Study strategies for long non-coding RNAs and their roles in regulating gene expression

Identification of candidate long non-coding RNAs in response to myocardial infarction

(2014) Jennifer Zangrando et al.   BMC GENOMICS

Regulation of lncRNA expression

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

Long Noncoding RNAs in Patients With Acute Myocardial Infarction

(2014) Mélanie Vausort et al.   CIRCULATION RESEARCH

Identification of Candidate Long Noncoding RNAs Associated with Left Ventricular Hypertrophy

(2014) Lu Zhang et al.   CTS-Clinical and Translational Science

The ways of action of long non-coding RNAs in cytoplasm and nucleus

(2014) Kun Zhang et al.   GENE

Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis

(2014) Xiaodong Song et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Pseudogene PTENP1 Functions as a Competing Endogenous RNA to Suppress Clear-Cell Renal Cell Carcinoma Progression

(2014) G. Yu et al.   MOLECULAR CANCER THERAPEUTICS

Attenuated ability of BACE1 to cleave the amyloid precursor protein via silencing long noncoding RNA BACE1-AS expression

(2014) TE LIU et al.   Molecular Medicine Reports

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation

(2014) P. Wang et al.   SCIENCE

Dominance of chemokine ligand 2 and matrix metalloproteinase-2 and -9 and suppression of pro-inflammatory cytokines in the epidural compartment after intervertebral disc extrusion in a canine model

(2014) Philemon Karli et al.   Spine Journal

Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications

(2014) Weihong Zhao et al.   Scientific Reports

Elucidating gene function and function evolution through comparison of co-expression networks of plants

(2014) Bjoern O. Hansen et al.   Frontiers in Plant Science

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

Divergent transcription is associated with promoters of transcriptional regulators

(2013) Cyrille Lepoivre et al.   BMC GENOMICS

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

Tackling Structures of Long Noncoding RNAs

(2013) Irina Novikova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Noncoding RNA in Oncogenesis: A New Era of Identifying Key Players

(2013) Guorui Deng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detecting and Comparing Non-Coding RNAs in the High-Throughput Era

(2013) Giovanni Bussotti et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Guided by RNAs: X-Inactivation as a Model for lncRNA Function

(2013) John E. Froberg et al.   JOURNAL OF MOLECULAR BIOLOGY

3S: Shotgun secondary structure determination of long non-coding RNAs

(2013) Irina V. Novikova et al.   METHODS

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

(2013) Matthew D. Simon et al.   NATURE

Emerging epigenetic mechanisms of long non-coding RNAs

(2013) K. Schaukowitch et al.   NEUROSCIENCE

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Ets-1 facilitates nuclear entry of NFAT proteins and their recruitment to the IL-2 promoter

(2013) H.-W. Tsao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function of lncRNAs and approaches to lncRNA-protein interactions

(2013) JuanJuan Zhu et al.   Science China-Life Sciences

Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data

(2012) Wen Huang et al.   ANIMAL GENETICS

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

(2012) Saakshi Jalali et al.   Biology Direct

Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

(2012) Georges St Laurent et al.   BMC GENOMICS

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

Non-coding RNAs in Alzheimer's Disease

(2012) Lin Tan et al.   MOLECULAR NEUROBIOLOGY

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

Combined RNAi and localization for functionally dissecting long noncoding RNAs

(2012) Debojyoti Chakraborty et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

(2012) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

Strategies to identify long noncoding RNAs involved in gene regulation

(2012) Catherine Lee et al.   Cell and Bioscience

Chromatin Isolation by RNA Purification (ChIRP)

(2012) Ci Chu et al.   Jove-Journal of Visualized Experiments

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

(2011) Ana C Tahira et al.   Molecular Cancer

Molecular Mechanisms of Long Noncoding RNAs

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

Antisense expression increases gene expression variability and locus interdependency

(2011) Z. Xu et al.   Molecular Systems Biology

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Exploring long non-coding RNAs through sequencing

(2011) Sophie R. Atkinson et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Long Noncoding RNAs, Chromatin, and Development

(2011) Daniel P. Caley et al.   TheScientificWorldJOURNAL

MacroRNA underdogs in a microRNA world: Evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA

(2010) Leonard Lipovich et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

(2010) Danilo Licastro et al.   BMC GENOMICS

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

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2010) H. Kawaji et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

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

(2009) Mitchell Guttman et al.   NATURE

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

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

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

Noncoding RNA in development

(2008) Paulo P. Amaral et al.   MAMMALIAN GENOME

A Novel H19 Antisense RNA Overexpressed in Breast Cancer Contributes to Paternal IGF2 Expression

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

Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock

(2008) Peter D. Mariner et al.   MOLECULAR CELL

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs

(2008) Kouji Hirota et al.   NATURE

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

(2008) Wenqiang Yu et al.   NATURE

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

Intersection of the RNA Interference and X-Inactivation Pathways

(2008) Y. Ogawa et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE