LncRNA Structural Characteristics in Epigenetic Regulation

Expression and role of long non-coding RNA H19 in carcinogenesis

(2018) Toshiyuki Ishiwata   Frontiers in Bioscience-Landmark

The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene

(2017) Nicholas Lister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energy stress-induced lncRNA FILNC1 represses c-Myc-mediated energy metabolism and inhibits renal tumor development

(2017) Zhen-Dong Xiao et al.   Nature Communications

The lncRNA BORG Drives Breast Cancer Metastasis and Disease Recurrence

(2017) Alex J. Gooding et al.   Scientific Reports

A comprehensive overview and evaluation of circular RNA detection tools

(2017) Xiangxiang Zeng et al.   PLoS Computational Biology

Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines

(2017) Wei Chen et al.   Scientific Reports

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

The ins and outs of lncRNA structure: How, why and what comes next?

(2016) Amanda J. Blythe et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1

(2016) Ming Sun et al.   CANCER RESEARCH

Characters, functions and clinical perspectives of long non-coding RNAs

(2016) Ruifang Wu et al.   MOLECULAR GENETICS AND GENOMICS

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways

(2016) Guiyou Liu et al.   Multiple Sclerosis Journal

An inducible long noncoding RNA amplifies DNA damage signaling

(2016) Adam M Schmitt et al.   NATURE GENETICS

AR promotes RCC via lncRNA interaction

(2016) Annette Fenner   Nature Reviews Urology

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

(2016) Tanvir Alam et al.   NUCLEIC ACIDS RESEARCH

A high-throughput approach to profile RNA structure

(2016) Riccardo Delli Ponti et al.   NUCLEIC ACIDS RESEARCH

LncRNA GClnc1 Promotes Gastric Carcinogenesis and May Act as a Modular Scaffold of WDR5 and KAT2A Complexes to Specify the Histone Modification Pattern

(2016) T.-T. Sun et al.   Cancer Discovery

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways

(2016) Guiyou Liu et al.   Multiple Sclerosis Journal

Pairwise RNA secondary structure alignment with conserved stem pattern

(2015) Jimmy Ka Ho Chiu et al.   BIOINFORMATICS

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data

(2015) Danny Incarnato et al.   BIOINFORMATICS

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

Revealing protein–lncRNA interaction

(2015) Fabrizio Ferrè et al.   BRIEFINGS IN BIOINFORMATICS

lncRNA-MIAT Regulates Microvascular Dysfunction by Functioning as a Competing Endogenous RNANovelty and Significance

(2015) Biao Yan et al.   CIRCULATION RESEARCH

The long noncoding RNA regulation at the MYC locus

(2015) Jian-Feng Xiang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

LncRNAs: emerging biomarkers in gastric cancer

(2015) Yu Gu et al.   Future Oncology

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

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

(2015) Colleen A. McHugh et al.   NATURE

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Detailed probing of RNA structure in vivo

(2015) Darren J. Burgess   NATURE REVIEWS GENETICS

Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder

(2015) Q. Chen et al.   SCIENCE

Control of Chromatin Structure by Long Noncoding RNA

(2015) Gudrun Böhmdorfer et al.   TRENDS IN CELL BIOLOGY

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase

(2015) Jichun Zhou et al.   Nature Communications

ALDB: A Domestic-Animal Long Noncoding RNA Database

(2015) Aimin Li et al.   PLoS One

lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals

(2014) Zhen Xing et al.   CELL

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Regulation of lncRNA expression

(2014) Zhuomin Wu et al.   CELLULAR & MOLECULAR BIOLOGY LETTERS

Regulation of Inflammatory Phenotype in Macrophages by a Diabetes-Induced Long Noncoding RNA

(2014) M. A. Reddy et al.   DIABETES

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

Negative regulation of lncRNA GAS5 by miR-21

(2013) Z Zhang et al.   CELL DEATH AND DIFFERENTIATION

Long non-coding RNAs: modulators of nuclear structure and function

(2013) Jan H Bergmann et al.   CURRENT OPINION IN CELL BIOLOGY

A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

(2013) Guohui Wan et al.   EMBO JOURNAL

Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage–hair hypoplasia

(2013) Leslie E. Rogler et al.   HUMAN MOLECULAR GENETICS

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

(2013) Jinyu Wu et al.   RNA Biology

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

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

(2011) M. M. Duszczyk et al.   RNA

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

The H19 locus: Role of an imprinted non-coding RNA in growth and development

(2010) Anne Gabory et al.   BIOESSAYS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

RNA traffic control of chromatin complexes

(2010) Magdalena J Koziol et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

(2010) Kyoko L. Yap et al.   MOLECULAR CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Maternally Expressed Gene 3 (MEG3) Noncoding Ribonucleic Acid: Isoform Structure, Expression, and Functions

(2009) Xun Zhang et al.   ENDOCRINOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

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

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

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

(2008) T. Nagano et al.   SCIENCE