Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

Chromosome territories and the global regulation of the genome

(2019) Andrew J. Fritz et al.   GENES CHROMOSOMES & CANCER

RNA: Nuclear Glue for Folding the Genome

(2019) Ryu-Suke Nozawa et al.   TRENDS IN CELL BIOLOGY

Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition

(2019) Jiah Kim et al.   JOURNAL OF CELL SCIENCE

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

(2019) Rui Xiao et al.   CELL

Role of nuclear RNA in regulating chromatin structure and transcription

(2019) Davide Michieletto et al.   CURRENT OPINION IN CELL BIOLOGY

Chromatin-associated RNAs as facilitators of functional genomic interactions

(2019) Xiao Li et al.   NATURE REVIEWS GENETICS

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

The NSL complex maintains nuclear architecture stability via lamin A/C acetylation

(2019) Adam Karoutas et al.   NATURE CELL BIOLOGY

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery

(2018) Xiaobin Zheng et al.   MOLECULAR CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

The senescent cell epigenome

(2018) Na Yang et al.   Aging-US

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

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

The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

(2017) Hui Fan et al.   GENOME RESEARCH

Identifying Nuclear Matrix-Attached DNA Across the Genome

(2017) Jason R. Dobson et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription

(2017) Michael S Werner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture

(2017) K. M. Creamer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

(2017) Marion Cremer et al.   Epigenetics & Chromatin

Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription

(2017) Michael S Werner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transformation-induced changes in the DNA-nuclear matrix interface, revealed by high-throughput analysis of DNA halos

(2017) Rosemary H. C. Wilson et al.   Scientific Reports

Prion-like domains as epigenetic regulators, scaffolds for subcellular organization, and drivers of neurodegenerative disease

(2016) Zachary M. March et al.   BRAIN RESEARCH

RNA as a fundamental component of interphase chromosomes: could repeats prove key?

(2016) Lisa L Hall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha

(2016) Kevin Gesson et al.   GENOME RESEARCH

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

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

(2015) Colleen A. McHugh et al.   NATURE

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

(2015) A. Minajigi et al.   SCIENCE

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes

(2015) Michael S. Werner et al.   Cell Reports

Genome-wide mapping of matrix attachment regions in Drosophila melanogaster

(2014) Rashmi U Pathak et al.   BMC GENOMICS

Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes

(2014) Lisa L. Hall et al.   CELL

Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit

(2014) Pavan Kumar Puvvula et al.   Nature Communications

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Higher-order unfolding of satellite heterochromatin is a consistent and early event in cell senescence

(2013) Eric C. Swanson et al.   JOURNAL OF CELL BIOLOGY

Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations

(2013) Ashwat Visvanathan et al.   PLoS One

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

(2013) Hashem Koohy et al.   PLoS One

Probing DNA shape and methylation state on a genomic scale with DNase I

(2013) A. Lazarovici et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes

(2011) Mignon A. Keaton et al.   PLoS One

SAF-A Forms a Complex with BRG1 and Both Components Are Required for RNA Polymerase II Mediated Transcription

(2011) Dzeneta Vizlin-Hodzic et al.   PLoS One

Coding RNAs with a non-coding function: Maintenance of open chromatin structure

(2011) Maïwen Caudron-Herger et al.   Nucleus

Nuclear Matrix Proteome Analysis ofDrosophila melanogaster

(2010) Satish Kallappagoudar et al.   MOLECULAR & CELLULAR PROTEOMICS

Cyclin E is recruited to the nuclear matrix during differentiation, but is not recruited in cancer cells

(2010) Jennifer Munkley et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Matrin 3: Chromosomal distribution and protein interactions

(2009) Michael J. Zeitz et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

The Peculiarities of Large Intron Splicing in Animals

(2009) Samuel Shepard et al.   PLoS One

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY