Project Details
Description
The mammalian genome folds into tens of thousands of long-range looping interactions. A
critical unknown is whether and how chromatin loops control gene expression, and a major
unresolved question is how the temporal progression of loops relates to transcription dynamics.
One major barrier to answering this question is that loops change on a range of timescales,
necessitating the use of tools and model systems amenable to tracking and engineering loops
longitudinally and in real time on both short and long timing. Here, we propose to develop and
apply new engineering and imaging tools to measure, induce, and perturb loops with precise
temporal control in three different biological systems spanning minutes, hours, and weeks. At
the shortest timescale (minutes, Aim 1), we will examine loop dynamics in human induced
pluripotent stem cell-derived neurons in response to electrical stimulation, revealing how
interaction frequency is functionally connected to transcriptional bursting of immediate early and
secondary response genes. On the timescale of hours (Aim 3), we will elucidate how the
architectural protein YY1 connects enhancer-promoter loops that re-assemble upon the exit
from mitosis by erythroid cells. On the timescale of weeks (Aim 2), we will use a cellular “Time
Machine” to longitudinally track the rare cells that undergo cellular reprogramming, allowing us
to dissect the functionality of loop formation and dissolution with single-cell and subcellular
resolution during the reprogramming of somatic cells to pluripotency and transition of melanoma
cancer cells to a resistant phenotype. Our team consists of a highly productive and collaborative
set of junior and senior investigators with complementary expertise and overlapping interests,
including Dr. Gerd Blobel (epigenetics, mitosis, loop engineering), Dr. Eric Joyce (Oligopaints
imaging), Dr. Bomyi Lim (nascent transcript live cell imaging), Dr. Jennifer Phillips-Cremins
(chromatin architecture, loop engineering, neurobiology), Dr. Stanley Qi (CRISPR genome
engineering, live cell imaging), and Dr. Arjun Raj (single cell genomics, RNA imaging,
reprogramming). We will develop and apply live and fixed cell imaging techniques for chromatin
contacts, and in the same cells image nascent transcription. We will build a cadre of synthetic
architectural proteins to engineer loops in a time-dependent inducible manner. Successful
application of our engineering and imaging tools across biological systems will yield a
comprehensive and rigorous assessment of the cause-and-effect relationship between loops
and distinct biological phenotypes across timescales.
Status | Active |
---|---|
Effective start/end date | 9/16/20 → 6/30/24 |
Funding
- National Institute of Diabetes and Digestive and Kidney Diseases: $1,108,388.00
- National Institute of Diabetes and Digestive and Kidney Diseases: $1,122,096.00
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