Research Overview in the Laboratory of Prof. Mazhar Adli

epigenomes
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.

Multiple Levels of Genome Regulation

Genetic information is encoded in four letters of A G C and T. All cells '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. Therefore, in addition to the DNA sequence information, chromatin organization provides an additional layer of regulation on the genomic information. There are multiple components of this non-genetic regulation, which is called epigenetic (Epi- in Greek means above or over). The tertiary level of genome regulation is dictated by the organization of nuclear architecture and long-range chromosomal interactions.

Epigenetics and Epigenomics

These latter two modes of genome regulation are considered epigenetic mechanisms. Epigenetics 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 Research Focus

chromatin maps
Our lab is focused on the latter two modes of genome regulation and aims to identify epigenetic mechanisms and epigenomic features that will help us better understand chromatin structure, function and nuclear organization. In the lab, we apply state-of-the-art genomic and epigenomic tools and aim to develop additional technologies to answer the following specific questions.

  • How are chromatin and cellular states established during normal development?
We are using primary as well as in vitro cultured hematopoietic stem and progenitor cells (blood stem cells) to study this question. The beauty of the hematopoietic system is that we can program the hematopoietic stem cells into specific lineages and then isolate and carefully characterize cell populations at distinct cellular states. By studying the temporal chromatin landscape in these populations, we are aiming to identify how chromatin sates are established and how they are related to unique cellular phenotypes.

  • What are the epigenetic determinants of differentiation programs of stem and progenitor cells?
Dynamic regulation of chromatin structure is essential for cell-type-specific gene expression programs and proper lineage fate choices during development. Chromatin regulators (CRs) are key players in this process, and aberrant chromatin regulation is an increasingly recognized mechanism implicated in cancer. Recently, recurrent mutations in CRs have been reported in hematopoietic malignancies and various other cancers. These findings have further highlighted the importance of understanding the chromatin regulatory networks in normal and malignant hematopoietic development. Here we are aiming to identify chromatin regulators and factors that are essential for specific cellular states of hematopoietic stem cell differentiation program.

  • How does aberrant regulation of epigenetic information lead to cellular transformation and malignant development?
Mutations in chromatin regulators are being recognized as one of the hallmarks of multiple diseases including cancer. We are studying the epigenome of normal and malignant cellular states to identify epigenomic features that are unique to the malignant state. We recently identified loss of H3K37me3 repressive histone mark as a hallmark of ASXL1 mutations in myeloid malignancies. Our article has been recently published as a cover article in Cancer Cell, August 2012.

  • Develop new technologies to study chromatin structure in rarely available but biologically important cell populations.
Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) has become a standard tool for whole-genome mapping of histone modifications, transcription factors and chromatin-associated proteins. However, the technique is plagued by inefficiencies at ChIP and sequencing steps that necessitate large amounts of starting materials, typically on the order of millions or tens of millions of cells. We have previously developed a Nano -ChIP-Seq technology (Adli et al, Nature Methods, 2011. Adli &Bernstein, Nature Protocols, 2011) that potentially overcomes some of these limitations. The method provides two-to-three orders of magnitude improvement over the conventional ChIP-Seq method (10,000 cells vs ~20M cells), however studying the chromatin maps of homogenously isolated rare cell populations is still a bottleneck in the epigenomic research community. Therefore, in addition to improving the Nano-ChIP-Seq technology, we aim to develop additional genomic tools to study chromatin structure and function in rare cells with the ultimate goal of studying the epigenome at the single cell level.