title: Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation.
abstract: Applications of embryonic stem cells (ESCs) require faithful chromatin changes during differentiation, but the fate of the X chromosome state in differentiating ESCs is unclear. Female human ESC lines either carry two active X chromosomes (XaXa), an Xa and inactive X chromosome with or without XIST RNA coating (XiXIST+Xa;XiXa), or an Xa and an eroded Xi (XeXa) where the Xi no longer expresses XIST RNA and has partially reactivated. Here, we established XiXa, XeXa, and XaXa ESC lines and followed their X chromosome state during differentiation. Surprisingly, we found that the X state pre-existing in primed ESCs is maintained in differentiated cells. Consequently, differentiated XeXa and XaXa cells lacked XIST, did not induce X inactivation, and displayed higher X-linked gene expression than XiXa cells. These results demonstrate that X chromosome dosage compensation is not required for ESC differentiation. Our data imply that XiXIST+Xa ESCs are most suited for downstream applications and show that all other X states are abnormal byproducts of our ESC derivation and propagation method.
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Sanjeet
authors.initials: S
authors.lastname: Patel
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Bonora
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Sahakyan
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Kim
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Chronis
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Langerman
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Sorel
authors.initials: S
authors.lastname: Fitz-Gibbon
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Liudmilla
authors.initials: L
authors.lastname: Rubbi
authors.affiliation: Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Rhys J P
authors.initials: RJP
authors.lastname: Skelton
authors.affiliation: Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Reza
authors.initials: R
authors.lastname: Ardehali
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Lowry
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Amander T
authors.initials: AT
authors.lastname: Clark
authors.affiliation: Department of Biological Chemistry, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: kplath@mednet.ucla.edu.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Plath
mesh_terms: D002454:Cell Differentiation / Q000187:drug effects / Q000235:genetics*; D002460:Cell Line; D019175:DNA Methylation / Q000235:genetics; D005260:Female; D005786:Gene Expression Regulation / Q000187:drug effects; D020868:Gene Silencing / Q000187:drug effects; D000066449:Human Embryonic Stem Cells / Q000187:drug effects / Q000378:metabolism*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D057026:Induced Pluripotent Stem Cells / Q000187:drug effects / Q000378:metabolism; D008297:Male; D017423:Sequence Analysis, RNA; D014212:Tretinoin / Q000494:pharmacology; D049951:X Chromosome Inactivation / Q000235:genetics*
chemical_list: D014212:Tretinoin
keywords: DNA methylation; X-chromosome dosage compensation; X-inactivation; Xi-erosion; Xist; human embryonic stem cells; human induced pluripotent stem cells; inactive X chromosome