# Dissecting the establishment and regulation of human pluripotency

> **NIH NIH P01** · HARVARD UNIVERSITY · 2020 · $2,107,347

## Abstract

Human pluripotent cells hold great promise for numerous biomedical applications including eventual
use in regenerative medicine and personalized therapies. However, achieving this important goal requires a
better understanding of the regulatory circuitry that establishes and maintains molecular and functional
pluripotency. Our previous proposal has provided many profound new insights, data sets and tools for the
scientific community. We characterized transcription factor and epigenome dynamics, uncovered hundreds of
new non-coding DNA and long non-coding RNA (lncRNA) elements and began to assemble a comprehensive,
multi-layered pluripotent gene regulatory network. Through advancements in technology, experimental
systems and computational analysis we are now uniquely poised to take the next leap forward in “Dissecting
the establishment and regulation of human pluripotency”.
 Our current objective is to leverage these latest biological, experimental and computational advances to
close important gaps and provide a comprehensive, functional characterization of the regulatory landscape and
hierarchies in pluripotent stem cells as well as their dynamics during reprogramming. Specifically we will focus
on the following pressing questions that have arisen over the past years:
1) What is the exact nature of the pluripotent state(s) (Projects 1-3)? We already a comprehensive catalogue of
the regulatory elements and defining features to will help distinguish these states and will complete these at
unprecedented resolution. Why does the naïve state emerge only transiently during human reprogramming
(Project 1 and 3)? What are the implications of deregulating the pluripotent network including its cis regulatory
elements (Project 3)? What is the contribution of genetic variation and coding/non-coding transcription (Project
2 and 3)?
2) How is the pluripotent genome organized in three-dimensional space to establish pluripotency gene-
expression programs (Project 1-3)? It is becoming clear that lncRNAs can bind and influence the organization
of chromatin within the nucleus. We aim to understand molecular underpinnings of how RNA (Project 2), DNA
(Project 3) and epigenetic/transcription factors (Project 1) establish the nuclear architecture of the pluripotent
genome. We will develop novel visualization and genomic technologies in living and fixed cells to chart the
dynamic of reorganizing these factors (Project 2) and their functional implications in the process of
reprograming as well as during the maintenance of pluripotency (Project 1, 2 and 3).
3) What are the cis regulatory elements that reinforce the pluripotent state (Project 3)? In our previous proposal
we have identified numerous DNA cis regulatory modules (CRMs) and began to unravel RNA CRMs that guide
nuclear localization. We now aim to functionally characterize the sequences and motifs within CRMs on a
genome-wide scale (Project 2 and 3).

## Key facts

- **NIH application ID:** 9959199
- **Project number:** 5P01GM099117-09
- **Recipient organization:** HARVARD UNIVERSITY
- **Principal Investigator:** Andreas Gnirke
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,107,347
- **Award type:** 5
- **Project period:** 2011-08-01 → 2022-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9959199

## Citation

> US National Institutes of Health, RePORTER application 9959199, Dissecting the establishment and regulation of human pluripotency (5P01GM099117-09). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9959199. Licensed CC0.

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