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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
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Special Emphasis Panel (ZGM1-GDB-8)
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Harvard University
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Hacisuleyman, Ezgi; Goff, Loyal A; Trapnell, Cole et al. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21:198-206
Rinn, John; Guttman, Mitchell (2014) RNA Function. RNA and dynamic nuclear organization. Science 345:1240-1
Smith, Zachary D; Chan, Michelle M; Humm, Kathryn C et al. (2014) DNA methylation dynamics of the human preimplantation embryo. Nature 511:611-5
Lu, Yu; Loh, Yuin-Han; Li, Hu et al. (2014) Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 15:92-101
Trapnell, Cole; Cacchiarelli, Davide; Grimsby, Jonna et al. (2014) The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32:381-6
Ichida, Justin K; TCW, Julia; T C W, Julia et al. (2014) Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol 10:632-9
Federation, Alexander J; Bradner, James E; Meissner, Alexander (2014) The use of small molecules in somatic-cell reprogramming. Trends Cell Biol 24:179-87
Karnik, Rahul; Meissner, Alexander (2013) Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Cell Stem Cell 13:14-21
Sun, Lei; Goff, Loyal A; Trapnell, Cole et al. (2013) Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A 110:3387-92
Smith, Zachary D; Meissner, Alexander (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14:204-20

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