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

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

(2019) Dario Nicetto et al.   SCIENCE

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

(2018) Chenfei Wang et al.   NATURE CELL BIOLOGY

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst

(2018) Jan J Zylicz et al.   eLife

Nuclear Dynamics of Histone H3 Trimethylated on Lysine 9 and/or Phosphorylated on Serine 10 in Mouse Cloned Embryos As New Markers of Reprogramming?

(2018) Karlla Ribeiro-Mason et al.   Cellular Reprogramming

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

(2017) Atsuko Shirai et al.   eLife

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

SUV4-20 activity in the preimplantation mouse embryo controls timely replication

(2016) André Eid et al.   GENES & DEVELOPMENT

Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin

(2016) Katerina Tsouroula et al.   MOLECULAR CELL

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

(2016) Xiaoyu Liu et al.   NATURE

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing

(2016) Wenqiang Liu et al.   Cell Discovery

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons

(2015) Yuki Hatanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Shogo Matoba et al.   CELL

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

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

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

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Heterochromatin establishment at pericentromeres depends on nuclear position

(2013) J. W. Jachowicz et al.   GENES & DEVELOPMENT

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

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

Live visualization of chromatin dynamics with fluorescent TALEs

(2013) Yusuke Miyanari et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Cell Profiling of Epigenetic Modifiers Identifies PRDM14 as an Inducer of Cell Fate in the Mammalian Embryo

(2013) Adam Burton et al.   Cell Reports

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

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

(2012) Abdenour Soufi et al.   CELL

Transient JMJD2B-Mediated Reduction of H3K9me3 Levels Improves Reprogramming of Embryonic Stem Cells into Cloned Embryos

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

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Recent advancements in cloning by somatic cell nuclear transfer

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

Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo

(2011) A. Burton et al.   Briefings in Functional Genomics

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Epigenetic reprogramming in mammalian reproduction: Contribution from histone variants

(2010) Angèle Santenard et al.   Epigenetics

Heterochromatin formation in the mouse embryo requires critical residues of the histone variant H3.3

(2010) Angèle Santenard et al.   NATURE CELL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal

(2009) Myriam Hemberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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