The overall goal of this component project is to identify and reverse engineer the cis-regulatory modules (CRMs) that direct the activation, maintenance and repression of gene expression in human pluripotent cells. The project innovates by applying high-throughput and quantitative genomic technologies to dissect key components of the pluripotency gene regulatory network (CRMs) at unprecedented resolution and scale. First, we will generate a genome-wide map of putative CRMs with specific activity in pluripotent cells, using computational analysis of new and existing TF localization and chromatin profiling data. We will then select genomic loci that harbor genes which correct regulation have previously been shown to be important for maintenance of pluripotency and self-renewal for in-depth validation and functional analysis. Second, we will select representative CRMs from these loci for systematic dissection of the relationship between their sequences and regulatory activities at single-nucleotide resolution. Third, we will classify pluripotency CRMs according to whether they are activated eariy or late in the reprogramming process, and then explore the mechanistic basis for these differences using systematic perturbation experiments. Finally, we will then use data from all of our experiments to construct quantitative models of pluripotency CRMs that integrate interactions between their DNA sequences, local chromatin structure and trans-regulatory factors.

Public Health Relevance

(See Instructions): The goal of this project is to uncover how the rules that govern gene expression in stem cells are encoded in human DNA. Insights into this question will help us understand the genetic basis for human development and disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
1P01GM099117-01
Application #
8206145
Study Section
Special Emphasis Panel (ZGM1-GDB-8 (IP))
Project Start
Project End
Budget Start
2011-08-01
Budget End
2012-07-31
Support Year
1
Fiscal Year
2011
Total Cost
$472,938
Indirect Cost
Name
Harvard University
Department
Type
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Pasque, Vincent; Karnik, Rahul; Chronis, Constantinos et al. (2018) X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs. Stem Cell Reports 10:1537-1550
Charlton, Jocelyn; Downing, Timothy L; Smith, Zachary D et al. (2018) Global delay in nascent strand DNA methylation. Nat Struct Mol Biol 25:327-332
Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L et al. (2018) Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell 69:1039-1045.e3
Shukla, Chinmay J; McCorkindale, Alexandra L; Gerhardinger, Chiara et al. (2018) High-throughput identification of RNA nuclear enrichment sequences. EMBO J 37:
Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L et al. (2018) Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell 70:188-189
Ichida, Justin K; Staats, Kim A; Davis-Dusenbery, Brandi N et al. (2018) Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons. Development 145:
Maass, Philipp G; Barutcu, A Rasim; Shechner, David M et al. (2018) Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol 25:176-184
Choi, Jiho; Clement, Kendell; Huebner, Aaron J et al. (2017) DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell 20:706-719.e7
Melé, Marta; Mattioli, Kaia; Mallard, William et al. (2017) Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res 27:27-37
Smith, Zachary D; Shi, Jiantao; Gu, Hongcang et al. (2017) Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549:543-547

Showing the most recent 10 out of 62 publications