GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers

Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

(2021) Marina Kulik et al.   NUCLEIC ACIDS RESEARCH

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression

(2021) Andrea Cerase et al.   Communications Biology

Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution

(2021) Guido Pacini et al.   Nature Communications

Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

(2021) Rutger A.F. Gjaltema et al.   MOLECULAR CELL

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Initiation of a conserved trophectoderm program in human, cow and mouse embryos

(2020) Claudia Gerri et al.   NATURE

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development

(2019) Shangli Cheng et al.   Cell Reports

The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells

(2019) Victor Heurtier et al.   Nature Communications

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

(2019) Rafael Galupa et al.   MOLECULAR CELL

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products

(2018) Giulia Furlan et al.   MOLECULAR CELL

Emerging Principles of Gene Expression Programs and Their Regulation

(2018) Scott D. Pope et al.   MOLECULAR CELL

X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation

(2018) Rafael Galupa et al.   Annual Review of Genetics

GATA transcription factors in development and disease

(2018) Mathieu Tremblay et al.   DEVELOPMENT

Maternal Eed knockout causes loss of H3K27me3 imprinting and random X inactivation in the extraembryonic cells

(2018) Azusa Inoue et al.   GENES & DEVELOPMENT

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice

(2018) Cristina Gontan et al.   Nature Communications

A Gata4 nuclear GFP transcriptional reporter to study endoderm and cardiac development in the mouse

(2018) Claire S. Simon et al.   Biology Open

Genomic imprinting ofXistby maternal H3K27me3

(2017) Azusa Inoue et al.   GENES & DEVELOPMENT

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

(2017) Yu Zhang et al.   NATURE GENETICS

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

(2017) Christian Krendl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators

(2016) Yuchen Gao et al.   NATURE METHODS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Characterization of Histone Modifications Associated with Inactive X-Chromosome in Trophoblast Stem Cells, eXtra-Embryonic Endoderm Cells and in In Vitro Derived Undifferentiated and Differentiated Epiblast Like Stem Cells

(2016) Cathérine Dupont et al.   PLoS One

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells

(2015) Sissy E. Wamaitha et al.   GENES & DEVELOPMENT

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

(2015) A. Minajigi et al.   SCIENCE

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

(2015) Sharon F. Briggs et al.   STEM CELLS

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

GATA6 Levels Modulate Primitive Endoderm Cell Fate Choice and Timing in the Mouse Blastocyst

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

Developmental plasticity, cell fate specification and morphogenesis in the early mouse embryo

(2014) I. Bedzhov et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2014) Q. Deng et al.   SCIENCE

Differentiation-dependent requirement of Tsix long non-coding RNA in imprinted X-chromosome inactivation

(2014) Emily Maclary et al.   Nature Communications

A prominent and conserved role for YY1 in Xist transcriptional activation

(2014) Mélanie Makhlouf et al.   Nature Communications

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

(2014) Greg Finak et al.   PLoS Computational Biology

MOF-associated complexes ensure stem cell identity and Xist repression

(2014) Tomasz Chelmicki et al.   eLife

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Tsix RNA and the Germline Factor, PRDM14, Link X Reactivation and Stem Cell Reprogramming

(2013) Bernhard Payer et al.   MOLECULAR CELL

The Pluripotency Factor-Bound Intron 1 of Xist Is Dispensable for X Chromosome Inactivation and Reactivation In Vitro and In Vivo

(2013) Alissa Minkovsky et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Site-Specific Silencing of Regulatory Elements as a Mechanism of X Inactivation

(2012) J. Mauro Calabrese et al.   CELL

Dual-specificity MAP kinase phosphatases (MKPs)

(2012) Christopher J. Caunt et al.   FEBS Journal

RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation

(2012) Cristina Gontan et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functional Analysis of Rex1 During Preimplantation Development

(2012) María Climent et al.   STEM CELLS AND DEVELOPMENT

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development

(2011) Ikuhiro Okamoto et al.   NATURE

RNF12 Activates Xist and Is Essential for X Chromosome Inactivation

(2011) Tahsin Stefan Barakat et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation

(2010) Di Tian et al.   CELL

Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice

(2010) JongDae Shin et al.   NATURE

Molecular coupling of Tsix regulation and pluripotency

(2010) Pablo Navarro et al.   NATURE

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates

(2010) Ziyang Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

RNF12 Is an X-Encoded Dose-Dependent Activator of X Chromosome Inactivation

(2009) Iris Jonkers et al.   CELL

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

(2009) Mary E. Donohoe et al.   NATURE

Synergy of Eed and Tsix in the repression of Xist gene and X-chromosome inactivation

(2008) Shinwa Shibata et al.   EMBO JOURNAL

X Chromosome Activity in Mouse XX Primordial Germ Cells

(2008) Susana M. Chuva de Sousa Lopes et al.   PLoS Genetics

Molecular Coupling of Xist Regulation and Pluripotency

(2008) P. Navarro et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY