Mammalian epigenetic mechanisms

On the presence and role of human gene-body DNA methylation

(2015) Daudi Jjingo et al.   Oncotarget

Ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG), components of the demethylation pathway, are direct targets of miRNA-29a

(2013) Pei Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Control of the Hippo Pathway by Set7-Dependent Methylation of Yap

(2013) Menno J. Oudhoff et al.   DEVELOPMENTAL CELL

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

(2013) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

On how mammalian transcription factors recognize methylated DNA

(2013) Bethany A. Buck-Koehntop et al.   Epigenetics

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

(2013) G. C. A. Taylor et al.   GENOME RESEARCH

Biochemical Analysis of Histone Deacetylase-independent Transcriptional Repression by MeCP2

(2013) Joshua W. M. Theisen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA

(2013) Ahmet Can Berkyurek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis of the Versatile DNA Recognition Ability of the Methyl-CpG Binding Domain of Methyl-CpG Binding Domain Protein 4

(2013) Junji Otani et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Novel mutation in the replication focus targeting sequence domain ofDNMT1causes hereditary sensory and autonomic neuropathy IE

(2013) Junhui Yuan et al.   JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM

Histone H3K27 Trimethylation Inhibits H3 Binding and Function of SET1-Like H3K4 Methyltransferase Complexes

(2013) D.-H. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication

(2013) Atsuya Nishiyama et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Methylation of SUV39H1 by SET7/9 results in heterochromatin relaxation and genome instability

(2013) D. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alteration of genic 5-hydroxymethylcytosine patterning in olfactory neurons correlates with changes in gene expression and cell identity

(2013) Bradley M. Colquitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA-143 is downregulated in breast cancer and regulates DNA methyltransferases 3A in breast cancer cells

(2013) Enders K. O. Ng et al.   TUMOR BIOLOGY

DNA methylation and transcriptional noise

(2013) Iksoo Huh et al.   Epigenetics & Chromatin

Crosstalk between SET7/9-dependent methylation and ARTD1-mediated ADP-ribosylation of histone H1.4

(2013) Ingrid Kassner et al.   Epigenetics & Chromatin

A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue

(2013) Tina Rönn et al.   PLoS Genetics

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

PKM2 Phosphorylates Histone H3 and Promotes Gene Transcription and Tumorigenesis

(2012) Weiwei Yang et al.   CELL

Appearance and heterochromatin localization of HP1α in early mouse embryos depends on cytoplasmic clock and H3S10 phosphorylation

(2012) Maciej Meglicki et al.   CELL CYCLE

Genome-wide aberrant DNA methylation of microRNA host genes in hepatocellular carcinoma

(2012) Jing Shen et al.   Epigenetics

Haploinsufficiency of Dnmt1 impairs leukemia stem cell function through derepression of bivalent chromatin domains

(2012) J. J. Trowbridge et al.   GENES & DEVELOPMENT

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

(2012) S. F. Pinter et al.   GENOME RESEARCH

Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy

(2012) Juliane Winkelmann et al.   HUMAN MOLECULAR GENETICS

MBD2 and Multiple Domains of CHD4 Are Required for Transcriptional Repression by Mi-2/NuRD Complexes

(2012) J. Ramirez et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone H3 Lysine 56 Methylation Regulates DNA Replication through Its Interaction with PCNA

(2012) Yongxin Yu et al.   MOLECULAR CELL

DNA methylation and microRNA dysregulation in cancer

(2012) Hiromu Suzuki et al.   Molecular Oncology

Chromatin 'resetting' during transcription elongation: a central role for methylated H3K36

(2012) Jill S Butler et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

(2012) Scott B Rothbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA methylation dynamics during the mammalian life cycle

(2012) J. A. Hackett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus

(2012) K. Nishi et al.   RNA

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

Active DNA demethylation by Gadd45 and DNA repair

(2012) Christof Niehrs et al.   TRENDS IN CELL BIOLOGY

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

(2012) Julia Arand et al.   PLoS Genetics

Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity

(2012) Mitsuhiro Endoh et al.   PLoS Genetics

Co-mutation of histone H2AX S139A with Y142A rescues Y142A-induced ionising radiation sensitivity

(2012) James A.L. Brown et al.   FEBS Open Bio

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Physical activity and breast cancer survival: an epigenetic link through reduced methylation of a tumor suppressor gene L3MBTL1

(2011) Hongmei Zeng et al.   BREAST CANCER RESEARCH AND TREATMENT

Phosphorylation of H2AX at Ser139 and a New Phosphorylation Site Ser16 by RSK2 Decreases H2AX Ubiquitination and Inhibits Cell Transformation

(2011) Feng Zhu et al.   CANCER RESEARCH

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Mouse miRNA-709 directly regulates miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system

(2011) Rui Tang et al.   CELL RESEARCH

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

(2011) M. Pawlak et al.   GENES & DEVELOPMENT

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

EZH1 and EZH2 cogovern histone H3K27 trimethylation and are essential for hair follicle homeostasis and wound repair

(2011) E. Ezhkova et al.   GENES & DEVELOPMENT

The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

(2011) Farisa Syeda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Critical Role of Monoubiquitination of Histone H2AX Protein in Histone H2AX Phosphorylation and DNA Damage Response

(2011) Ching-Yuan Wu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation

(2011) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Isoform-specific phosphorylation of human linker histone H1.4 in mitosis by the kinase Aurora B

(2011) S. P. Hergeth et al.   JOURNAL OF CELL SCIENCE

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing

(2011) Michael Reuter et al.   NATURE

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

(2011) Christopher J Klein et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

DiseaseMeth: a human disease methylation database

(2011) J. Lv et al.   NUCLEIC ACIDS RESEARCH

DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin

(2011) Burkhard Jakob et al.   NUCLEIC ACIDS RESEARCH

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

(2011) Y. Tao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Male germ cells express abundant endogenous siRNAs

(2011) Rui Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

(2011) Khursheed Iqbal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Regulation of UGT1A1 and HNF1 transcription factor gene expression by DNA methylation in colon cancer cells

(2010) Anne-Sophie Belanger et al.   BMC MOLECULAR BIOLOGY

MicroRNA-205-directed transcriptional activation of tumor suppressor genes in prostate cancer

(2010) Shahana Majid et al.   CANCER

Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4

(2010) Chengyang Huang et al.   CELL RESEARCH

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

A Modified “Cross-talk” between Histone H2B Lys-120 Ubiquitination and H3 Lys-79 Methylation

(2010) Agus Darwanto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II

(2010) Yupeng Zheng et al.   JOURNAL OF CELL BIOLOGY

Epigenetic inactivation of the tumor suppressor gene RIZ1 in hepatocellular carcinoma involves both DNA methylation and histone modifications

(2010) Cuijuan Zhang et al.   JOURNAL OF HEPATOLOGY

Histone H1 Poly[ADP]-Ribosylation Regulates the Chromatin Alterations Required for Learning Consolidation

(2010) A. Fontan-Lozano et al.   JOURNAL OF NEUROSCIENCE

Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18

(2010) Baolong Bao et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Role of ATM and the Damage Response Mediator Proteins 53BP1 and MDC1 in the Maintenance of G2/M Checkpoint Arrest

(2010) A. Shibata et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

(2010) Christian Popp et al.   NATURE

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons

(2010) Jian Feng et al.   NATURE NEUROSCIENCE

A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability

(2010) Pierre-Olivier Estève et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

(2010) J. Song et al.   SCIENCE

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

Learning How to Read ADP-Ribosylation

(2009) Henning Kleine et al.   CELL

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Importin 8 Is a Gene Silencing Factor that Targets Argonaute Proteins to Distinct mRNAs

(2009) Lasse Weinmann et al.   CELL

DNA hypomethylation restricted to the murine forebrain induces cortical degeneration and impairs postnatal neuronal maturation

(2009) Leah K. Hutnick et al.   HUMAN MOLECULAR GENETICS

Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase

(2009) Yoko Hayashi-Takanaka et al.   JOURNAL OF CELL BIOLOGY

MeCP2-Mediated Transcription Repression in the Basolateral Amygdala May Underlie Heightened Anxiety in a Mouse Model of Rett Syndrome

(2009) M. Adachi et al.   JOURNAL OF NEUROSCIENCE

Chromatin Binding of SRp20 and ASF/SF2 and Dissociation from Mitotic Chromosomes Is Modulated by Histone H3 Serine 10 Phosphorylation

(2009) Rebecca J. Loomis et al.   MOLECULAR CELL

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Rethinking how DNA methylation patterns are maintained

(2009) Peter A. Jones et al.   NATURE REVIEWS GENETICS

CRM1 mediates nuclear-cytoplasmic shuttling of mature microRNAs

(2009) D. Castanotto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Analysis of skewed X-chromosome inactivation in females with rheumatoid arthritis and autoimmune thyroid diseases

(2009) Ghazi Chabchoub et al.   ARTHRITIS RESEARCH & THERAPY

WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity

(2008) Andrew Xiao et al.   NATURE

The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men

(2008) Xiang-Jiao Yang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis

(2008) L.-X. Yan et al.   RNA

MeCP2, a Key Contributor to Neurological Disease, Activates and Represses Transcription

(2008) M. Chahrour et al.   SCIENCE

CpG island density and its correlations with genomic features in mammalian genomes

(2008) Leng Han et al.   GENOME BIOLOGY