# Epigenetic control of the human X chromosome

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2021 · $427,382

## Abstract

PROJECT SUMMARY
The overall goal of this proposal is to study the regulation of X-chromosome dosage compensation by long-
noncoding (lnc) RNAs in human embryonic stem cells (hESCs) to fundamentally advance the understanding of
early human development, the regulation of pluripotency states, and mechanisms of gene regulation by lncRNAs.
X-chromosome dosage compensation is an essential process that equalizes X-linked gene expression between
females and males and is initiated early in development. In mammals, it is mediated by X-chromosome
inactivation (XCI), the transcriptional silencing of genes on one of the two X-chromosomes in females.
Mechanistic studies of XCI have been carried out in mice and established that the lncRNA Xist, encoded on the
X chromosome, spreads along the X chromosome to mediate XCI. Although XCI occurs in both mouse and
human post-implantation development, the regulation of X-chromosome dosage in pre-implantation embryos
has evolved differently between the two species. In pre-implantation development, mouse embryos undergo an
imprinted form of XCI, while human embryos lack imprinted XCI and instead regulate gene expression by
dampening transcription on both X-chromosomes. X-chromosome dampening (XCD) is different from XCI as it
occurs on both X chromosomes in contrast to the complete transcriptional silencing of one X. Additional
remarkable differences between human and mouse include the unprecedented expression and accumulation of
XIST on the active (dampened) X-chromosomes and the expression of the primate- and pluripotency-specific
lncRNA XACT from the X in human pre-implantation embryos. Thus, X-linked gene dosage in humans is
regulated first by XCD and upon implantation by XCI, and remarkably, XIST expression is uncoupled from
silencing when XCD takes place. A mechanistic understanding of XCD, lack of silencing by XIST in pre-
implantation embryos, XIST's transition to mediating XCI, and the role of the lncRNA XACT is lacking, and it is
not known if XIST has any role in human pre-implantation cells or XCD. We discovered that naïve hESCs
recapitulate in vitro many of the unique features of human X-chromosome dosage compensation, including XCD,
expression of XIST on active X-chromosomes, XACT expression, and initiation of XCI upon differentiation. Here,
we will take advantage of naïve hESCs to investigate how XIST expression does not induce silencing early in
development and later acquires the ability to silence, to reveal regulatory mechanisms of human XCD and XCI,
and if XACT controls XIST functions. We have the following Specific Aims: 1) We will define the function of XIST
in naïve hESCs, its requirement for XCD, and mechanisms of XCD. 2) We will define chromatin targets and
protein interactors of XIST to understand its differential silencing ability in naïve and primed hESCs. 3) We will
characterize the function and localization of the lncRNA XACT. Understanding the mechanisms of human X-
chromosome dosage compensati...

## Key facts

- **NIH application ID:** 10152632
- **Project number:** 5R01HD098387-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** Kathrin Plath
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $427,382
- **Award type:** 5
- **Project period:** 2019-05-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10152632

## Citation

> US National Institutes of Health, RePORTER application 10152632, Epigenetic control of the human X chromosome (5R01HD098387-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10152632. Licensed CC0.

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