Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation

Anna Sahakyan; Rachel Kim; Constantinos Chronis; Shan Sabri; Giancarlo Bonora; Thorold W Theunissen; Edward Kuoy; Justin Langerman; Amander T Clark; Rudolf Jaenisch; Kathrin Plath

doi:10.1016/j.stem.2016.10.006

Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation

Cell Stem Cell. 2017 Jan 5;20(1):87-101. doi: 10.1016/j.stem.2016.10.006. Epub 2016 Dec 15.

Authors

Affiliations

¹ Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁴ Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁵ Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁶ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
⁷ Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁸ Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
⁹ Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: kplath@mednet.ucla.edu.

Abstract

Naive human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocysts, but their X chromosome state has remained unresolved. Here, we show that the inactive X chromosome (X_i) of primed hESCs was reactivated in naive culture conditions. Like cells of the blastocyst, the resulting naive cells contained two active X chromosomes with XIST expression and chromosome-wide transcriptional dampening and initiated XIST-mediated X inactivation upon differentiation. Both establishment of and exit from the naive state (differentiation) happened via an XIST-negative X_aX_a intermediate. Together, these findings identify a cell culture system for functionally exploring the two X chromosome dosage compensation processes in early human development: X dampening and X inactivation. However, remaining differences between naive hESCs and embryonic cells related to mono-allelic XIST expression and non-random X inactivation highlight the need for further culture improvement. As the naive state resets X_i abnormalities seen in primed hESCs, it may provide cells better suited for downstream applications.

Keywords: X chromosome; X chromosome dampening; X chromosome inactivation; XIST; embryonic stem cells; human development; human stem cells; lncRNA; naive pluripotency; pluripotent stem cells.

Published by Elsevier Inc.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Blastocyst / cytology
Blastocyst / metabolism
Cell Differentiation / genetics
Cells, Cultured
Chromosomes, Human, X / genetics*
DNA Methylation / genetics
Female
Histones / metabolism
Human Embryonic Stem Cells / cytology
Human Embryonic Stem Cells / metabolism
Humans
Lysine / metabolism
Methylation
Pluripotent Stem Cells / cytology
Pluripotent Stem Cells / metabolism*
RNA, Long Noncoding / genetics
RNA, Long Noncoding / metabolism
X Chromosome Inactivation / genetics*

Substances

Histones
RNA, Long Noncoding
XIST non-coding RNA
Lysine

Abstract

Publication types

MeSH terms

Substances

Grants and funding