Our research interests focus on the similarities and differences in chromatin structure among different cell types and how chromatin remodeling factors that modulate these differences regulate cell fate. The long-term goals of our laboratory are to comprehensively understand the functions, targets, regulation, and mechanisms of action of non-coding RNAs (ncRNAs) and chromatin regulatory factors with critical functions in gene regulatory networks.
Embryonic stem (ES) cells are of considerable biomedical interest because of their following two properties: the unlimited capacity to proliferate without accumulation of genetic or epigenetic alterations that alter their identity (self-renewal) and the ability to differentiate into any of the approximately two hundred different cell types found in the adult organism (pluripotency). Because of these properties, ES cells are excellent candidates for the development of new therapies for degenerative diseases. However, while therapeutic trials with ES cell-derived tissue-specific cells have begun, a major obstacle in the development of stem cell-based therapies is the inability to robustly differentiate ES cells into homogeneous populations of committed progenitors. On one hand, it is not currently possible to obtain large amounts of most cell types from differentiating ES cells. On the other hand, if undifferentiated ES cells remain within the population of cells transplanted into a patient, tumors may arise from this population. Therefore, a more comprehensive understanding of the factors regulating ES cell self-renewal and differentiation pathways should aid the design of more robust differentiation protocols that facilitate the development of ES cell-based therapies.
An unexpected finding from genome-scale studies is that the majority of the human genome is transcribed. Although protein-coding regions comprise only ~2% of the human genome, at least 75% is transcribed at detectable levels. These findings have led to a re-evaluation of the mammalian genome – if non-coding regions are transcribed, the resulting non-coding RNAs (ncRNAs) may have important functions. This possibility has tremendous ramifications for biomedical research, since clinical samples subjected to diagnostic sequencing are typically examined at only a subset of important genes, and only in their coding sequences.
One key regulatory mechanism shared among eukaryotes is the control of access to regulatory sequences by transcription factors through alteration of nucleosome occupancy or positioning. Nucleosome remodeling factors use the energy from ATP hydrolysis to reposition, deposit, or remove nucleosomes at regulatory regions by altering histone-DNA contacts. The actions of nucleosome remodeling factors are critical for transcription, DNA repair, and other essential cellular functions. Given their key roles in regulation of gene expression and genome integrity, it is perhaps not surprising that nucleosome remodeling factors are among the most commonly mutated or epigenetically silenced genes in human cancers and neurological disorders. However, the mechanisms by which loss of nucleosome remodeling factors function contributes to cancer and disease development are largely unknown.
Our lab will address a number outstanding questions regarding transcription regulation in murine ES cells and human cancer cells. Please contact us directly if you are interested in our work.
Enabling our studies, our research spans the disciplines of genomics, cell and molecular biology, biochemistry, and genetics.
Systems: we study mammalian cells in culture. We focus on mouse embryonic stem cells in order to understand cell fate, but also use other mouse cell lines and immortalized human cancer cell lines.
Techniques: we mainly use molecular biology and applied genomic techniques. In addition, we use some biochemistry and cell biology to address our questions. Specifically we use PCR, RT-qPCR, ChIP-qPCR, CRISPR/Cas9 targeting to generate cell lines, 3C, RNA-seq, nascent RNA-seq, ChIP-seq, (uli)CUT&RUN, ATAC-seq, MNase-seq, and Hi-C. We perform our own bioinformatic analyses on genome-wide datasets that we generate.