title: Local compartment changes and regulatory landscape alterations in histone H1-depleted cells.
abstract: BACKGROUND
  Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. Here we have used a combination of genome-wide approaches including DNA methylation, histone modification and DNase I hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function.
  
  
  RESULTS
  We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associating domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs.
  
  
  CONCLUSIONS
  Our data show that cells require normal histone H1 levels to expose their proper regulatory landscape. Reducing the levels of histone H1 results in massive epigenetic changes and altered topological organization particularly at the most active chromosomal domains. Changes in TAD configuration coincide with epigenetic landscape changes but not with transcriptional output changes, supporting the emerging concept that transcriptional control and nuclear positioning of TADs are not causally related but independently controlled by the locally associated trans-acting factors.
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. g.geeven@hubrecht.eu.
authors.forename: Geert
authors.initials: G
authors.lastname: Geeven
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. zhuyun1104@gmail.com.
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA. byungju@hotmail.com.
authors.forename: Byung Ju
authors.initials: BJ
authors.lastname: Kim
authors.affiliation: Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA. boris.bartholdy@einstein.yu.edu.
authors.forename: Boris A
authors.initials: BA
authors.lastname: Bartholdy
authors.affiliation: Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA. seung-min.yang@einstein.yu.edu.
authors.forename: Seung-Min
authors.initials: SM
authors.lastname: Yang
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA. todd.macfarlan@nih.gov.
authors.forename: Todd S
authors.initials: TS
authors.lastname: Macfarlan
authors.affiliation: Gene Expression Laboratory and the Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, CA, 92037, USA. wesgifford@gmail.com.
authors.forename: Wesley D
authors.initials: WD
authors.lastname: Gifford
authors.affiliation: Gene Expression Laboratory and the Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, CA, 92037, USA. Pfaff@Salk.edu.
authors.forename: Samuel L
authors.initials: SL
authors.lastname: Pfaff
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. m.verstegen@hubrecht.eu.
authors.forename: Marjon J A M
authors.initials: MJ
authors.lastname: Verstegen
authors.affiliation: Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
authors.forename: Hugo
authors.initials: H
authors.lastname: Pinto
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. m.vermunt@hubrecht.eu.
authors.forename: Marit W
authors.initials: MW
authors.lastname: Vermunt
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. m.creyghton@hubrecht.eu.
authors.forename: Menno P
authors.initials: MP
authors.lastname: Creyghton
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. p.wijchers@hubrecht.eu.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Wijchers
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. jstam@uw.edu.|Department of Medicine, Division of Oncology, University of Washington, Seattle, WA, 98195, USA. jstam@uw.edu.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.affiliation: Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA. arthur.skoultchi@einstein.yu.edu.
authors.forename: Arthur I
authors.initials: AI
authors.lastname: Skoultchi
authors.affiliation: Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. w.delaat@hubrecht.eu.
authors.forename: Wouter
authors.initials: W
authors.lastname: de Laat
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D044127:Epigenesis, Genetic; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D051379:Mice
chemical_list: D002843:Chromatin; D006657:Histones