Architectural RNA in chromatin organization

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

(2020) Fabian Erdel et al.   MOLECULAR CELL

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

RIC-seq for global in situ profiling of RNA–RNA spatial interactions

(2020) Zhaokui Cai et al.   NATURE

Deciphering Hi-C: from 3D genome to function

(2019) Siyuan Kong et al.   CELL BIOLOGY AND TOXICOLOGY

The role of transcription in shaping the spatial organization of the genome

(2019) Bas van Steensel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

(2019) Aaron J. Plys et al.   GENES & DEVELOPMENT

GRID-seq for comprehensive analysis of global RNA–chromatin interactions

(2019) Bing Zhou et al.   Nature Protocols

Differential contribution of steady‐state RNA and active transcription in chromatin organization

(2019) A Rasim Barutcu et al.   EMBO REPORTS

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

Xist RNA in action: Past, present, and future

(2019) Agnese Loda et al.   PLoS Genetics

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo et al.   MOLECULAR CELL

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Enhancer LncRNAs Influence Chromatin Interactions in Different Ways

(2019) Yue Hou et al.   Frontiers in Genetics

Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs

(2018) Maria Samata et al.   Annual Review of Biochemistry

Unexpected conformational variations of the human centromeric chromatin complex

(2018) Jitendra Thakur et al.   GENES & DEVELOPMENT

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

(2018) Briana Van Treeck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing

(2018) Iain A. Sawyer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

The functions and unique features of long intergenic non-coding RNA

(2017) Julia D. Ransohoff et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulatory feedback from nascent RNA to chromatin and transcription

(2017) Lenka Skalska et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

(2017) Seth W. Cheetham 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

AI in Action: Combing the genome for the roots of autism

(2017) Elizabeth Pennisi   SCIENCE

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

(2017) Seth W. Cheetham et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modular function of long noncoding RNA, COLDAIR, in the vernalization response

(2017) Dong-Hwan Kim et al.   PLoS Genetics

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

(2017) Atsuko Shirai et al.   eLife

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

(2017) Whitney L Johnson et al.   eLife

Architectural RNAs (arcRNAs): A class of long noncoding RNAs that function as the scaffold of nuclear bodies

(2016) Takeshi Chujo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structure of centromere chromatin: from nucleosome to chromosomal architecture

(2016) Thomas Schalch et al.   CHROMOSOMA

CENPT bridges adjacent CENPA nucleosomes on young human α-satellite dimers

(2016) Jitendra Thakur et al.   GENOME RESEARCH

CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development

(2016) Mridula K. Ray et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

(2016) Jesse M. Engreitz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Classification and characterization of human endogenous retroviruses; mosaic forms are common

(2016) Laura Vargiu et al.   Retrovirology

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Auxin/AID versus conventional knockouts: distinguishing the roles of CENP-T/W in mitotic kinetochore assembly and stability

(2016) Laura Wood et al.   Open Biology

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

(2016) Diana M Mitrea et al.   eLife

Regulation of the ESC transcriptome by nuclear long noncoding RNAs

(2015) Jan H. Bergmann et al.   GENOME RESEARCH

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs

(2014) A. A. Alekseyenko et al.   GENES & DEVELOPMENT

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Human Heterochromatin Protein 1α Promotes Nucleosome Associations That Drive Chromatin Condensation

(2014) Abdelhamid M. Azzaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Centromere: Epigenetic Control of Chromosome Segregation during Mitosis

(2014) Frederick G. Westhorpe et al.   Cold Spring Harbor Perspectives in Biology

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Role of small nuclear RNAs in eukaryotic gene expression

(2013) Saba Valadkhan et al.   Essays in Biochemistry

Suv4-20h2 mediates chromatin compaction and is important for cohesin recruitment to heterochromatin

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Getting RNA and Protein in Phase

(2012) Stephanie C. Weber et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge

(2011) D. J. Grau et al.   GENES & DEVELOPMENT

A scaffold for X chromosome inactivation

(2011) Anna Tattermusch et al.   HUMAN GENETICS

Chromodomain-Mediated Oligomerization of HP1 Suggests a Nucleosome-Bridging Mechanism for Heterochromatin Assembly

(2011) Daniele Canzio et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization

(2011) M. M. Duszczyk et al.   RNA

Biogenesis and function of nuclear bodies

(2011) Yuntao S. Mao et al.   TRENDS IN GENETICS

Heterochromatin maintenance and establishment: Lessons from the mouse pericentromere

(2011) Geneviève Almouzni et al.   Nucleus

RNAi-dependent formation of heterochromatin and its diverse functions

(2010) Shiv IS Grewal   CURRENT OPINION IN GENETICS & DEVELOPMENT

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

roX RNAs: Non-coding regulators of the male X chromosome in flies

(2010) Ibrahim Ilik et al.   RNA Biology

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Paraspeckles: nuclear bodies built on long noncoding RNA

(2009) Charles S. Bond et al.   JOURNAL OF CELL BIOLOGY

RNA turnover and chromatin-dependent gene silencing

(2008) Marc Bühler   CHROMOSOMA

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Heterochromatin and RNAi Are Required to Establish CENP-A Chromatin at Centromeres

(2008) H. D. Folco et al.   SCIENCE

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE