Long noncoding RNAs in cancer: mechanisms of action and technological advancements

Direct non transcriptional role of NF-Y in DNA replication

(2016) Paolo Benatti et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

LncRNA-UCA1 exerts oncogenic functions in non-small cell lung cancer by targeting miR-193a-3p

(2016) Wei Nie et al.   CANCER LETTERS

Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins

(2016) Sungyul Lee et al.   CELL

Systemic genome screening identifies the outcome associated focal loss of long noncoding RNA PRAL in hepatocellular carcinoma

(2016) Chuan-chuan Zhou et al.   HEPATOLOGY

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Noncoding RNAs and the control of signalling via nuclear receptor regulation in health and disease

(2015) Paul Cathcart et al.   BEST PRACTICE & RESEARCH CLINICAL ENDOCRINOLOGY & METABOLISM

MALAT1 promotes colorectal cancer cell proliferation/migration/invasion via PRKA kinase anchor protein 9

(2015) Min-Hui Yang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

The up-regulation of long non-coding RNA AFAP1-AS1 is associated with the poor prognosis of NSCLC patients

(2015) Jun Deng et al.   BIOMEDICINE & PHARMACOTHERAPY

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

(2015) Xiaohui Yan et al.   CANCER CELL

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

(2015) Bodu Liu et al.   CANCER CELL

CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus

(2015) M. R. Russell et al.   CANCER RESEARCH

HBXIP and LSD1 Scaffolded by lncRNA Hotair Mediate Transcriptional Activation by c-Myc

(2015) Yinghui Li et al.   CANCER RESEARCH

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21

(2015) Ping Wang et al.   CELLULAR SIGNALLING

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

(2015) Biao Yan et al.   CIRCULATION RESEARCH

A BRCA1-interacting lncRNA regulates homologous recombination

(2015) V. Sharma et al.   EMBO REPORTS

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

DNMT1-associated long non-coding RNAs regulate global gene expression and DNA methylation in colon cancer

(2015) Callie R. Merry et al.   HUMAN MOLECULAR GENETICS

Long non-coding RNA MEG3 functions as a competing endogenous RNA to regulate gastric cancer progression

(2015) Weizhao Peng et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Long noncoding RNA CCAT1 promotes hepatocellular carcinoma progression by functioning as let-7 sponge

(2015) Liang Deng et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

The H19 Long non-coding RNA in cancer initiation, progression and metastasis – a proposed unifying theory

(2015) Eli Raveh et al.   Molecular Cancer

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA

(2015) Chen Davidovich et al.   MOLECULAR CELL

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

(2015) Anna Postepska-Igielska et al.   MOLECULAR CELL

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

(2015) Michael B Clark et al.   NATURE METHODS

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method

(2015) Tsutomu Suzuki et al.   Nature Protocols

TERRA and the state of the telomere

(2015) Karsten Rippe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

(2015) Scott T. Younger et al.   NUCLEIC ACIDS RESEARCH

MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells

(2015) Gero Doose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNAPCA3

(2015) Ahmad Salameh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

(2015) Chen Davidovich et al.   RNA

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

TERRA and the state of the telomere

(2015) Karsten Rippe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

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

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

(2015) Joseph Mazar et al.   Oncotarget

MYC regulates the non-coding transcriptome

(2015) Jonathan R. Hart et al.   Oncotarget

LEIGClong non-coding RNA acts as a tumor suppressor in gastric carcinoma by inhibiting the epithelial-to-mesenchymal transition

(2014) Yuehua Han et al.   BMC CANCER

The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation

(2014) Gaurav Kumar Pandey et al.   CANCER CELL

A Functional Genomic Approach Identifies FAL1 as an Oncogenic Long Noncoding RNA that Associates with BMI1 and Represses p21 Expression in Cancer

(2014) Xiaowen Hu et al.   CANCER CELL

A Long Noncoding RNA Activated by TGF-β Promotes the Invasion-Metastasis Cascade in Hepatocellular Carcinoma

(2014) Ji-hang Yuan et al.   CANCER CELL

PCAT-1 , a Long Noncoding RNA, Regulates BRCA2 and Controls Homologous Recombination in Cancer

(2014) John R. Prensner et al.   CANCER RESEARCH

lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals

(2014) Zhen Xing et al.   CELL

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth

(2014) Katharina M. Michalik et al.   CIRCULATION RESEARCH

Linc-RNA-RoR acts as a “sponge” against mediation of the differentiation of endometrial cancer stem cells by microRNA-145

(2014) Xi Zhou et al.   GYNECOLOGIC ONCOLOGY

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at theKcnq1locus

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

Long Noncoding RNA MRUL Promotes ABCB1 Expression in Multidrug-Resistant Gastric Cancer Cell Sublines

(2014) Y. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

lincRNA-RoR and miR-145 Regulate Invasion in Triple-Negative Breast Cancer via Targeting ARF6

(2014) Gabriel Eades et al.   MOLECULAR CANCER RESEARCH

Long Noncoding RNA TARID Directs Demethylation and Activation of the Tumor Suppressor TCF21 via GADD45A

(2014) Khelifa Arab et al.   MOLECULAR CELL

Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

(2014) Julia Liz et al.   MOLECULAR CELL

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

(2014) Nadya Dimitrova et al.   MOLECULAR CELL

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

A decade of discovery in cancer genomics

(2014) Kenneth Offit   Nature Reviews Clinical Oncology

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

RETRACTED: Long non-coding RNAINXSis a critical mediator ofBCL-XSinduced apoptosis

(2014) Carlos DeOcesano-Pereira et al.   NUCLEIC ACIDS RESEARCH

Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5

(2014) T. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CCAT2 is a lung adenocarcinoma-specific long non-coding RNA and promotes invasion of non-small cell lung cancer

(2014) Mantang Qiu et al.   TUMOR BIOLOGY

Long noncoding RNA PANDA and scaffold-attachment-factor SAFA control senescence entry and exit

(2014) Pavan Kumar Puvvula et al.   Nature Communications

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Induction of the liver cancer-down-regulated long noncoding RNA uc002mbe.2 mediates trichostatin-induced apoptosis of liver cancer cells

(2013) Hui Yang et al.   BIOCHEMICAL PHARMACOLOGY

Cell cycle regulation by long non-coding RNAs

(2013) Masatoshi Kitagawa et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer

(2013) Ken-ichi Takayama et al.   EMBO JOURNAL

From human genome to cancer genome: The first decade

(2013) D. A. Wheeler et al.   GENOME RESEARCH

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

(2013) H. Ling et al.   GENOME RESEARCH

HOX antisense lincRNA HOXA-AS2 is an apoptosis repressor in allTransretinoic acid treated NB4 promyelocytic leukemia cells

(2013) Hang Zhao et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Reciprocal Regulation of HIF-1α and LincRNA-p21 Modulates the Warburg Effect

(2013) Fan Yang et al.   MOLECULAR CELL

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Linking the SWI/SNF complex to prostate cancer

(2013) Ryan S Lee et al.   NATURE GENETICS

Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion

(2013) Guocan Wang et al.   NATURE GENETICS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Widespread purifying selection on RNA structure in mammals

(2013) Martin A. Smith et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

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

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

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

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

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Long non-coding RNAgadd7interacts with TDP-43 and regulatesCdk6mRNA decay

(2012) Xuefeng Liu et al.   EMBO JOURNAL

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

Regulation of mammalian cell differentiation by long non-coding RNAs

(2012) Wenqian Hu et al.   EMBO REPORTS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients' poor recurrence-free survival after hepatectomy

(2012) Sheng-Xian Yuan et al.   HEPATOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma

(2012) Sharon J Diskin et al.   NATURE GENETICS

Systematic reconstruction of RNA functional motifs with high-throughput microfluidics

(2012) Lance Martin et al.   NATURE METHODS

The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type

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

AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans

(2012) Q. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The hallmarks of cancer

(2012) Tony Gutschner et al.   RNA Biology

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan 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

Role of Noncoding RNA ANRIL in Genesis of Plexiform Neurofibromas in Neurofibromatosis Type 1

(2011) Eric Pasmant et al.   JNCI-Journal of the National Cancer Institute

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

(2011) Ci Chu et al.   MOLECULAR CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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

(2011) Kevin C. Wang et al.   NATURE

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1

(2010) F. Mohammad et al.   DEVELOPMENT

Combined analysis of specific KRAS mutation, BRAF and microsatellite instability identifies prognostic subgroups of sporadic and hereditary colorectal cancer

(2010) Inti Zlobec et al.   INTERNATIONAL JOURNAL OF CANCER

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

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

(2010) Jason G Underwood et al.   NATURE METHODS

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase

(2010) Sophie Redon et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

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

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

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer

(2008) M Mourtada-Maarabouni et al.   ONCOGENE

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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