Mazhar Adli
Assistant Professor of Biochemistry & Molecular Genetics
Ph.D., U. North Carolina Chapel Hill
Chromatin Biology & Epigenomics

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The human body contains more than 200 different cell types. Although these cells are genotypically the same, i.e., they posses the same genetic information, they are functionally and phenotypically different. Our lab integrates genomic and epigenomic technologies such as RNA-Seq and ChIP-Seq as well as imaging technologies (Flow cytometry, confocal microscopy) to understand how chromatin architecture is organized and functions differently in diverse cellular states. We are particularly focused on studying chromatin biology during normal and malignant development.

Genetic information is encoded in four letters of A G C and T. All cells in the body 'read' this four letter genetic information to function. There are multiple levels of regulation during this process of 'reading' the genetic information. The primary level of regulation takes place at the DNA sequence level, in which the four letters of nucleic acids are organized in certain combinations and function as 'regulatory DNA elements' such as promoters, genes and enhancers. The secondary level of organization and regulation is controlled at the chromatin level where DNA is wrapped around special proteins called 'histone' proteins, forming nucleosomes. Nucleosomes can tightly or loosely package DNA and hence provide differential accessibility of genomic information. The tertiary level of genome regulation is dictated by the organization of nuclear architecture and long-range chromosomal interactions.

These latter two modes of genome regulation are considered epigenetic mechanisms. Epigenetics (Epi- in Greek means above or over) can be defined in its simplest form as the study of heritable changes in gene expression and cellular states that are not caused by changes in genetic information. There are several sources of epigenetic information. Among those, methylation of DNA cytosine residues and post-translation modifications on histone proteins are relatively better-understood components of epigenetic information. Studying these epigenetic information at the whole genome level is called Epigenomics. The study of the epigenomic maps of diverse histone modifications and DNA methylation provide unprecedented information about global chromatin landscape, organization and function.

Our lab is focused on the role chromatin organization in genome regulation during normal and malignant development such as cancer. We aim to identify epigenetic mechanisms and epigenomic features that will help us better understand the dynamic chromatin structure, function and nuclear organization during cellular differentiation programs such as stem cell self renewal and differentiation. In the lab, we apply state-of-the-art genomic and epigenomic tools and seek to develop additional technologies to answer the following specific questions.

  • How are chromatin and cellular states established during normal development?
  • What are the epigenetic determinants of differentiation programs of stem and progenitor cells?
  • How does aberrant regulation of epigenetic information lead to cellular transformation and malignant development?
  • How can we study chromatin structure in rarely available but biologically important cell populations and ultimately at single-cell-level?

Selected References

Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B,Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, Sanders SJ,Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG,Hisama FM, Leclair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L,Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB,Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, Walsh CA. (2013) "Using Whole-Exome Sequencing to Identify Inherited Causes of Autism." Neuron. Jan 77:259-273. doi: 10.1016/j.neuron.2012.11.002. [PubMed]

Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M,Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R,Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE. (2013) "Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues." Cell. Jan 15. pii: S0092-8674(12)01555-3. doi: 10.1016/j.cell.2012.12.033.[Epub ahead of print] [PubMed]

Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, Pandey S, Patel JP,Chung YR, Koche R, Perna F, Zhao X, Taylor JE, Park CY, Carroll M, Melnick A,Nimer SD, Jaffe JD, Aifantis I, Bernstein BE, Levine RL. (2012) "ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression." Cancer Cell. Aug 22:180-93. doi: 10.1016/j.ccr.2012.06.032. [PubMed]

Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F,Saunders LM, Mullally A, Abdel-Wahab O, Leung L, Weinstein A, Marubayashi S, GoelA, Gönen M, Estrov Z, Ebert BL, Chiosis G, Nimer SD, Bernstein BE, Verstovsek S, Levine RL. (2012) "Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy." Nature. Sep 489(7414):155-9. doi: 10.1038/nature11303. [PubMed]

Adli M, Bernstein BE. (2011) "Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq." Nat Protoc. Sep 6(10):1656-68. doi: 10.1038/nprot.2011.402. [PubMed]

Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, HarviewCL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A,Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC,Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S,Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, SiegelDS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T,Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, GolubTR. (2011) "Initial genome sequencing and analysis of multiple myeloma." Nature. Mar 471(7339):467-72. doi: 10.1038/nature09837. [PubMed]

Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. (2011) "Reprogramming factor expression initiates widespread targeted chromatin remodeling." Cell Stem Cell. Jan 8:96-105. doi: 10.1016/j.stem.2010.12.001. [PubMed]

Adli M, Zhu J, Bernstein BE. (2010) "Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors." Nat Methods. 7:615-8. doi: 10.1038/nmeth.1478. Epub 2010 Jul 11. [PubMed]

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A,Milos PM, Bernstein BE. (2010) "Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA." Nat Methods. 7:47-9. doi: 10.1038/nmeth.1404. Epub 2009 Nov 29. [PubMed]

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A,Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES,Koseki H, Bernstein BE. (2008) "Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains." PLoS Genet. 4(10):e1000242. doi: 10.1371/journal.pgen.1000242. Epub 2008Oct 31. [PubMed]