Roles for Non-coding RNAs in Spatial Genome Organization

Transcription alterations of KCNQ1 associated with imprinted methylation defects in the Beckwith–Wiedemann locus

(2019) Federica Maria Valente et al.   GENETICS IN MEDICINE

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila

(2019) Sergey V. Ulianov et al.   Nature Communications

Point centromere activity requires an optimal level of centromeric noncoding RNA

(2019) Yick Hin Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disruption of nuclear speckles reduces chromatin interactions in active compartments

(2019) Shibin Hu et al.   Epigenetics & Chromatin

Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease

(2019) Oliver H. Tam et al.   Mobile DNA

Transposable Elements and Their Epigenetic Regulation in Mental Disorders: Current Evidence in the Field

(2019) Błażej Misiak et al.   Frontiers in Genetics

Phase Separation as a Melting Pot for DNA Repeats

(2019) Amanda C. Hall et al.   TRENDS IN GENETICS

Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression

(2018) Feng Wang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures

(2018) Zhongliang Zhao et al.   GENES & DEVELOPMENT

TERRA and the histone methyltransferase Dot1 cooperate to regulate senescence in budding yeast

(2018) Jennifer J. Wanat et al.   PLoS One

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline

(2018) Elizaveta Radion et al.   Epigenetics & Chromatin

Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair

(2018) Roxanne Oshidari et al.   Nature Communications

Tau Activates Transposable Elements in Alzheimer’s Disease

(2018) Caiwei Guo et al.   Cell Reports

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases

(2018) Elizabeth M. Black et al.   Genes

The Long Noncoding RNA NEAT1 Exerts Antihantaviral Effects by Acting as Positive Feedback for RIG-I Signaling

(2017) Hongwei Ma et al.   JOURNAL OF VIROLOGY

Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization

(2017) Marie-Laure Diebold-Durand et al.   MOLECULAR CELL

Tuned SMC Arms Drive Chromosomal Loading of Prokaryotic Condensin

(2017) Frank Bürmann et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus

(2017) Caitlin Hult et al.   NUCLEIC ACIDS RESEARCH

Integrity of the human centromere DNA repeats is protected by CENP-A, CENP-C, and CENP-T

(2017) Simona Giunta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF driven TERRA transcription facilitates completion of telomere DNA replication

(2017) Kate Beishline et al.   Nature Communications

Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids

(2017) Shira Sagie et al.   Nature Communications

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

(2017) Oscar Velazquez Camacho et al.   eLife

CENP-A chromatin disassembly in stressed and senescent murine cells

(2017) Sabrine Hédouin et al.   Scientific Reports

Cajal body function in genome organization and transcriptome diversity

(2016) Iain A. Sawyer et al.   BIOESSAYS

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Mitotic noncoding RNA processing promotes kinetochore and spindle assembly inXenopus

(2016) Andrew W. Grenfell et al.   JOURNAL OF CELL BIOLOGY

DNA damage signalling targets the kinetochore to promote chromatin mobility

(2016) Jonathan Strecker et al.   NATURE CELL BIOLOGY

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

(2016) Carmen Adriaens et al.   NATURE MEDICINE

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

(2016) C.-K. Chen et al.   SCIENCE

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

lncRNA-Induced Nucleosome Repositioning Reinforces Transcriptional Repression of rRNA Genes upon Hypotonic Stress

(2016) Zhongliang Zhao et al.   Cell Reports

Centromeric Transcription Regulates Aurora-B Localization and Activation

(2016) Michael D. Blower   Cell Reports

CENP-A, a protein required for chromosome segregation in mitosis, declines with age in islet but not exocrine cells

(2016) Seung-Hee Lee et al.   Aging-US

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

(2015) Lian Zhu et al.   CURRENT OPINION IN CELL BIOLOGY

Alu element-containing RNAs maintain nucleolar structure and function

(2015) M. Caudron-Herger et al.   EMBO JOURNAL

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

(2015) Francesca Bersani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) A. Minajigi et al.   SCIENCE

Perinuclear tethers license telomeric DSBs for a broad kinesin- and NPC-dependent DNA repair process

(2015) Daniel K.C. Chung et al.   Nature Communications

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

(2015) Fan Yang et al.   GENOME BIOLOGY

Non-coding RNA: what is functional and what is junk?

(2015) Alexander F. Palazzo et al.   Frontiers in Genetics

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

(2014) Suhas S.P. Rao et al.   CELL

lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs

(2014) Nataša Savić et al.   Cell Stem Cell

Nuclear bodies: new insights into assembly/dynamics and disease relevance

(2014) Judith E Sleeman et al.   CURRENT OPINION IN CELL BIOLOGY

Roles for Pbp1 and Caloric Restriction in Genome and Lifespan Maintenance via Suppression of RNA-DNA Hybrids

(2014) Jayesh S. Salvi et al.   DEVELOPMENTAL CELL

Involvement of satellite I noncoding RNA in regulation of chromosome segregation

(2014) Takashi Ideue et al.   GENES TO CELLS

Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division

(2014) Silvana Rošić et al.   JOURNAL OF CELL BIOLOGY

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at theKcnq1locus

(2014) He Zhang et al.   JOURNAL OF CELL BIOLOGY

Cutting Edge: Developmental Stage-Specific Recruitment of Cohesin to CTCF Sites throughout Immunoglobulin Loci during B Lymphocyte Development

(2014) S. C. Degner et al.   JOURNAL OF IMMUNOLOGY

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

(2014) Katsutoshi Imamura et al.   MOLECULAR CELL

The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies

(2014) Martin Machyna et al.   MOLECULAR CELL

Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing

(2014) Holger Bierhoff et al.   MOLECULAR CELL

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

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

Tumor hypoxia induces nuclear paraspeckle formation through HIF-2α dependent transcriptional activation of NEAT1 leading to cancer cell survival

(2014) H Choudhry et al.   ONCOGENE

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer

(2014) Dimple Chakravarty et al.   Nature Communications

Dynamic control of Cajal body number during zebrafish embryogenesis

(2014) Magdalena Strzelecka et al.   Nucleus

A far downstream enhancer for murine Bcl11b controls its T-cell specific expression

(2013) L. Li et al.   BLOOD

Cellular Senescence in Yeast Is Regulated by rDNA Noncoding Transcription

(2013) Kimiko Saka et al.   CURRENT BIOLOGY

The chromatin remodelling complex NoRC safeguards genome stability by heterochromatin formation at telomeres and centromeres

(2013) Anna Postepska-Igielska et al.   EMBO REPORTS

Flexible Long-Range Loops in the VH Gene Region of the Igh Locus Facilitate the Generation of a Diverse Antibody Repertoire

(2013) Jasna Medvedovic et al.   IMMUNITY

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

Environmental cues induce a long noncoding RNA–dependent remodeling of the nucleolus

(2013) Mathieu D. Jacob et al.   MOLECULAR BIOLOGY OF THE CELL

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PML bodies provide an important platform for the maintenance of telomeric chromatin integrity in embryonic stem cells

(2013) Fiona T. M. Chang et al.   NUCLEIC ACIDS RESEARCH

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Crowding Effects on the Formation and Maintenance of Nuclear Bodies: Insights from Molecular-Dynamics Simulations of Simple Spherical Model Particles

(2012) Eun Jin Cho et al.   BIOPHYSICAL JOURNAL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes

(2012) T.-M. Kim et al.   GENOME RESEARCH

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

(2012) J. H. Bergmann et al.   JOURNAL OF CELL SCIENCE

Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA

(2012) Timothy E. Audas et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Active transcription and essential role of RNA polymerase II at the centromere during mitosis

(2012) F. L. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noncoding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells

(2012) J. Verma-Gaur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Telomeres and disease: Enter TERRA

(2012) André Maicher et al.   RNA Biology

The genetics of dyskeratosis congenita

(2012) Philip J. Mason et al.   Cancer Genetics

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

Dyskerin, telomerase and the DNA damage response

(2011) BaiWei Gu et al.   CELL CYCLE

Perinuclear Cohibin Complexes Maintain Replicative Life Span via Roles at Distinct Silent Chromatin Domains

(2011) Janet N.Y. Chan et al.   DEVELOPMENTAL CELL

Telomerase and idiopathic pulmonary fibrosis

(2011) Mary Armanios   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

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

(2011) Kevin C. Wang et al.   NATURE

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Nucleation of nuclear bodies by RNA

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

SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin

(2011) Christèle Maison et al.   NATURE GENETICS

Epigenetic Silencing of Nucleolar rRNA Genes in Alzheimer's Disease

(2011) Maciej Pietrzak et al.   PLoS One

Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

(2011) D. T. Ting et al.   SCIENCE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Biogenesis and function of nuclear bodies

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

Ribosomopathies: human disorders of ribosome dysfunction

(2010) A. Narla et al.   BLOOD

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Skewed X inactivation in manifesting carriers of Duchenne muscular dystrophy

(2010) Mieko Yoshioka et al.   CLINICAL GENETICS

Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore

(2010) Jan H Bergmann et al.   EMBO JOURNAL

CENP-A Reduction Induces a p53-Dependent Cellular Senescence Response To Protect Cells from Executing Defective Mitoses

(2010) K. Maehara et al.   MOLECULAR AND CELLULAR BIOLOGY

Changes in Hox genes’ structure and function during the evolution of the squamate body plan

(2010) Nicolas Di-Poï et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Telomeres: protecting chromosomes against genome instability

(2010) Roderick J. O'Sullivan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The nuclear envelope in genome organization, expression and stability

(2010) Karim Mekhail et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

(2010) Joke G. van Bemmel et al.   PLoS One

Hyper telomere recombination accelerates replicative senescence and may promote premature aging

(2010) R. T. Hagelstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b

(2010) L. Li et al.   SCIENCE

DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA

(2010) Yaqing Du et al.   PLoS Genetics

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

(2010) Kohta Ikegami et al.   GENOME BIOLOGY

Short Telomeres are Sufficient to Cause the Degenerative Defects Associated with Aging

(2009) Mary Armanios et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Telomeres and telomerase in cancer

(2009) S. E. Artandi et al.   CARCINOGENESIS

Yeast telomerase and the SUN domain protein Mps3 anchor telomeres and repress subtelomeric recombination

(2009) H. Schober et al.   GENES & DEVELOPMENT

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

TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres

(2009) Zhong Deng et al.   MOLECULAR CELL

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase

(2009) Federica Ferri et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CpG-island promoters drive transcription of human telomeres

(2009) S. G. Nergadze et al.   RNA

Dicer independent small RNAs associate with telomeric heterochromatin

(2009) F. Cao et al.   RNA

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

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

LINE dancing in the human genome: transposable elements and disease

(2009) Victoria P Belancio et al.   Genome Medicine

Nucleolus, Ribosomes, and Cancer

(2008) Lorenzo Montanaro et al.   AMERICAN JOURNAL OF PATHOLOGY

Polycomb Group Proteins Ezh2 and Rnf2 Direct Genomic Contraction and Imprinted Repression in Early Mouse Embryos

(2008) Rémi Terranova et al.   DEVELOPMENTAL CELL

Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes

(2008) C. R. Brown et al.   GENES & DEVELOPMENT

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH

Kcnq1ot1/Lit1 Noncoding RNA Mediates Transcriptional Silencing by Targeting to the Perinucleolar Region

(2008) F. Mohammad et al.   MOLECULAR AND CELLULAR BIOLOGY

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Role for perinuclear chromosome tethering in maintenance of genome stability

(2008) Karim Mekhail et al.   NATURE

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

De Novo Formation of a Subnuclear Body

(2008) T. E. Kaiser et al.   SCIENCE