Non-coding RNAs: Biological Functions And Applications.
Baby Santosh, Akhil Varshney, Pramod Kumar Yadava
Published 2015 · Medicine, Biology
Download PDFAnalyze on Scholarcy
Analyses of the international human genome sequencing results in 2004 converged to a consensual number of ~20,000 protein-coding genes, spanning over <2% of the total genomic sequence. Therefore, the developmental and physiological complexity of human beings remains unaccounted if viewed only in terms of the number of protein-coding genes; the epigenetic influences involving chromatin remodelling and RNA interference and alternative precursor messenger RNA splicing of functional protein-coding transcripts as well as post-translational modifications of proteins increase the diversity and the functionality of the proteome and likely explain the increased complexity. In addition, there has been an explosion of research addressing possible functional roles for the other 98% of the human genome that does not encode proteins. In fact, >90% of the human genome is likely to be transcribed yielding a complex network of overlapping transcripts that include tens of thousands of long RNAs with little or no protein forming capacity; they are collectively called non-coding RNA. This review highlights the fundamental concepts of biological roles of non-coding RNA and their importance in regulation of cellular physiology under disease conditions like cancer.
This paper references
TERRA biogenesis, turnover and implications for function.
Sascha Feuerhahn (2010)
Genome-wide transcription and the implications for genomic organization
Philipp Kapranov (2007)
P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner.
Archa H Fox (2005)
Identification and consequences of miRNA–target interactions — beyond repression of gene expression
Jean Hausser (2014)
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains
John N Hutchinson (2006)
Murray MF Dykxhoorn DM Beresford PJ Riess J Lee S-K et al Novina CD (2014)
Long non-coding RNAs: insights into functions
Tim R. Mercer (2009)
Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions.
Adrian P Bracken (2006)
Polycomb complexes repress developmental regulators in murine embryonic stem cells
Laurie A. Boyer (2006)
Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia
George Adrian Calin (2002)
An ultraconserved lnc to miRNA processing.
Brian S. Plosky (2014)
Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer.
Yi-Wen Huang (2009)
siRNA-directed inhibition of HIV-1 infection
Carl D. Novina (2002)
Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors.
Meihua Li (2009)
Control of alternative splicing through siRNA-mediated transcriptional gene silencing
Mariano Alló (2009)
Non-coding RNAs: hope or hype?
Alexander Hüttenhofer (2005)
MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer
Ping Ji (2003)
Intersection of the RNA Interference and X-Inactivation Pathways
Yuya Ogawa (2008)
Multiple Roles for the Non-Coding RNA SRA in Regulation of Adipogenesis and Insulin Sensitivity
Bin Xu (2010)
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
Qun Pan (2008)
A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT
Aarron T. Willingham (2005)
MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases
Maria Angelica Cortez (2009)
The Noncoding RNA Taurine Upregulated Gene 1 Is Required for Differentiation of the Murine Retina
Tamara L. Young (2005)
Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II
Stefan Schoeftner (2008)
Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control
Alexei A. Aravin (2007)
A noncoding RNA is a potential marker of cell fate during mammary gland development.
Melanie R Ginger (2006)
A Steroid Receptor Coactivator, SRA, Functions as an RNA and Is Present in an SRC-1 Complex
Rainer B. Lanz (1999)
Long non-coding RNAs: new players in cell differentiation and development
Alessandro Fatica (2014)
MicroRNA expression profiles classify human cancers
Jun Lu (2005)
Epigenetic mutations of the imprinted IGF2-H19 domain in Silver–Russell syndrome (SRS): results from a large cohort of patients with SRS and SRS-like phenotypes
Deborah Bartholdi (2008)
The Transcriptional Landscape of the Mammalian Genome
Piero Carninci (2005)
Long noncoding RNAs: functional surprises from the RNA world.
Jeremy E. Wilusz (2009)
Regulation and function of miRNA-21 in health and disease
Regalla Kumarswamy (2011)
Telomeres and human disease: ageing, cancer and beyond
María A. Blasco (2005)
Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center.
Thomas H. King (2003)
lncRNA H19/miR-675 axis represses prostate cancer metastasis by targeting TGFBI.
Miaojun Zhu (2014)
MiR-205 in cancer: an angel or a devil?
Ai-Ying Qin (2013)
The role of microRNAs in skin fibrosis
Olubukola Babalola (2013)
The H19 lincRNA is a developmental reservoir of miR-675 which suppresses growth and Igf1r
Andrew Keniry (2012)
Non-coding RNAs in cancer initiation and progression and as novel biomarkers.
Serge Patrick Nana-Sinkam (2011)
Therapeutic targeting of microRNAs: current status and future challenges
Zhonghan Li (2014)
Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
Katalin Fejes-Tóth (2009)
Telomeric noncoding RNA: telomeric repeat-containing RNA in telomere biology.
Emilio Cusanelli (2014)
Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas.
George Adrian Calin (2007)
Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
Igor Martianov (2007)
MEG3 noncoding RNA: a tumor suppressor.
Yunli Zhou (2012)
Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients.
Chantal Sellier (2010)
Non-coding RNAs in human disease
Manel Esteller (2011)
Noncoding RNAs of Trithorax Response Elements Recruit Drosophila Ash1 to Ultrabithorax
Tilman Sanchez-Elsner (2006)
Nuclear speckles: a model for nuclear organelles
Angus I. Lamond (2003)
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
Thomas R. Cech (2014)
RNA-mediated response to heat shock in mammalian cells
Ilya Shamovsky (2006)
Non-coding RNAs: hope or hype? Trends Genet: TIG
A Huttenhofer (2005)
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
Sayda M. Elbashir (2001)
Long non-coding RNAs: modulators of nuclear structure and function.
Jan H. Bergmann (2014)
Noncoding RNA in development
Paulo P. Amaral (2008)
miR-15 and miR-16 Are Direct Transcriptional Targets of E2F1 that Limit E2F-Induced Proliferation by Targeting Cyclin E
Matan Ofir (2011)
Transcriptional noise and the fidelity of initiation by RNA polymerase II
Kevin Struhl (2007)
The Genetic Signatures of Noncoding RNAs
John S. Mattick (2009)
Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA
Jae Bok Heo (2011)
Paraspeckles A Novel Nuclear Domain
Archa H Fox (2002)
Relationship Between Downregulation of miRNAs and Increase of Oxidative Stress in the Development of Diabetic Cardiac Dysfunction: Junctin as a Target Protein of miR-1
Samet Serdar Yildirim (2013)
Epigenetic regulation of miR-196b expression in gastric cancer.
Kuo-Wang Tsai (2010)
RNA-mediated neuromuscular disorders.
Laura P. W. Ranum (2006)
Non-coding RNAs: regulators of disease.
Ryan J. Taft (2010)
CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer
Amaia Lujambio (2010)
3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA
Jeremy E. Wilusz (2008)
miR-128 and its target genes in tumorigenesis and metastasis.
Molin Li (2013)
DNA methylation and microRNA dysregulation in cancer.
Hiromu Suzuki (2012)
The 5'-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter.
Scott W. Blume (2003)
Liu CG Ferracin M Hyslop T Spizzo R Sevignani C et al. Calin GA (2014)
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression.
Delphine Bernard (2010)
Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
Rajnish A. Gupta (2010)
Regulating Gene Expression through RNA Nuclear Retention
Kannanganattu V Prasanth (2005)
Telomerase Efficiently Elongates Highly Transcribing Telomeres in Human Cancer Cells
Benjamin O. Farnung (2012)
The widespread regulation of microRNA biogenesis, function and decay
Jacek Krol (2010)
Noncoding RNA Gas5 Is a Growth Arrest– and Starvation-Associated Repressor of the Glucocorticoid Receptor
Tomoshige Kino (2010)
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation.
Vidisha Tripathi (2010)
Posttranscriptional gene regulation by long noncoding RNA.
Je-Hyun Yoon (2013)
MicroRNA-106b-25 cluster expression is associated with early disease recurrence and targets caspase-7 and focal adhesion in human prostate cancer
Robert S. Hudson (2013)
new players in cell differentiation and development
A Fatica (2014)
Molecular classification of solid tumours: towards pathway-driven therapeutics
Charles Swanton (2009)
A novel role of miR-302/367 in reprogramming.
Chih-Hao Kuo (2012)
SR proteins and related factors in alternative splicing.
Shengrong Lin (2007)
The long non-coding RNA H19-derived miR-675 modulates human gastric cancer cell proliferation by targeting tumor suppressor RUNX1.
Ming Hui Zhuang (2014)
The miR-106b-25 polycistron, activated by genomic amplification, functions as an oncogene by suppressing p21 and Bim.
Takatsugu Kan (2009)
The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock
Tiffany A Allen (2004)
MicroRNA-Based Therapeutics for Cancer
Vivien Wang (2012)
Transcriptional regulation by calcium, calcineurin, and NFAT.
Patrick G. Hogan (2003)
Telomeric Repeat–Containing RNA and RNA Surveillance Factors at Mammalian Chromosome Ends
Claus M. Azzalin (2007)
Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes
Oliver H Tam (2008)
This paper is referenced by
DNA methylation in Parkinson's disease.
U Wüllner (2016)
Two lncRNAs Expression Profiles in Salt Stressed Barley (Hordeum vulgare L.) Roots
Elif Karlik (2018)
Knockdown of NEAT1 repressed the malignant progression of glioma through sponging miR-107 and inhibiting CDK14.
Yingwei Zhen (2019)
Recent Advances In Nutritional Sciences: An Overview Of Glycans And MiRNAs
Marcello Menapace (2018)
lncRNA CRNDE promotes the proliferation and metastasis by acting as sponge miR-539-5p to regulate POU2F1 expression in HCC
Zhi-xi Li (2020)
Epigenetics in Schistosomes: What We Know and What We Need Know
Weiwei Liu (2016)
Methodologies of Neuroepigenetic Research: Background, Challenges and Future Perspectives.
Clara Snijders (2018)
Long Non-Coding RNAs: Epigenetic Regulators in Cancer.
Asma Vafadar (2019)
Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation
Duy Ngoc Do (2017)
Online Databases and Circular RNAs.
Seyed Hamid Aghaee-Bakhtiari (2018)
Peroxisome biogenesis in mammalian cells: The impact of genes and environment.
Rebecca L. Farr (2016)
Role of epigenetics in aetiology and therapies for Type 1 Diabetes Mellitus: A narrative review
Yahaya Tajudeen (2019)
YRNAs overexpression and potential implications in allergy
María Isidoro-García (2019)
Oncogenesis and tumor inhibition by microRNAs and its potential therapeutic applications; a systematic review.
Maryam Karkhane (2019)
Long noncoding RNAs: emerging regulators of tumor angiogenesis.
Su-rui Sheng (2017)
Genome-wide identification and prediction of long non-coding RNAs in half-smooth tongue sole Cynoglossus semilaevis
Xiaoli Jiang (2019)
ODNA: a manually curated database of noncoding RNAs associated with orthopedics
Changcheng You (2019)
Long noncoding RNA TUG1 promotes cell proliferation and migration of renal cell carcinoma via regulation of YAP.
Shan Liu (2018)
LncRNAs: genetic and epigenetic effects in plants
Elif Karlik (2019)
Circulating long non-coding RNAs in cancer: current status and future perspectives
Peng Qi (2016)
Cell organelles and inherited metabolic diseases
Amr S. Gouda (2016)
The emerging role of the long non-coding RNA HOTAIR in breast cancer development and treatment
Hossein Mozdarani (2020)
New gene expression regulators: Long non-coding RNAs
Nermin Gozukirmizi (2019)
long noncoding rna aFaP 1-as 1 , a potential novel biomarker to predict the clinical outcome of cancer patients : a meta-analysis
Fang-teng Liu (2016)
High glucose regulates ERp29 in hepatocellular carcinoma by LncRNA MEG3-miRNA 483-3p pathway.
Xin Li (2019)
Alternative Splicing in the Cytochrome P450 Superfamily Expands Protein Diversity to Augment Gene Function and Redirect Human Drug Metabolism
Andrew J Annalora (2017)
Clinical importance of long non-coding RNA LINC00460 expression in EGFR-mutant lung adenocarcinoma
Yuta Nakano (2019)
Isoform-Specific Expression During Embryo Development in Arabidopsis and Soybean
Delasa Aghamirzaie (2016)
Clinicopathological and prognostic value of lncRNA PANDAR expression in solid tumors: Evidence from a systematic review and meta-analysis.
Hassan Mehrad-Majd (2019)
Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.
Heeyoun Hwang (2015)
HOTAIR rs920778 polymorphism is associated with ovarian cancer susceptibility and poor prognosis in a Chinese population.
Haifeng Qiu (2017)
GENOME-WIDE ANALYSIS OF LONG NON-CODING RNA (LNCRNA) OF AUTOIMMUNE THYROID DISEASES USING BIOINFORMATICS APPROACHES
Shobana Sugumar (2016)See more