title: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
abstract: BACKGROUND
  During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X chromosome. Here, we use mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation (XCI) and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq.
  
  
  RESULTS
  Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Allele-specific RNA-seq of neural progenitor cells generated from the female ESCs identifies three regions distal to the X-inactivation center that escape XCI. These regions, which stably escape during propagation and maintenance of XCI, coincide with topologically associating domains (TADs) as present in the female ESCs. Also, the previously characterized gene clusters escaping XCI in human fibroblasts correlate with TADs.
  
  
  CONCLUSIONS
  The gene silencing observed during XCI provides further insight in the establishment of the repressive complex formed by the inactive X chromosome. The association of escape regions with TADs, in mouse and human, suggests that TADs are the primary targets during propagation of XCI over the X chromosome.
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. H.Marks@ncmls.ru.nl.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Marks
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. H.Kerstens@ncmls.ru.nl.
authors.forename: Hindrik H D
authors.initials: HH
authors.lastname: Kerstens
authors.affiliation: Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. Stefan.Barakat@ed.ac.uk.
authors.forename: Tahsin Stefan
authors.initials: TS
authors.lastname: Barakat
authors.affiliation: Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands. Erik.Splinter@cergentis.com.
authors.forename: Erik
authors.initials: E
authors.lastname: Splinter
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. R.Dirks@ncmls.ru.nl.
authors.forename: René A M
authors.initials: RA
authors.lastname: Dirks
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. G.vanMierlo@science.ru.nl.
authors.forename: Guido
authors.initials: G
authors.lastname: van Mierlo
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. O.Joshi@ncmls.ru.nl.
authors.forename: Onkar
authors.initials: O
authors.lastname: Joshi
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. S.Wang@ncmls.ru.nl.
authors.forename: Shuang-Yin
authors.initials: SY
authors.lastname: Wang
authors.affiliation: Biology Department, Queen's University, Kingston, ON, Canada. tomas.babak@queensu.ca.
authors.forename: Tomas
authors.initials: T
authors.lastname: Babak
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. Kees.Albers@radboudumc.nl.
authors.forename: Cornelis A
authors.initials: CA
authors.lastname: Albers
authors.affiliation: Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. tk360@cam.ac.uk.
authors.forename: Tüzer
authors.initials: T
authors.lastname: Kalkan
authors.affiliation: Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK. Austin.Smith@cscr.cam.ac.uk.
authors.forename: Austin
authors.initials: A
authors.lastname: Smith
authors.affiliation: INRA, UMR1198 Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France. Alice.Jouneau@jouy.inra.fr.
authors.forename: Alice
authors.initials: A
authors.lastname: Jouneau
authors.affiliation: Hubrecht Institute, University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands. W.Laat@hubrecht.eu.
authors.forename: Wouter
authors.initials: W
authors.lastname: de Laat
authors.affiliation: Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. J.Gribnau@erasmusmc.nl.
authors.forename: Joost
authors.initials: J
authors.lastname: Gribnau
authors.affiliation: Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6500HB, Nijmegen, The Netherlands. H.Stunnenberg@ncmls.ru.nl.
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
mesh_terms: D000483:Alleles; D000818:Animals; D002843:Chromatin / Q000737:chemistry; D058732:Embryoid Bodies / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D005260:Female; D020868:Gene Silencing; D006801:Humans; D051379:Mice; D058953:Neural Stem Cells / Q000378:metabolism; D017423:Sequence Analysis, RNA; D049951:X Chromosome Inactivation
chemical_list: D002843:Chromatin