Cajal body function in genome organization and transcriptome diversity

Transcription Dynamics in Living Cells

(2016) Tineke L. Lenstra et al.   Annual Review of Biophysics

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

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

Cycling in the nucleus: regulation of RNA 3′ processing and nuclear organization of replication-dependent histone genes

(2016) Valentina Romeo et al.   CURRENT OPINION IN CELL BIOLOGY

Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis

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Nuclear bodies: Built to boost

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Locus-specific gene repositioning in prostate cancer

(2016) Marc Leshner et al.   MOLECULAR BIOLOGY OF THE CELL

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

(2016) Marina Falaleeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific genomic cues regulate Cajal body assembly

(2016) Iain A. Sawyer et al.   RNA Biology

The Spliceosome: The Ultimate RNA Chaperone and Sculptor

(2016) Panagiotis Papasaikas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Recent advances in dynamic m6A RNA modification

(2016) Guangchao Cao et al.   Open Biology

The reciprocal regulation between splicing and 3′-end processing

(2016) Daisuke Kaida   Wiley Interdisciplinary Reviews-RNA

Spectral imaging to visualize higher-order genomic organization

(2016) Iain A. Sawyer et al.   Nucleus

Spectral imaging to visualize higher-order genomic organization

(2016) Iain A. Sawyer et al.   Nucleus

Understanding Spatial Genome Organization: Methods and Insights

(2016) Vijay Ramani et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Gene Positioning Effects on Expression in Eukaryotes

(2015) Huy Q. Nguyen et al.   Annual Review of Genetics

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

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

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization

(2015) Mauro D. Locati et al.   NUCLEIC ACIDS RESEARCH

Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing

(2015) Silvia Jimeno-González et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA: master or servant?

(2015) Karla M. Neugebauer   RNA

Alternative mRNA transcription, processing, and translation: insights from RNA sequencing

(2015) Eleonora de Klerk et al.   TRENDS IN GENETICS

MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex

(2015) Hidehisa Takahashi et al.   Nature Communications

SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies

(2015) Ivan Novotný et al.   Cell Reports

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods

(2015) Jeanette Baran-Gale et al.   Frontiers in Genetics

Introns and gene expression: Cellular constraints, transcriptional regulation, and evolutionary consequences

(2014) Patricia Heyn et al.   BIOESSAYS

Genes with a large intronic burden show greater evolutionary conservation on the protein level

(2014) Olga Gorlova et al.   BMC EVOLUTIONARY BIOLOGY

Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis

(2014) S.-K. Park et al.   GENES & DEVELOPMENT

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II

(2014) S. Hutten et al.   JOURNAL OF CELL SCIENCE

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

(2014) Martin Machyna et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Novel regulatory principles of the spliceosomal Brr2 RNA helicase and links to retinal disease in humans

(2014) Sina Mozaffari-Jovin et al.   RNA Biology

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes

(2013) Michael H Farkas et al.   BMC GENOMICS

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories

(2013) Dietmar Rieder et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs

(2013) Harmony R. Salzler et al.   DEVELOPMENTAL CELL

Role of small nuclear RNAs in eukaryotic gene expression

(2013) Saba Valadkhan et al.   Essays in Biochemistry

U1A Regulates 3′ Processing of the Survival Motor Neuron mRNA

(2013) Eileen Workman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP

(2013) Reagan W. Ching et al.   JOURNAL OF CELL BIOLOGY

The Little Elongation Complex Functions at Initiation and Elongation Phases of snRNA Gene Transcription

(2013) Deqing Hu et al.   MOLECULAR CELL

Molecular crowding shapes gene expression in synthetic cellular nanosystems

(2013) Cheemeng Tan et al.   Nature Nanotechnology

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human snRNA genes use polyadenylation factors to promote efficient transcription termination

(2013) Dawn O’Reilly et al.   NUCLEIC ACIDS RESEARCH

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

(2013) Andreas R. Gruber et al.   Wiley Interdisciplinary Reviews-RNA

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

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

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

(2012) Tom Sexton et al.   CELL

Nuclear bodies: multifunctional companions of the genome

(2012) Miroslav Dundr   CURRENT OPINION IN CELL BIOLOGY

Transcription factories: genetic programming in three dimensions

(2012) Lucas Brandon Edelman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The integrator complex is required for integrity of Cajal bodies

(2012) H. Takata et al.   JOURNAL OF CELL SCIENCE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

In Vitro RNase and Nucleic Acid Binding Activities Implicate Coilin in U snRNA Processing

(2012) Hanna J. Broome et al.   PLoS One

Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming

(2012) H. Berndt et al.   RNA

Transcription factories

(2012) Dietmar Rieder et al.   Frontiers in Genetics

N6-methyl-adenosine (m6A) in RNA: An Old Modification with A Novel Epigenetic Function

(2012) Yamei Niu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Seed and grow: a two-step model for nuclear body biogenesis: Figure 1.

(2011) Miroslav Dundr   JOURNAL OF CELL BIOLOGY

Ultrastructural study of transcription factories in mouse erythroblasts

(2011) C. H. Eskiw et al.   JOURNAL OF CELL SCIENCE

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Nucleation of nuclear bodies by RNA

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

Biogenesis and function of nuclear bodies

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

snRNA 3′ end formation: the dawn of the Integrator complex

(2010) Jiandong Chen et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Regulation of snRNA gene expression by theDrosophila melanogastersmall nuclear RNA activating protein complex (DmSNAPc)

(2010) Ko-Hsuan Hung et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

3D shortcuts to gene regulation

(2010) Ofir Hakim et al.   CURRENT OPINION IN CELL BIOLOGY

In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies

(2010) Ivan Novotný et al.   MOLECULAR BIOLOGY OF THE CELL

Deciphering the splicing code

(2010) Yoseph Barash 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

Making the message clear: visualizing mRNA localization

(2010) Timothy T. Weil et al.   TRENDS IN CELL BIOLOGY

Interchromosomal association and gene regulation in trans

(2010) Adam Williams et al.   TRENDS IN GENETICS

The Cajal Body and Histone Locus Body

(2010) Z. Nizami et al.   Cold Spring Harbor Perspectives in Biology

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Nuclear Bodies: Random Aggregates of Sticky Proteins or Crucibles of Macromolecular Assembly?

(2009) A. Gregory Matera et al.   DEVELOPMENTAL CELL

Cajal-body formation correlates with differential coilin phosphorylation in primary and transformed cell lines

(2009) S. M. Hearst et al.   JOURNAL OF CELL SCIENCE

Cell type specific chromosome territory organization in the interphase nucleus of normal and cancer cells

(2009) Narasimharao V. Marella et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

Expression of human snRNA genes from beginning to end

(2008) Sylvain Egloff et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The Meaning of Gene Positioning

(2008) Takumi Takizawa et al.   CELL

SMN Deficiency Causes Tissue-Specific Perturbations in the Repertoire of snRNAs and Widespread Defects in Splicing

(2008) Zhenxi Zhang et al.   CELL

Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

(2008) A. L. Saltzman et al.   MOLECULAR AND CELLULAR BIOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Association between the Igk and Igh immunoglobulin loci mediated by the 3′ Igk enhancer induces 'decontraction' of the Igh locus in pre–B cells

(2008) Susannah L Hewitt et al.   NATURE IMMUNOLOGY

The assembly of a spliceosomal small nuclear ribonucleoprotein particle

(2008) S. B. Patel et al.   NUCLEIC ACIDS RESEARCH

De Novo Formation of a Subnuclear Body

(2008) T. E. Kaiser et al.   SCIENCE