# Mechanisms of transcription factor-guided enhancer reorganization and heterochromatin disassembly during reprogramming to iPSCs

> **NIH NIH P01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2020 · $423,739

## Abstract

PROJECT SUMMARY
The overall goal of this proposal is to reveal the molecular mechanisms by which the reprogramming factors
Oct4 (O), Sox2 (S), Klf4 (K), and cMyc (M) revert somatic cells to iPSCs. Conversion of somatic cells to
pluripotency is the most robust example of cellular reprogramming. In many other cases of transcription factor
(TF)-induced cell fate conversion, for example the direct conversion of fibroblasts to neurons, cells fail to
completely silence the starting cell transcriptome. Thus, uncovering mechanisms by which OSKM inactivate
the somatic program and activate the pluripotency program during reprogramming to iPSCs will reveal
important principles of how cell identity is maintained and effectively converted, and enable novel approaches
to make cellular reprogramming, including lineage conversions, more efficient and faithful. In preliminary
studies, we determined the genomic locations of OSKM early in reprogramming of mouse fibroblasts and in the
pluripotent state, which revealed a dramatic change of OSKM targets during reprogramming and engendered
new hypotheses about the action of OSKM. Early in reprogramming, the essential reprogramming factors OSK
only engage a small set of pluripotency enhancers and, unexpectedly, bind extensively to somatically active
enhancers. At this early time point, when very few transcriptional changes occur, we observed that almost all
somatic enhancers lose active chromatin marks. Explaining how somatic enhancer decommissioning may
occur, we found that somatic TFs are redistributed away from somatic enhancers early in reprogramming, to
other genomic sites bound by OSK. Our findings lead to the unique hypothesis that OSK orchestrate
reprogramming by mediating the activation of pluripotency enhancers as well as the silencing of somatic
enhancers, and we speculate that the effect of OSK on somatic TFs is similarly important for reprogramming
as step-wise pluripotency enhancer activation. Another crucial step that we defined in the reprogramming
process is the reactivation of the inactive X chromosome (Xi). We discovered that Xi-reactivation is associated
with DNA demethylation and is one of the final steps of reprogramming. How the disassembly of this
heterochromatic structure is achieved is unknown. Based on our studies and collaborations with the Zaret lab
on silencing via heterochromatin and the Hochedlinger lab on post-transcriptional control, we are well
positioned to unveil the mechanisms underlying OSK's step-wise engagement of pluripotency enhancers,
somatic enhancer decommissioning by OSK, and Xi-reactivation, with these Aims: 1) To uncover the
mechanisms by which OSK target and modulate somatic and pluripotency enhancers early in reprogramming.
2) To define the co-factors required for the step-wise selection and activation of pluripotency enhancers by
OSK. 3) To delineate mechanisms of Xi-reactivation and heterochromatin disassembly. While we will perform
most experiments on fibroblast repr...

## Key facts

- **NIH application ID:** 9930459
- **Project number:** 5P01GM099134-09
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** Kathrin Plath
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $423,739
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9930459

## Citation

> US National Institutes of Health, RePORTER application 9930459, Mechanisms of transcription factor-guided enhancer reorganization and heterochromatin disassembly during reprogramming to iPSCs (5P01GM099134-09). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9930459. Licensed CC0.

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