature Genetics. 2009 Mar;41(3):365-70. [Epub 2009 Feb 15] Erratum in: Nature Genetics. 2010 May;42(5):464. , 19219043

5 - Savas JN, Makusky A, Ottosen S, Baillat D, Then F, Dranic D, Shiekhattar R, et al., Huntington's disease protein contributes to RNA-mediated gene silencing through association with Argonaute and P bodies., Proceedings of the National Academy of the Sciences, USA. 2008 Aug 5;105(31):10820-5. [E-pub 2008 Jul 31], 18669659

6 - Messick TE, Russell NS, Iwata AJ, Sarachan KL, Shiekhattar R, Shanks JR, Reyes-Turcu FE, Wilkinon KD, Marmorstein R., Structural basis for ubiquitin recognition by the otu1 ovarian tumor domain protein., Journal of Biological Chemistry. 2008 April 18; 283(16):11038-49. [Epub 2008 Feb 12], 18270205

7 - Di Croce L, Shiekhattar R., Thrilling transcription through threonine phosphorylation., Nature Cell Biology. 2008 January; 10(1):5-6. (Comment on: Nature Cell Biology. 2008 January; 10(1):53-60.), 18172424

8 - Smith ER, Lee MG, Winter B, Droz NM, Eissenberg JC, Shiekhattar R, Shilatifard A., Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II., Molecular and Cellular Biology. 2008 February; 28(3):1041-6. [Epub 2007 Nov 26], 18039863

9 - Allis CD. Berger SL. Cote J. Dent S. Jenuwien T. Kouzarides T. Pillus L. Reinberg D. Shi Y. Shiekhattar R. et al., New nomenclature for chromatin-modifying enzymes., Cell. 131(4):633-6, 2007 Nov 16., 18022353

10 - Ingvarsdottir K, Edwards C, Lee MG, Lee JS, Schultz DC, Shilatifard A, Shiekhattar R, Berger SL., Histone H3 K4 demethylation during activation and attenuation of GAL1 transcription in S. cerevisiae., Molecular and Cellular Biology. 2007 November; 27(22):7856-64. , 17875926