Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Short-term gain, long-term pain: the senescence life cycle and cancer

(2019) Adelyne Sue Li Chan et al.   GENES & DEVELOPMENT

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Cellular Senescence: Defining a Path Forward

(2019) Vassilis Gorgoulis et al.   CELL

Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization

(2019) Osamu Iwasaki et al.   Nature Communications

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

(2018) Federico Comoglio et al.   GENOME RESEARCH

Mechanisms and functions of cellular senescence

(2018) Nicolás Herranz et al.   JOURNAL OF CLINICAL INVESTIGATION

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

(2018) Anne Zirkel et al.   MOLECULAR CELL

NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence

(2018) Aled J. Parry et al.   Nature Communications

Redefining the ancestral origins of the interleukin-1 superfamily

(2018) Jack Rivers-Auty et al.   Nature Communications

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Organizational principles of 3D genome architecture

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

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages

(2018) Stefan Schoenfelder et al.   Nature Communications

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response

(2016) Petros Kolovos et al.   GENOME RESEARCH

NOTCH1 mediates a switch between two distinct secretomes during senescence

(2016) Matthew Hoare et al.   NATURE CELL BIOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

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

BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance

(2016) N. Tasdemir et al.   Cancer Discovery

Reorganization of chromosome architecture in replicative cellular senescence

(2016) Steven W. Criscione et al.   Science Advances

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

(2015) Aaron T.L. Lun et al.   BMC BIOINFORMATICS

Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2

(2015) Masashi Minamino et al.   CURRENT BIOLOGY

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence

(2013) M. Sadaie et al.   GENES & DEVELOPMENT

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

A complex secretory program orchestrated by the inflammasome controls paracrine senescence

(2013) Juan Carlos Acosta et al.   NATURE CELL BIOLOGY

Radmis, a Novel Mitotic Spindle Protein that Functions in Cell Division of Neural Progenitors

(2013) Takahito Yumoto et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

(2012) Tamir Chandra et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Lessons from senescence: Chromatin maintenance in non-proliferating cells

(2011) Taranjit Singh Rai et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The essence of senescence

(2010) T. Kuilman et al.   GENES & DEVELOPMENT

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Autophagy mediates the mitotic senescence transition

(2009) A. R.J. Young et al.   GENES & DEVELOPMENT

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Cell surface-bound IL-1  is an upstream regulator of the senescence-associated IL-6/IL-8 cytokine network

(2009) A. V. Orjalo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin Complex Promotes Transcriptional Termination between Convergent Genes in S. pombe

(2008) Monika Gullerova et al.   CELL

The Organization of Histone H3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

(2008) Hiroshi Kimura et al.   CELL STRUCTURE AND FUNCTION

Opposing roles for p16Ink4a and p19Arf in senescence and ageing caused by BubR1 insufficiency

(2008) Darren J. Baker et al.   NATURE CELL BIOLOGY