Cohesin-dependence of neuronal gene expression relates to chromatin loop length

BET inhibition disrupts transcription but retains enhancer-promoter contact

(2021) Nicholas T. Crump et al.   Nature Communications

Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin

(2021) Felix D. Weiss et al.   Nature Communications

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

(2020) Rachel Patton McCord et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

(2020) Jonathan A. Beagan et al.   NATURE NEUROSCIENCE

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Enhancer RNAs predict enhancer–gene regulatory links and are critical for enhancer function in neuronal systems

(2020) Nancy V N Carullo et al.   NUCLEIC ACIDS RESEARCH

Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data

(2019) Thomas G. Gilgenast et al.   Cell Systems

Sensory experience remodels genome architecture in neural circuit to drive motor learning

(2019) Tomoko Yamada et al.   NATURE

HiChIRP reveals RNA-associated chromosome conformation

(2019) Maxwell R. Mumbach et al.   NATURE METHODS

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF)

(2018) Somi Kim et al.   JOURNAL OF NEUROSCIENCE

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

(2018) Ji Hun Kim et al.   METHODS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Different Neuronal Activity Patterns Induce Different Gene Expression Programs

(2018) Kelsey M. Tyssowski et al.   NEURON

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Immediate Early Genes, Memory and Psychiatric Disorders: Focus on c-Fos, Egr1 and Arc

(2018) Francisco T. Gallo et al.   Frontiers in Behavioral Neuroscience

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries

(2018) James H. Sun et al.   CELL

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Activity-Regulated Transcription: Bridging the Gap between Neural Activity and Behavior

(2018) Ee-Lynn Yap et al.   NEURON

Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior

(2017) Yuki Fujita et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Abnormal Microglia and Enhanced Inflammation-Related Gene Transcription in Mice with Conditional Deletion ofCtcfinCamk2a-Cre-Expressing Neurons.

(2017) Bryan E. McGill et al.   JOURNAL OF NEUROSCIENCE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration

(2017) Debbie L.C. van den Berg et al.   NEURON

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

Spatial genome organization and cognition

(2016) Prashanth Rajarajan et al.   NATURE REVIEWS NEUROSCIENCE

Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc

(2016) Dev Sharan Sams et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Initiation and maintenance of pluripotency gene expression in the absence of cohesin

(2015) Thais Lavagnolli et al.   GENES & DEVELOPMENT

Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

(2015) Jae-Yeol Joo et al.   NATURE NEUROSCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability

(2013) Anne Gregor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A unique role of cohesin-SA1 in gene regulation and development

(2012) Silvia Remeseiro et al.   EMBO JOURNAL

Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex

(2012) Gerard M J Beaudoin et al.   Nature Protocols

CTCF Is Required for Neural Development and Stochastic Expression of Clustered Pcdh Genes in Neurons

(2012) Teruyoshi Hirayama et al.   Cell Reports

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

(2011) Vlad C. Seitan et al.   NATURE

SFARI Gene: an evolving database for the autism research community

(2010) S. Banerjee-Basu et al.   Disease Models & Mechanisms

Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes

(2010) K. Tachibana-Konwalski et al.   GENES & DEVELOPMENT

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

My5C: web tools for chromosome conformation capture studies

(2009) Bryan R Lajoie et al.   NATURE METHODS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Organ System Defects and Transcriptional Dysregulation in the Nipbl+/− Mouse, a Model of Cornelia de Lange Syndrome

(2009) Shimako Kawauchi et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

From Synapse to Nucleus: Calcium-Dependent Gene Transcription in the Control of Synapse Development and Function

(2008) Paul L. Greer et al.   NEURON

A Biological Function for the Neuronal Activity-Dependent Component of Bdnf Transcription in the Development of Cortical Inhibition

(2008) Elizabeth J. Hong et al.   NEURON

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY