Biochemistry Department

Sihem Cheloufi


sihem cheloufi

Sihem Cheloufi
Assistant Professor of Biochemistry


PubMed Citations


Dr. Cheloufi obtained her B.Sc. degree in Molecular Genetics from King’s College University of London. She then moved to Cold Spring Harbor Laboratory where she joined Dr. Gregory Hannon’s group for her thesis project. Her doctorate work focused on investigating the role of small non-coding RNAs during mammalian development. She was awarded her Ph.D. in Genetics in 2010. Following her graduation, she joined the laboratory of Dr. Konrad Hochedlinger where she worked on identifying the key regulators of chromatin plasticity during cellular reprogramming. In 2017, she joined the department of Biochemistry at the UC Riverside as assistant professor. 

Research Focus

Understanding the mechanisms that specify and maintain the identity of over 200 cell types of the human body is key to developing strategies for regenerative medicine and to cure human diseases. Although all cells have the same genetic blueprint, they follow different developmental trajectories. Epigenetic regulators, including chromatin associated proteins and non-coding RNAs are key determinants of cell identity during this process. The mechanisms by which these molecules stabilize cell identity during normal tissue homeostasis and across generations remain poorly understood. To address this problem, my research team investigates chromatin remodeling and regulatory RNA pathways using cellular reprogramming and differentiation systems such as hematopoiesis, osteogenesis, adipogenesis and neurogenesis. Using these paradigms, we investigate genetically engineered stem and progenitor cells to identify the consequences of manipulating epigenetic pathways. Our work employs systems biology approaches, bioengineering tools, in-vivo mouse models and patient derived iPSCs to decipher the basic principles of cell identity control. The ultimate goal of our research is to apply our findings to generate clinically relevant cell types, differentiate cancer cells and extend organismal life span.


2015       Harvard Medical School epigenetics seed grant award

2015       Keystone Symposia Future of Science Fund Scholarship

2013       The Department of Defense (DoD) Peer-Reviewed Cancer Research Program (PRCRP) visionary postdoctoral fellowship award http://cdmrp.army.mil/prcrp/research_highlights/17chelouti_highlight

2007       Society for Developmental Biology travel award

2003       Sigma Xi Travel Award, SUNY at Stony Brook

2001       Certificate of Merit from the Daily Telegraph Young Science Writer Awards

1997       Undergraduate Scholarship Award, the Algerian Ministry of Education and Scientific Research

Selected Publications
  • Li Y, Basavappa M, Lu J, Dong S, Cronkite DA, Prior JT, Reinecker HC, Hertzog P, Han Y, Li WX, Cheloufi S, Karginov FV, Ding SW, Jeffrey KL. (2016) Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells. Nature Microbiology. 2:16250. PMCID: PMC5488270
  • Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G and Hochedlinger K. (2016). A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Reports, 6, 1-13. PMCID: PMC4939549
  • Cheloufi S, Elling U, Hopfgartner B, Jung Y, Murn J, Maria Ninova Badeaux A, Ang CE, Tennen D, Ferrari F, Wesche D, Abazova N, Hogue M, Tasdemir N, Rathert P, Vidal S, Fellner M, Wenzel D, Zinner M, Stadtfeld M, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park P, Penninger JM, Zuber J, Hochedlinger K (2015) The histone chaperone CAF-1 safeguards somatic cell identity. Nature 528, 218–224. PMCID: PMC4866648
  • Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, et al. (2015). Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes and Development 29, 501-512. PMCID: PMC4358403
  • Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, et al. (2013). Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 12, 699-712. PMCID: PMC3725985
  • Polo JM, Anderssen E, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei, S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S, Hochedlinger K (2012). A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617-1632. PMCID: PMC3608203
  • Van Stry M, Oguin TH 3rd, Cheloufi S, Vogel P, Watanabe M, Pillai MR, Dash P, Thomas PG, Hannon GJ, Bix M (2012). Enhanced susceptibility of Ago1/3 double-null mice to influenza A virus infection. Journal of Virology 86, 4151-4157. PMCID: PMC3318639
  •  Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ (2010). A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465, 584-589. PMCID: PMC2995450
  • Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, et al. (2010). A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328, 1694-1698. PMCID: PMC3093307
  • Chong MM, Zhang G, Cheloufi S, Neubert TA, Hannon GJ, Littman DR (2010). Canonical and alternate functions of the microRNA biogenesis machinery. Genes and Development 24, 1951-1960. PMCID: PMC2932976
  • Karginov FV, Cheloufi S, Chong MM, Stark A, Smith AD, Hannon GJ (2010). Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Molecular Cell 38, 781-788. PMCID: PMC2914474
Review Articles
  • Cheloufi S, Hochedlinger K. Emerging roles of the histone chaperone CAF-1 in cellular plasticity. (2017) Current Opinion in Genetics and Development, 46:83-94

  1. Structurally designed shRNAs, Gregory J. Hannon, Huntington, N.Y. (US); and Sihem Cheloufi, Boston, Mass. (US) Filed on October 04th 2011 and issued on September 25th 2012.

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