Post date: 06/05/19
Research Goal
The work performed in my laboratory will help determine how the 3-dimensional organization of DNA within each cell affects cellular function and identity throughout development.
Current Research
Importance of chromatin insulators
It has become increasingly apparent that proper control of gene expression requires complex organization of DNA at the level of chromatin. Chromatin insulators are DNA-protein complexes that influence gene expression by establishing chromatin domains subject to distinct transcriptional controls, likely through alteration of their spatial organization. Insulators enforce the strict specific and temporal expression of loci with complex enhancer and/or promoter configuration. Examples include metazoan Hox genes, master regulators of body segmentation, and the vertebrate beta-globin locus, which changes in expression during erythroid development. Loss of insulator activity can result in substantial positive or negative changes in gene expression, culminating in disease, defects in development, and/or lethality. For example, deletion of insulator binding sites at the H19/IGF2 imprinting center have been implicated in Beckwith-Wiedemann syndrome and Wilms’ Tumor. Moreover, recent studies have shown that loss of insulator activity in IDH1 mutant gliomas and T cell acute lymphoblastic leukemias leads to disruption of boundaries between chromatin domains and subsequent oncogene activation.
The gypsy chromatin insulator
We primarily utilize the biochemically and genetically tractable model system Drosophila, which harbors the largest diversity of known chromatin insulator complexes. Defined by the specific binding of the Su(Hw) zinc finger DNA-binding protein, gypsy insulator complexes tend to associate with gene-poor, transcriptionally inert regions of the genome. Within the nucleus, gypsy insulator complexes concentrate at approximately 200nm diameter ovoid structures termed insulator bodies, which are tethered stably to the nuclear matrix. The proper localization of insulator bodies is highly correlated with gypsy chromatin insulator function, but their precise function and spatial relationship with respect to the genome is not well understood. We are investigating the cofactors required for and the ultrastructure of insulator bodies within the surrounding chromatin environment.
Tissue-specific regulation of insulator activity
We recently identified two novel, tissue-specific negative regulators of gypsy insulator function that affect both enhancer blocking and barrier activities. Shep can bind directly to Su(Hw) as well as another core component of the gypsy insulator complex, potentially competing with inter- or intra-insulator complex interactions and thereby neutralizing insulator activity. Shep is required for neuronal remodeling during development and is highly enriched in the CNS, perhaps serving to negatively regulate insulator function in these cell types to promote CNS-specific gene expression programs. Shep harbors two highly conserved RNA recognition motifs (RRMs), and genetic evidence points to a functional relationship between its RNA-binding capability and insulator function. In contrast, Rump, which contains 3 RRMs, antagonizes gypsy insulator activity in tissues outside of the CNS.
RNA-dependent insulator function
Using RNA immunoprecipitation followed by deep sequencing (RIP-seq), we made the striking finding that certain mRNAs, including that encoding Su(Hw) itself, associate stably with gypsy insulator complexes. Expression of untranslatable versions of these mRNAs alters insulator body localization and promotes insulator activity. We speculate that these, and possibly other mRNAs, also harbor a noncoding function, such as acting as a scaffold for insulator complexes at specific subnuclear locations. We continue to delve into the mechanisms by which these mRNAs function and the roles of associated RNA-binding proteins in insulator regulation.
This work was highlighted in Editors' Choice, Riddihough G. Noncoding mRNAs. Science, (341)6149: 938, 2013.) Link: http://www.sciencemag.org/content/341/6149/twil.full
Roles and Responsibilities
A postbaccalaureate IRTA position is available in Dr. Elissa Lei’s lab on the main NIH campus in Bethesda, MD. We combine computational approaches with molecular biology, biochemistry, genetics, cellular biology and behavioral biology to study mechanisms by which genome 3D organization influences neuronal maturation during development. Our research employs both fruit fly and mouse as our model organisms to provide fundamental mechanistic information. The trainee will have an opportunity to broaden their experience in basic research and cutting-edge technologies, including molecular techniques (e.g., CRISPR-based generation of transgenic animals, cloning, high throughput sequencing), developmental neuroscience, and computational biology.
About You
Applications are invited from highly motivated biologists with a B.S. or M.S. degree with a strong background in genetics and molecular biology. Previous experience in laboratory research is required.
Application
Interested individuals should send a cover letter including career goals and research interests, curriculum vitae, and the names and contact information of three references via e-mail to Dr. Dahong Chen (dahong.chen@nih.gov).
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