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

Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation

(2021) Moritz Bauer et al.   Nature Communications

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

(2021) Guido Pacini et al.   Nature Communications

RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes

(2021) Elin Enervald et al.   EMBO JOURNAL

Enhancer-associated H3K4 methylation safeguards in vitro germline competence

(2021) Tore Bleckwehl et al.   Nature Communications

The regulatory landscapes of developmental genes

(2020) Christopher Chase Bolt et al.   DEVELOPMENT

Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective

(2020) Jan J. Żylicz et al.   Annual Review of Biochemistry

Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X‐Chromosome Inactivation

(2020) Verena Mutzel et al.   BIOESSAYS

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution

(2019) Peter Hansen et al.   BMC GENOMICS

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

Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation

(2019) Anne Laugesen et al.   MOLECULAR CELL

Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

(2019) Qing V. Li et al.   NATURE GENETICS

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

(2019) Josef Redolfi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A symmetric toggle switch explains the onset of random X inactivation in different mammals

(2019) Verena Mutzel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features

(2019) Lisa Barros de Andrade e Sousa et al.   GENOME RESEARCH

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments

(2019) Chen-Yu Wang et al.   Nature Communications

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

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

Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development

(2019) Xianfa Yang et al.   CELL RESEARCH

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

(2019) Rafael Galupa et al.   MOLECULAR CELL

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Epigenome editing strategies for the functional annotation of CTCF insulators

(2019) Daniel R. Tarjan et al.   Nature Communications

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

(2019) Josh Tycko et al.   Nature Communications

Identifying Novel Enhancer Elements with CRISPR-Based Screens

(2018) Jason C. Klein et al.   ACS Chemical Biology

Exit from Naive Pluripotency Induces a Transient X Chromosome Inactivation-like State in Males

(2018) Elsa J. Sousa et al.   Cell Stem Cell

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

(2018) Giulia Furlan et al.   MOLECULAR CELL

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

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

The Implication of Early Chromatin Changes in X Chromosome Inactivation

(2018) Jan Jakub Żylicz et al.   CELL

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

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

Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

(2018) Noa Gil et al.   Cell Systems

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

(2017) Yu Zhang et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression

(2017) Smitha Sripathy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An RNA-Seq atlas of gene expression in mouse and rat normal tissues

(2017) Julia F. Söllner et al.   Scientific Data

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

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

(2016) Sophie Petropoulos et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Co-repressor CBFA2T2 regulates pluripotency and germline development

(2016) Shengjiang Tu et al.   NATURE

Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development

(2016) Kelly M. Anderson et al.   NATURE

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

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

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body

(2016) Masaki Hosogane et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

Activin/Nodal signalling in stem cells

(2015) S. Pauklin et al.   DEVELOPMENT

Chromatin-Mediated Reversible Silencing of Sense-Antisense Gene Pairs in Embryonic Stem Cells Is Consolidated upon Differentiation

(2015) Friedemann Loos et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone H3 Lysine 36 Trimethylation Is Established over theXistPromoter by AntisenseTsixTranscription and Contributes to RepressingXistExpression

(2015) Tatsuya Ohhata et al.   MOLECULAR AND CELLULAR BIOLOGY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding

(2014) Andrew G Chapman et al.   BMC GENETICS

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

(2014) Marvin E. Tanenbaum et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network

(2014) Edda G. Schulz et al.   Cell Stem Cell

Nascent RNA interaction keeps PRC2 activity poised and in check

(2014) Syuzo Kaneko et al.   GENES & DEVELOPMENT

The Trans-Activator RNF12 and Cis-Acting Elements Effectuate X Chromosome Inactivation Independent of X-Pairing

(2014) Tahsin Stefan Barakat et al.   MOLECULAR CELL

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Live Cell Imaging of the Nascent Inactive X Chromosome during the Early Differentiation Process of Naive ES Cells towards Epiblast Stem Cells

(2014) Aurélia Guyochin et al.   PLoS One

Genetic and pharmacological reactivation of the mammalian inactive X chromosome

(2014) S. Bhatnagar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Q. Deng et al.   SCIENCE

A prominent and conserved role for YY1 in Xist transcriptional activation

(2014) Mélanie Makhlouf et al.   Nature Communications

Ftx is dispensable for imprinted X-chromosome inactivation in preimplantation mouse embryos

(2014) Miki Soma et al.   Scientific Reports

Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

(2014) Shen-Hsi Yang et al.   Cell Reports

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

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

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

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

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

Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition

(2012) D. Acampora et al.   DEVELOPMENT

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

RNF12 Controls Embryonic Stem Cell Fate and Morphogenesis in Zebrafish Embryos by Targeting Smad7 for Degradation

(2012) Long Zhang et al.   MOLECULAR CELL

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation

(2012) Cristina Gontan et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Michael B. Stadler et al.   NATURE

A PiggyBac-Based Recessive Screening Method to Identify Pluripotency Regulators

(2011) Ge Guo et al.   PLoS One

Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells

(2011) Tatyana B Nesterova et al.   Epigenetics & Chromatin

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

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

(2010) Di Tian et al.   CELL

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

(2010) Corinne Chureau et al.   HUMAN MOLECULAR GENETICS

Molecular coupling of Tsix regulation and pluripotency

(2010) Pablo Navarro et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation

(2010) Morgan E Royce-Tolland et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

High-resolution analysis of epigenetic changes associated with X inactivation

(2009) H. Marks et al.   GENOME RESEARCH

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

(2009) Mary E. Donohoe et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

X Inactivation Counting and Choice Is a Stochastic Process: Evidence for Involvement of an X-Linked Activator

(2008) Kim Monkhorst et al.   CELL

A proximal conserved repeat in the Xist gene is essential as a genomic element for X-inactivation in mouse

(2008) Y. Hoki et al.   DEVELOPMENT

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