Sex-specific multi-level 3D genome dynamics in the mouse brain

Conditional knock out of transcription factor CTCF in excitatory neurons induces cognitive deficiency

(2021) Dong Il Choi et al.   Molecular Brain

The dynamics of chromatin architecture in brain development and function

(2021) Izabela Harabula et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cell type-specific chromatin accessibility analysis in the mouse and human brain

(2021) Devin Rocks et al.   Epigenetics

Oestrogen engages brain MC4R signalling to drive physical activity in female mice

(2021) William C. Krause et al.   NATURE

Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals

(2020) M Jordan Rowley et al.   GENOME RESEARCH

On the existence and functionality of topologically associating domains

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

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

(2020) Arya Kaul et al.   Nature Protocols

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer

(2020) Joanna Achinger-Kawecka et al.   Nature Communications

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

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

Ovariectomy-induced depressive-like behavior and brain glucose metabolism changes in female rats are not affected by chronic mild stress

(2020) M.A. Khayum et al.   PSYCHONEUROENDOCRINOLOGY

The Thyrotropin-Releasing Hormone-Degrading Ectoenzyme, a Therapeutic Target?

(2020) Jean-Louis Charli et al.   Frontiers in Pharmacology

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

(2020) Asaf Marco et al.   NATURE NEUROSCIENCE

Oestradiol as a neuromodulator of learning and memory

(2020) Lisa R. Taxier et al.   NATURE REVIEWS NEUROSCIENCE

Structural plasticity of the hippocampus in response to estrogens in female rodents

(2019) Paul A. S. Sheppard et al.   Molecular Brain

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

(2019) Tomoko Yamada et al.   NATURE

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

Chromatin organization in the female mouse brain fluctuates across the oestrous cycle

(2019) Ivana Jaric et al.   Nature Communications

Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus

(2019) Jordi Fernandez-Albert et al.   NATURE NEUROSCIENCE

A Portal to Visualize Transcriptome Profiles in Mouse Models of Neurological Disorders

(2019) Al-Ouran et al.   Genes

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

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

Signaling by Steroid Hormones in the 3D Nuclear Space

(2018) François Le Dily et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2018) Somi Kim et al.   JOURNAL OF NEUROSCIENCE

Hormone-control regions mediate steroid receptor–dependent genome organization

(2018) François Le Dily et al.   GENOME RESEARCH

Organizational principles of 3D genome architecture

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

The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders

(2018) Chao Chen et al.   Science Translational Medicine

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

The X chromosome in space

(2017) Teddy Jégu et al.   NATURE REVIEWS GENETICS

Pituitary adenylate cyclase activating polypeptide (PACAP), stress, and sex hormones

(2017) S. Bradley King et al.   STRESS-THE INTERNATIONAL JOURNAL ON THE BIOLOGY OF STRESS

Inducible chromatin priming is associated with the establishment of immunological memory in T cells

(2016) S. L. Bevington et al.   EMBO JOURNAL

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Spatial genome organization and cognition

(2016) Prashanth Rajarajan et al.   NATURE REVIEWS NEUROSCIENCE

Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility

(2016) Rosemary C. Bagot et al.   NEURON

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells

(2016) Charlotte Moretti et al.   Epigenetics & Chromatin

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

In-vivo Dynamics of the Human Hippocampus across the Menstrual Cycle

(2016) Claudia Barth et al.   Scientific Reports

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer

(2015) Ronan Chaligné et al.   GENOME RESEARCH

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

(2015) Rashi Halder et al.   NATURE NEUROSCIENCE

Hippocampal volume and functional connectivity changes during the female menstrual cycle

(2015) Nina Lisofsky et al.   NEUROIMAGE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression

(2014) Samantha B. Peeters et al.   BIOESSAYS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

X-chromosome inactivation in development and cancer

(2014) Ronan Chaligné et al.   FEBS LETTERS

Sex differences in anxiety and depression clinical perspectives

(2014) Margaret Altemus et al.   FRONTIERS IN NEUROENDOCRINOLOGY

Estrogen receptor α in cancer-associated fibroblasts suppresses prostate cancer invasion via modulation of thrombospondin 2 and matrix metalloproteinase 3

(2013) Spencer Slavin et al.   CARCINOGENESIS

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Comprehensive behavioral analysis of pituitary adenylate cyclase-activating polypeptide (PACAP) knockout mice

(2012) Satoko Hattori et al.   Frontiers in Behavioral Neuroscience

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Post-traumatic stress disorder is associated with PACAP and the PAC1 receptor

(2011) Kerry J. Ressler et al.   NATURE

Reframing sexual differentiation of the brain

(2011) Margaret M McCarthy et al.   NATURE NEUROSCIENCE

Changes in Brain Size during the Menstrual Cycle

(2011) Georg Hagemann et al.   PLoS One

Epigenetic regulation of autosomal gene expression by sex chromosomes

(2011) Patrick J. Wijchers et al.   TRENDS IN GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

An improved method for generating BAC DNA suitable for FISH

(2008) J. Roohi et al.   CYTOGENETIC AND GENOME RESEARCH

Hippocampal structural changes across the menstrual cycle

(2008) Xenia Protopopescu et al.   HIPPOCAMPUS