Whole-genome sequencing of H3K4me3 and DNA methylation in human sperm reveals regions of overlap linked to fertility and development

Histone H3 lysine 4 trimethylation in sperm is transmitted to the embryo and associated with diet-induced phenotypes in the offspring

(2021) Ariane Lismer et al.   DEVELOPMENTAL CELL

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells

(2020) Donnchadh S. Dunican et al.   BMC BIOLOGY

Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation

(2020) J. Yuyang Lu et al.   Cell Reports

Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription

(2020) Mami Oikawa et al.   Nature Communications

Sperm histone H3 lysine 4 trimethylation is altered in a genetic mouse model of transgenerational epigenetic inheritance

(2020) Ariane Lismer et al.   NUCLEIC ACIDS RESEARCH

The genomic distribution of histone H3K4me2 in spermatogonia is highly conserved in sperm†

(2019) Romain Lambrot et al.   BIOLOGY OF REPRODUCTION

Resetting histone modifications during human parental-to-zygotic transition

(2019) Weikun Xia et al.   SCIENCE

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

GenPipes: an open-source framework for distributed and scalable genomic analyses

(2019) Mathieu Bourgey et al.   GigaScience

Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism

(2019) Donovan Chan et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

(2018) Tahsin Stefan Barakat et al.   Cell Stem Cell

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions

(2018) Kosuke Yamaguchi et al.   Cell Reports

Sperm epigenetics and influence of environmental factors

(2018) Ida Donkin et al.   Molecular Metabolism

Establishment of environmentally sensitive DNA methylation states in the very early human embryo

(2018) Noah J. Kessler et al.   Science Advances

Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

(2018) Mei Wang et al.   Cell Stem Cell

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

Preconception urinary phthalate concentrations and sperm DNA methylation profiles among men undergoing IVF treatment: a cross-sectional study

(2017) Haotian Wu et al.   HUMAN REPRODUCTION

Temporal trends in sperm count: a systematic review and meta-regression analysis

(2017) Hagai Levine et al.   HUMAN REPRODUCTION UPDATE

Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

(2017) Deqing Hu et al.   MOLECULAR CELL

Intergenerational impact of paternal lifetime exposures to both folic acid deficiency and supplementation on reproductive outcomes and imprinted gene methylation

(2017) Lundi Ly et al.   MOLECULAR HUMAN REPRODUCTION

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex

(2016) Hongjie Shen et al.   CELL

Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa

(2016) Hélène Royo et al.   DEVELOPMENTAL CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Intra- and inter-individual differences in human sperm DNA methylation

(2016) E. Dere et al.   Andrology

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

High-dose folic acid supplementation alters the human sperm methylome and is influenced by theMTHFRC677T polymorphism

(2015) Mahmoud Aarabi et al.   HUMAN MOLECULAR GENETICS

Epigenomic Landscape of Human Fetal Brain, Heart, and Liver

(2015) Liying Yan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation

(2015) Rodrigo A. Grandy et al.   MOLECULAR AND CELLULAR BIOLOGY

H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation

(2015) Yoshihiro Matsumura et al.   MOLECULAR CELL

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(2015) K. Siklenka et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Uniformity of Nucleosome Preservation Pattern in Mammalian Sperm and Its Connection to Repetitive DNA Elements

(2014) Birgit Samans et al.   DEVELOPMENTAL CELL

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

(2014) Benjamin R. Carone et al.   DEVELOPMENTAL CELL

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism

(2014) E. J. Radford et al.   SCIENCE

Genome-wide chromatin analysis in mature mouse and human spermatozoa

(2013) Mizue Hisano et al.   Nature Protocols

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

(2013) Serap Erkek et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes

(2013) R. Lambrot et al.   Nature Communications

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Novel Insights into DNA Methylation Features in Spermatozoa: Stability and Peculiarities

(2012) Csilla Krausz et al.   PLoS One

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men

(2011) S. S. Hammoud et al.   HUMAN REPRODUCTION

Fertility treatments and outcomes among couples seeking fertility care: data from a prospective fertility cohort in the United States

(2010) James F. Smith et al.   FERTILITY AND STERILITY

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

(2010) N Zamudio et al.   HEREDITY

Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

(2010) Urszula Brykczynska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

(2010) Eric M. Mendenhall et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Distinctive chromatin in human sperm packages genes for embryo development

(2009) Saher Sue Hammoud et al.   NATURE

Possible involvement of SINEs in mammalian-specific brain formation

(2008) T. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY