Starting in Summer 2022

“Dark” genome in cell fate decisions

Successful development of a single cell into a complex multicellular organism requires precise coordination of multiple regulatory layers that define cell fate. In mammals, the first lineage-specific transcription pattern emerges as drastic remodeling of 3D chromatin organization occurs. However, we still lack information about the functional relationship between these concurrent changes in gene expression and DNA structure during early development, and do not understand the precise molecular mechanisms by which they occur. To address this, my lab will employ a novel, genome-wide technology that allows simultaneous measurement of 3D nuclear organization and transcription within single cells, combined with systematic functional identification of key lineage specification regulators. Recent studies, including my previous work, show that DNA and RNA from the “dark” genome (i.e., transposons, repeats, lncRNAs) can affect global genome organization and gene expression and may act as a previously unappreciated driving force during early development. Thus, my lab will specifically focus on investigating the regulatory role of “dark” elements in shaping genome functions during first lineage-specification in mammals.


Keywords: early embryonic development, “dark” genome, 3D chromatin organization, gene expression, single cell omics


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