Diverse heterochromatin states restricting cell identity and reprogramming

SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers

(2022) Amandine Barral et al.   MOLECULAR CELL

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

(2022) Nathaniel L. Burge et al.   BIOCHEMISTRY

Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression

(2022) William Garland et al.   MOLECULAR CELL

Rolling back human pluripotent stem cells to an eight-cell embryo-like stage

(2022) Md. Abdul Mazid et al.   NATURE

Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance

(2022) Jan Padeken et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pioneer factors as master regulators of the epigenome and cell fate

(2022) Aurelio Balsalobre et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome

(2022) Spencer A. Haws et al.   CELL

Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development

(2022) Hanwen Yu et al.   Cell Stem Cell

Hijacking of transcriptional condensates by endogenous retroviruses

(2022) Vahid Asimi et al.   NATURE GENETICS

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

SUV39H2 epigenetic silencing controls fate conversion of epidermal stem and progenitor cells

(2021) Pierre Balmer et al.   JOURNAL OF CELL BIOLOGY

The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity

(2021) Jiadong Liu et al.   NATURE

Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos

(2021) Zhiyuan Chen et al.   NATURE GENETICS

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation

(2021) Wendan Ren et al.   Nature Communications

Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain

(2021) Christopher J. Playfoot et al.   GENOME RESEARCH

Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements

(2021) Ryan L. McCarthy et al.   NATURE CELL BIOLOGY

Dissecting OCT4 defines the role of nucleosome binding in pluripotency

(2021) Gareth A. Roberts et al.   NATURE CELL BIOLOGY

Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability

(2021) Sheldon Decombe et al.   Epigenetics & Chromatin

MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells

(2021) Iris Müller et al.   Nature Communications

Complete loss of H3K9 methylation dissolves mouse heterochromatin organization

(2021) Thomas Montavon et al.   Nature Communications

MAP2K6 remodels chromatin and facilitates reprogramming by activating Gatad2b-phosphorylation dependent heterochromatin loosening

(2021) Guangsuo Xing et al.   CELL DEATH AND DIFFERENTIATION

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development

(2021) Pia A. Johansson et al.   Cell Stem Cell

Seeking the truth behind the myth: Argonaute tales from “nuclearland”

(2021) Ezequiel Nazer et al.   MOLECULAR CELL

H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity

(2021) Stephen P. Methot et al.   NATURE CELL BIOLOGY

Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing

(2021) Kentaro Mochizuki et al.   Nature Communications

ChromID identifies the protein interactome at chromatin marks

(2020) Rodrigo Villaseñor et al.   NATURE BIOTECHNOLOGY

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

MicroRNA Clustering Assists Processing of Suboptimal MicroRNA Hairpins through the Action of the ERH Protein

(2020) Wenwen Fang et al.   MOLECULAR CELL

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes

(2020) Aditya Sankar et al.   NATURE CELL BIOLOGY

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3

(2020) Adam Burton et al.   NATURE CELL BIOLOGY

The roles of histone variants in fine-tuning chromatin organization and function

(2020) Sara Martire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction

(2020) Sean E. Healton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Field Guide to Eukaryotic Transposable Elements

(2020) Jonathan N. Wells et al.   Annual Review of Genetics

Interaction of the pioneer transcription factor GATA3 with nucleosomes

(2020) Hiroki Tanaka et al.   Nature Communications

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

(2019) Dario Nicetto et al.   SCIENCE

A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing

(2019) Guodong Xie et al.   Nature Communications

m6A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins

(2019) Ditipriya Hazra et al.   Genes

H3K27me3 is an epigenetic barrier while KDM6A overexpression improves nuclear reprogramming efficiency

(2019) Chuan Zhou et al.   FASEB JOURNAL

Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains

(2019) Kelvin See et al.   DEVELOPMENT

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

(2019) Julien Pontis et al.   Cell Stem Cell

H3K9me3 is required for inheritance of small RNAs that target a unique subset of newly evolved genes

(2019) Itamar Lev et al.   eLife

Structural Features of Transcription Factors Associating with Nucleosome Binding

(2019) Meilin Fernandez Garcia et al.   MOLECULAR CELL

H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

(2019) Andrey Poleshko et al.   eLife

Active and Repressed Chromatin Domains Exhibit Distinct Nucleosome Segregation during DNA Replication

(2019) Thelma M. Escobar et al.   CELL

Heterochromatin loosening by the Oct4 linker region facilitates Klf4 binding and iPSC reprogramming

(2019) Keshi Chen et al.   EMBO JOURNAL

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo et al.   MOLECULAR CELL

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression

(2019) Simone Tamburri et al.   MOLECULAR CELL

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes

(2018) Luisa Robbez-Masson et al.   GENOME RESEARCH

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

(2018) Chenfei Wang et al.   NATURE CELL BIOLOGY

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate

(2018) Alexandre Mayran et al.   NATURE GENETICS

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

The epigenetic control of stemness in CD8+T cell fate commitment

(2018) Luigia Pace et al.   SCIENCE

Heterochromatin: Guardian of the Genome

(2018) Aniek Janssen et al.   Annual Review of Cell and Developmental Biology

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

(2018) Nofar Mor et al.   Cell Stem Cell

The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin

(2018) Shujun Cai et al.   MOLECULAR BIOLOGY OF THE CELL

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Nimble and Ready to Mingle: Transposon Outbursts of Early Development

(2018) Diego Rodriguez-Terrones et al.   TRENDS IN GENETICS

Enhancer of rudimentary homologue interacts with scaffold attachment factor B at the nuclear matrix to regulate SR protein phosphorylation

(2017) Sotiria Drakouli et al.   FEBS Journal

Dynamic changes in H1 subtype composition during epigenetic reprogramming

(2017) Annalisa Izzo et al.   JOURNAL OF CELL BIOLOGY

Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation

(2017) Svetlana Petruk et al.   MOLECULAR CELL

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

(2017) Justin S. Becker et al.   MOLECULAR CELL

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo

(2017) Joanna W Jachowicz et al.   NATURE GENETICS

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

(2017) Oscar Velazquez Camacho et al.   eLife

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

(2017) Whitney L Johnson et al.   eLife

KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency

(2017) Jingwei Wei et al.   Scientific Reports

Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

(2016) Gabriela Ecco et al.   DEVELOPMENTAL CELL

The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system

(2016) Letizia Venturini et al.   EXPERIMENTAL HEMATOLOGY

A Histone Methyltransferase ESET Is Critical for T Cell Development

(2016) Shoichi Takikita et al.   JOURNAL OF IMMUNOLOGY

Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly

(2016) Tomoyasu Sugiyama et al.   MOLECULAR CELL

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

TRIM28 Is an Epigenetic Barrier to Induced Pluripotent Stem Cell Reprogramming

(2016) Denise Catherine Miles et al.   STEM CELLS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

The histone chaperone CAF-1 safeguards somatic cell identity

(2015) Sihem Cheloufi et al.   NATURE

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Epigenetic silencing of Oct4 by a complex containing SUV39H1 and Oct4 pseudogene lncRNA

(2015) Michele Scarola et al.   Nature Communications

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

Embryonic Development following Somatic Cell Nuclear Transfer Impeded by Persisting Histone Methylation

(2014) Shogo Matoba et al.   CELL

Direct Reprogramming of Human Fibroblasts to Functional and Expandable Hepatocytes

(2014) Pengyu Huang et al.   Cell Stem Cell

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis

(2014) Adam Burton et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic inheritance uncoupled from sequence-specific recruitment

(2014) K. Ragunathan et al.   SCIENCE

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

An epigenetic silencing pathway controlling T helper 2 cell lineage commitment

(2012) Rhys S. Allan et al.   NATURE

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs

(2012) Jiekai Chen et al.   NATURE GENETICS

Histone H4K20me3 and HP1  are late heterochromatin markers in development, but present in undifferentiated embryonic stem cells

(2011) T. Wongtawan et al.   JOURNAL OF CELL SCIENCE

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

A Strand-Specific Burst in Transcription of Pericentric Satellites Is Required for Chromocenter Formation and Early Mouse Development

(2010) Aline.V. Probst et al.   DEVELOPMENTAL CELL

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming

(2009) Sylvain Daujat et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos

(2008) Mareike Puschendorf et al.   NATURE GENETICS