DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis

An mTORC1-dependent switch orchestrates the transition between mouse spermatogonial stem cells and clones of progenitor spermatogonia

(2021) Shinnosuke Suzuki et al.   Cell Reports

Remethylation of Dnmt3a−/− hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing

(2020) Shamika Ketkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation disruption reshapes the hematopoietic differentiation landscape

(2020) Franco Izzo et al.   NATURE GENETICS

NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

(2020) Kenjiro Shirane et al.   NATURE GENETICS

Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis

(2020) Keren Cheng et al.   iScience

Sex-specific histone modifications in mouse fetal and neonatal germ cells

(2019) Yukiko Kawabata et al.   Epigenomics

Differential RA responsiveness directs formation of functionally distinct spermatogonial populations at the initiation of spermatogenesis in the mouse

(2019) Ellen K. Velte et al.   DEVELOPMENT

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2019) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage

(2019) Nathan C. Law et al.   Nature Communications

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

(2019) Soichiro Yamanaka et al.   DEVELOPMENTAL CELL

Defective germline reprogramming rewires the spermatogonial transcriptome

(2018) Lina Vasiliauskaitė et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Defective germline reprogramming rewires the spermatogonial transcriptome

(2018) Lina Vasiliauskaitė et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells In Vivo

(2018) Mira Jeong et al.   Cell Reports

A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq

(2018) Christopher Daniel Green et al.   DEVELOPMENTAL CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids

(2018) Brian P. Hermann et al.   Cell Reports

Genome-wide quantification of the effects of DNA methylation on human gene regulation

(2018) Amanda J Lea et al.   eLife

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains

(2016) Dominique C. Stephens et al.   NUCLEIC ACIDS RESEARCH

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity

(2016) Joan Barau et al.   SCIENCE

Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells

(2016) Andrew D. King et al.   Cell Reports

DMRT1 Is Required for Mouse Spermatogonial Stem Cell Maintenance and Replenishment

(2016) Teng Zhang et al.   PLoS Genetics

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis

(2015) Naoki Kubo et al.   BMC GENOMICS

DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination

(2015) Natasha Zamudio et al.   GENES & DEVELOPMENT

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Functional and molecular features of the Id4+ germline stem cell population in mouse testes

(2014) F. Chan et al.   GENES & DEVELOPMENT

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

(2014) P. Jermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional control of spermatogonial maintenance and differentiation

(2014) Hye-Won Song et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Microarray-Based Analysis of Cell-Cycle Gene Expression During Spermatogenesis in the Mouse1

(2010) Dipanwita Roy Choudhury et al.   BIOLOGY OF REPRODUCTION

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

(2010) H. Wu et al.   SCIENCE

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

(2008) A. M. Smith et al.   GENOME RESEARCH