Splicing regulation by long noncoding RNAs

Long noncoding RNA MALAT1 affects the efficacy of radiotherapy for esophageal squamous cell carcinoma by regulating Cks1 expression

(2017) Zhijun Li et al.   JOURNAL OF ORAL PATHOLOGY & MEDICINE

MicroRNA-mediated silence of onco-lncRNA MALAT1 in different ESCC cells via ligand-functionalized hydroxyl-rich nanovectors

(2017) Rui-Quan Li et al.   Nanoscale

Long noncoding RNA EGFR-AS1 mediates epidermal growth factor receptor addiction and modulates treatment response in squamous cell carcinoma

(2017) Daniel S W Tan et al.   NATURE MEDICINE

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein

(2017) Yoichiro Sugimoto et al.   Nature Protocols

Long non-coding RNA LINC01133 inhibits epithelial–mesenchymal transition and metastasis in colorectal cancer by interacting with SRSF6

(2016) Jianlu Kong et al.   CANCER LETTERS

Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation

(2016) Pushkar Malakar et al.   CANCER RESEARCH

Long non-coding RNA XIST exerts oncogenic functions in human nasopharyngeal carcinoma by targeting miR-34a-5p

(2016) Peng Song et al.   GENE

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

(2016) Caterina Catalanotto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Put your 3D glasses on: plant chromatin is on show

(2016) Natalia Y. Rodriguez-Granados et al.   JOURNAL OF EXPERIMENTAL BOTANY

LncRNA MALAT1 promotes development of mantle cell lymphoma by associating with EZH2

(2016) Xin Wang et al.   Journal of Translational Medicine

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

(2016) Huang Wu et al.   MOLECULAR CELL

The biogenesis and emerging roles of circular RNAs

(2016) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis

(2016) Emilie Elvira-Matelot et al.   PLANT CELL

Detection of generic differential RNA processing events from RNA-seq data

(2016) Van Du T Tran et al.   RNA Biology

Long non-coding RNA LINC01133 represses KLF2, P21 and E-cadherin transcription through binding with EZH2, LSD1 in non small cell lung cancer

(2016) Chongshuang Zang et al.   Oncotarget

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

The RNA Binding Protein Quaking Regulates Formation of circRNAs

(2015) Simon J. Conn et al.   CELL

Mutations within theLINC-HELLPnon-coding RNA differentially bind ribosomal and RNA splicing complexes and negatively affect trophoblast differentiation

(2015) Marie van Dijk et al.   HUMAN MOLECULAR GENETICS

Exon Skipping Is Correlated with Exon Circularization

(2015) Steven Kelly et al.   JOURNAL OF MOLECULAR BIOLOGY

Regulation of Splicing Factors by Alternative Splicing and NMD Is Conserved between Kingdoms Yet Evolutionarily Flexible

(2015) Liana F. Lareau et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA splicing in common disease

(2015) Tiago Faial   NATURE GENETICS

RNA mis-splicing in disease

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

A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature

(2015) Inma Gonzalez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differential Recruitment of Splice Variants from SR Pre-mRNAs to Polysomes During Development and in Response to Stresses

(2015) Saiprasad Goud Palusa et al.   PLANT AND CELL PHYSIOLOGY

Battles and hijacks: noncoding transcription in plants

(2015) Federico Ariel et al.   TRENDS IN PLANT SCIENCE

An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses

(2015) Xiangqiang Zhan et al.   Nature Communications

A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature

(2015) Inma Gonzalez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

(2014) Feng Ding et al.   BMC GENOMICS

Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex

(2014) Q Ji et al.   BRITISH JOURNAL OF CANCER

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1

(2014) Akira Ishizuka et al.   GENES TO CELLS

Natural antisense transcripts

(2014) O. Khorkova et al.   HUMAN MOLECULAR GENETICS

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

(2014) Federico Ariel et al.   MOLECULAR CELL

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

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

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

circRNA Biogenesis Competes with Pre-mRNA Splicing

(2014) Reut Ashwal-Fluss et al.   MOLECULAR CELL

Structural basis of the non-coding RNA RsmZ acting as a protein sponge

(2014) Olivier Duss et al.   NATURE

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

A day in the life of the spliceosome

(2014) A. Gregory Matera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

(2014) Yusuke Suenaga et al.   PLoS Genetics

Long Non-Coding RNA NEAT1 Associates with SRp40 to Temporally Regulate PPARγ2 Splicing during Adipogenesis in 3T3-L1 Cells

(2014) Denise Cooper et al.   Genes

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

(2013) Ignacio E Schor et al.   EMBO JOURNAL

Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins

(2013) Hypaitia B. Rauch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

(2013) G Barry et al.   MOLECULAR PSYCHIATRY

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

(2013) Matthew D. Simon et al.   NATURE

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

(2013) Fulai Jin et al.   NATURE

Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms

(2013) H.-L. Zhou et al.   NUCLEIC ACIDS RESEARCH

The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs

(2013) K. Dou et al.   NUCLEIC ACIDS RESEARCH

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions

(2013) Pil Joon Seo et al.   PLANTA

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

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

A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis

(2013) Chao-Feng Huang et al.   PLoS Genetics

The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis

(2012) Israel Ausin et al.   Epigenetics

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease

(2012) Andrea N. Ladd   MOLECULAR AND CELLULAR NEUROSCIENCE

Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana

(2012) Kang Yan et al.   MOLECULAR CELL

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

(2012) Edouard I. Severing et al.   PLoS One

Flowering time control: another window to the connection between antisense RNA and chromatin

(2012) Robert Ietswaart et al.   TRENDS IN GENETICS

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

(2012) Anireddy S. N. Reddy et al.   Frontiers in Plant Science

Dual RNAs in plants

(2011) Florian Bardou et al.   BIOCHIMIE

Structure and expression of two nuclear receptor genes in marsupials: insights into the evolution of the antisense overlap between the α-thyroid hormone receptor and Rev-erbα

(2011) Brandon C Rindfleisch et al.   BMC MOLECULAR BIOLOGY

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

(2011) Liuqing Yang et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1

(2011) Hitomi Tsuiji et al.   GENES TO CELLS

PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa

(2011) Goranka Tanackovic et al.   HUMAN MOLECULAR GENETICS

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Frequent pathway mutations of splicing machinery in myelodysplasia

(2011) Kenichi Yoshida et al.   NATURE

The long noncoding RNA RNCR2 directs mouse retinal cell specification.

(2010) Nicole A Rapicavoli et al.   BMC DEVELOPMENTAL BIOLOGY

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

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

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

17A, a novel non-coding RNA, regulates GABA B alternative splicing and signaling in response to inflammatory stimuli and in Alzheimer disease

(2010) Sara Massone et al.   NEUROBIOLOGY OF DISEASE

First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal

(2010) M. de la Mata et al.   RNA

Human tRNA-derived small RNAs in the global regulation of RNA silencing

(2010) D. Haussecker et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

New meaning in the message: Noncoding RNAs and their role in retinal development

(2009) Nicole A. Rapicavoli et al.   DEVELOPMENTAL DYNAMICS

Regulation of SR protein phosphorylation and alternative splicing by modulating kinetic interactions of SRPK1 with molecular chaperones

(2009) X.-Y. Zhong et al.   GENES & DEVELOPMENT

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Involvement of the Spliceosomal U4 Small Nuclear RNA in Heterochromatic Gene Silencing at Fission Yeast Centromeres

(2009) Madoka Chinen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

(2009) I. E. Schor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of proto-oncogene transcription, cell proliferation, and tumorigenesis in mice by PSF protein and a VL30 noncoding RNA

(2009) G. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of human noncoding RNAs in the control of tumorigenesis

(2009) L. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

The SR protein family of splicing factors: master regulators of gene expression

(2008) Jennifer C. Long et al.   BIOCHEMICAL JOURNAL

Akt2 Regulation of Cdc2-Like Kinases (Clk/Sty), Serine/Arginine-Rich (SR) Protein Phosphorylation, and Insulin-Induced Alternative Splicing of PKCβII Messenger Ribonucleic Acid

(2008) Kun Jiang et al.   ENDOCRINOLOGY

A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition

(2008) M. Beltran et al.   GENES & DEVELOPMENT

Conservation of the Protein Composition and Electron Microscopy Structure of Drosophila melanogaster and Human Spliceosomal Complexes

(2008) N. Herold et al.   MOLECULAR AND CELLULAR BIOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA

Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast

(2008) E. H. Bayne et al.   SCIENCE