Browse > Article
http://dx.doi.org/10.5483/BMBRep.2018.51.6.025

Long noncoding RNA: multiple players in gene expression  

Chen, Xiaochang (Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University)
Sun, Yunmei (Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University)
Cai, Rui (Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University)
Wang, Guoqiang (Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University)
Shu, Xiaoyan (School of Life Science and Engineering, Southwest University of Science and Technology)
Pang, Weijun (Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University)
Publication Information
BMB Reports / v.51, no.6, 2018 , pp. 280-289 More about this Journal
Abstract
Previously considered as a component of transcriptional noise, long noncoding RNAs (lncRNAs) were neglected as a therapeutic target, however, recently increasing evidence has shown that lncRNAs can participate in numerous biological processes involved in genetic regulation including epigenetic, transcriptional, and post-transcriptional regulation. In this review, we discuss the fundamental functions of lncRNAs at different regulatory levels and their roles in metabolic balance. Typical examples are introduced to illustrate their diverse molecular mechanisms. The comprehensive investigation and identification of key lncRNAs will not only contribute to insights into diseases, such as breast cancer and type II diabetes, but also provide promising therapeutic targets for related diseases.
Keywords
Disease; Epigenetics; LncRNAs; Post-transcription; Transcription;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Schmitt AM and Chang HY (2016) Long Noncoding RNAs in Cancer Pathways. Cancer Cell 29, 452-463   DOI
2 Schmitz SU, Grote P and Herrmann BG (2016) Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 73, 2491-2509   DOI
3 Gupta RA, Shah N, Wang KC et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076   DOI
4 Liu BD, Sun LJ, Liu Q et al (2015) A Cytoplasmic NF-kappa B Interacting Long Noncoding RNA Blocks I kappa B Phosphorylation and Suppresses Breast Cancer Metastasis. Cancer Cell 27, 370-381   DOI
5 Wang YY, He L, Du Y et al (2015) The Long Noncoding RNA IncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling. Cell Stem Cell 16, 413-425   DOI
6 Prensner JR, Iyer MK, Sahu A et al (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 45, 1392-1398   DOI
7 Takayama K, Horie-Inoue K, Katayama S et al (2013) Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J 32, 1665-1680   DOI
8 Gibb EA, Brown CJ and Lam WL (2011) The functional role of long non-coding RNA in human carcinomas. Mol Cancer 10, 38   DOI
9 Martin L and Chang HY (2012) Uncovering the role of genomic "dark matter" in human disease. J Clin Invest 122, 1589-1595   DOI
10 Ponting CP and Belgard TG (2010) Transcribed dark matter: meaning or myth? Hum Mol Genet 19, R162-R168   DOI
11 Lander ES (2011) Initial impact of the sequencing of the human genome. Nature 470, 187-197   DOI
12 Fatica A and Bozzoni I (2014) Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet 15, 7-21
13 Quinn JJ and Chang HY (2016) Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet 17, 47-62
14 Wang Z, Gerstein M and Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10, 57-63   DOI
15 Guttman M, Amit I, Garber M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227   DOI
16 Cabili MN, Trapnell C, Goff L et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25, 1915-1927   DOI
17 Ingolia NT, Brar GA, Rouskin S, McGeachy AM and Weissman JS (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534-1550   DOI
18 Ruiz-Orera J, Messeguer X, Subirana JA and Alba MM (2014) Long non-coding RNAs as a source of new peptides. Elife 3, e03523   DOI
19 Han P, Hang CT, Yang J and Chang CP (2011) Chromatin remodeling in cardiovascular development and physiology. Circ Res 108, 378-396   DOI
20 Rani N, Nowakowski TJ, Zhou HJ et al (2016) A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron 90, 1174-1188   DOI
21 Chang CP and Han P (2016) Epigenetic and lncRNA regulation of cardiac pathophysiology. Biochim Biophys Acta 1863, 1767-1771   DOI
22 Tsai MC, Spitale RC and Chang HY (2011) Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res 71, 3-7
23 Spitale RC, Tsai MC and Chang HY (2011) RNA templating the epigenome Long noncoding RNAs as molecular scaffolds. Epigenetics 6, 539-543   DOI
24 Mondal T, Subhash S, Vaid R et al (2015) MEG3 long noncoding RNA regulates the TGF-beta pathway genes through formation of RNA-DNA triplex structures. Nat Commun 6
25 Gupta RA, Shah N, Wang KC et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076   DOI
26 Wang KC, Yang YW, Liu B et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-U158   DOI
27 Fan JY, Xing Y, Wen XY et al (2015) Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis. Genome Biol 16
28 Chu C, Qu K, Zhong FL, Artandi SE and Chang HY (2011) Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. Mol Cell 44, 667-678   DOI
29 Yamanaka Y, Faghihi MA, Magistri M, Alvarez-Garcia O, Lotz M and Wahlestedt C (2015) Antisense RNA Controls LRP1 Sense Transcript Expression through Interaction with a Chromatin-Associated Protein, HMGB2. Cell Rep 11, 967-976   DOI
30 Anderson DM, Anderson KM, Chang CL et al (2015) A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance. Cell 160, 595-606   DOI
31 Flynn RA and Chang HY (2014) Long Noncoding RNAs in Cell-Fate Programming and Reprogramming. Cell Stem Cell 14, 752-761   DOI
32 Pang KC, Dinger ME, Mercer TR et al (2009) Genome-Wide Identification of Long Noncoding RNAs in CD8(+) T Cells. J Immunol 182, 7738-7748   DOI
33 Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22, 1775-1789   DOI
34 Batista PJ and Chang HY (2013) Long Noncoding RNAs: Cellular Address Codes in Development and Disease. Cell 152, 1298-1307   DOI
35 Gloss BS and Dinger ME (2016) The specificity of long noncoding RNA expression. Biochim Biophys Acta 1859, 16-22   DOI
36 Guttman M and Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482, 339-346   DOI
37 Yoon JH, Abdelmohsen K and Gorospe M (2014) Functional interactions among microRNAs and long noncoding RNAs. Semin Cell Dev Biol 34, 9-14   DOI
38 Han XR, Yang F, Cao HQ and Liang ZC (2015) Malat1 regulates serum response factor through miR-133 as a competing endogenous RNA in myogenesis. FASEB J 29, 3054-3064   DOI
39 Banfai B, Jia H, Khatun J et al (2012) Long noncoding RNAs are rarely translated in two human cell lines. Genome Res 22, 1646-1657   DOI
40 Guttman M, Russell P, Ingolia NT, Weissman JS and Lander ES (2013) Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins. Cell 154, 240-251   DOI
41 Gherzi R, Chen CY, Ramos A and Briata P (2014) KSRP controls pleiotropic cellular functions. Semin Cell Dev Biol 34, 2-8   DOI
42 Wang Y, Pang WJ, Wei N et al (2014) Identification, stability and expression of Sirt1 antisense long non-coding RNA. Gene 539, 117-124   DOI
43 Kim J, Noh JH, Lee SK et al (2017) LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis. Oncotarget 8, 49409-49420
44 Wang JS, Gong CG and Maquat LE (2013) Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev 27, 793-804   DOI
45 Giovarelli M, Bucci G, Ramos A et al (2014) H19 long noncoding RNA controls the mRNA decay promoting function of KSRP. Proc Natl Acad Sci U S A 111, E5023-E5028   DOI
46 Gong CG, Li ZZ, Ramanujan K et al (2015) A Long Non-coding RNA, LncMyoD, Regulates Skeletal Muscle Differentiation by Blocking IMP2-Mediated mRNA Translation. Dev Cell 34, 181-191   DOI
47 Trimarchi T, Bilal E, Ntziachristos P et al (2014) Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia. Cell 158, 593-606   DOI
48 Kornfeld JW and Bruning JC (2014) Regulation of metabolism by long, non-coding RNAs. Front Genet 5, 57
49 Liu XW, Xiao ZD, Han L et al (2016) LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nat Cell Biol 18, 431-442   DOI
50 Lin AF, Li CL, Xing Z et al (2016) The LINK-A lncRNA activates normoxic HIF1 alpha signalling in triple-negative breast cancer. Nat Cell Biol 18, 213   DOI
51 Zhao XY and Lin JD (2015) Long Noncoding RNAs: A New Regulatory Code in Metabolic Control. Trends Biochem Sci 40, 586-596   DOI
52 Pontier DB and Gribnau J (2011) Xist regulation and function eXplored. Hum Genet 130, 223-236   DOI
53 Zhou JC, Yang LH, Zhong TY et al (2015) H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase. Nat Commun 6, 10221   DOI
54 Pandey RR, Mondal T, Mohammad F et al (2008) Kcnq1ot1 antisense noncoding RNA mediates lineagespecific transcriptional silencing through chromatin-level regulation. Mol Cell 32, 232-246   DOI
55 Nagano T, Mitchell JA, Sanz LA et al (2008) The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin. Science 322, 1717-1720   DOI
56 Galupa R and Heard E (2015) X-chromosome inactivation: new insights into cis and trans regulation. Curr Opin Genet Dev 31, 57-66   DOI
57 Chew GL, Pauli A, Rinn JL, Regev A, Schier AF and Valen E (2013) Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development 140, 2828-2834   DOI
58 Bazzini AA, Johnstone TG, Christiano R et al (2014) Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33, 981-993   DOI
59 Rion N and Ruegg MA (2017) LncRNA-encoded peptides: More than translational noise? Cell Res 27, 604-605   DOI
60 Hung T, Wang YL, Lin MF et al (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43, 621-629   DOI
61 Wang P, Xue YQ, Han YM et al (2014) The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation. Science 344, 310-313   DOI
62 Tripathi V, Ellis JD, Shen Z et al (2010) The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation. Mol Cell 39, 925-938   DOI
63 Yoon JH, Abdelmohsen K, Srikantan S et al (2012) LincRNA-p21 Suppresses Target mRNA Translation. Mol Cell 47, 648-655   DOI
64 Yoon JH, Abdelmohsen K and Gorospe M (2013) Posttranscriptional Gene Regulation by Long Noncoding RNA. J Mol Biol 425, 3723-3730   DOI
65 Han JJ, Lee Y, Yeom KH et al (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887-901   DOI
66 Friedman RC, Farh KK-H, Burge CB and Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19, 92-105
67 Huang JZ, Chen M, Chen et al (2017) A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth. Mol Cell 68, 171-184 e176   DOI
68 Papaioannou D, Petri A, Thrue CA et al (2016) HOXB-AS3 Regulates Cell Cycle Progression and Interacts with the Drosophila Splicing Human Behavior (DSHB) Complex in NPM1-Mutated Acute Myeloid Leukemia. Blood 128, 1514
69 Liz J, Portela A, Soler M et al (2014) Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region. Mol Cell 55, 138-147   DOI
70 Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233   DOI
71 Shukla GC, Singh J and Barik S (2011) MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions. Mol Cell Pharmacol 3, 83-92
72 Wang GQ, Wang Y, Xiong Y et al (2016) Sirt1 AS lncRNA interacts with its mRNA to inhibit muscle formation by attenuating function of miR-34a. Sci Rep 6, 21865   DOI
73 Pang WJ, Lin LG, Xiong Y et al (2013) Knockdown of PU.1 AS lncRNA Inhibits Adipogenesis Through Enhancing PU.1 mRNA Translation. J Cell Biochem 114, 2500-2512   DOI
74 Wang LJ, Zhao Y, Bao XC et al (2015) LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res 25, 335-350   DOI
75 Sun L, Goff LA, Trapnell C et al (2013) Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A 110, 3387-3392   DOI
76 Wei SJ, Du M, Jiang ZH, Hausman GJ, Zhang LF and Dodson MV (2016) Long noncoding RNAs in regulating adipogenesis: new RNAs shed lights on obesity. Cell Mol Life Sci 73, 2079-2087   DOI
77 Wei N, Wang Y, Xu RX et al (2015) PU.1 antisense lncRNA against its mRNA translation promotes adipogenesis in porcine preadipocytes. Anim Genet 46, 133-140   DOI
78 Alvarez-Dominguez JR, Bai ZQ, Xu D et al (2015) De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development. Cell Metab 21, 764-776   DOI
79 Turner M, Galloway A and Vigorito E (2014) Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol 15, 484-491   DOI
80 Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L et al (2015) LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure. Mol Cell 60, 626-636   DOI
81 Paralkar VR, Taborda CC, Huang P et al (2016) Unlinking an lncRNA from Its Associated cis Element. Mol Cell 62, 104-110   DOI
82 Miao Y, Ajami NE, Huang TS et al (2018) Enhancerassociated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function. Nat Commun 9, 292   DOI
83 Yin YF, Yan PX, Lu JL et al (2015) Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation. Cell Stem Cell 16, 504-516   DOI
84 Lang KC, Lin IH, Teng HF et al (2009) Simultaneous overexpression of Oct4 and Nanog abrogates terminal myogenesis. Am J Physiol Cell Physiol 297, C43-C54   DOI
85 Knoll M, Lodish HF and Sun L (2015) Long non-coding RNAs as regulators of the endocrine system. Nat Rev Endocrinol 11, 151-160   DOI
86 Li P, Ruan XB, Yang L et al (2015) A Liver-Enriched Long Non-Coding RNA, lncLSTR, Regulates Systemic Lipid Metabolism in Mice. Cell Metab 21, 455-467   DOI
87 Satpathy AT and Chang HY (2015) Long Noncoding RNA in Hematopoiesis and Immunity. Immunity 42, 792-804   DOI
88 Hobson DJ, Wei W, Steinmetz LM and Svejstrup JQ (2012) RNA Polymerase II Collision Interrupts Convergent Transcription. Mol Cell 48, 365-374   DOI
89 Shearwin KE, Callen BP and Egan JB (2005) Transcriptional interference - a crash course. Trends Genet 21, 339-345   DOI
90 Palmer AC, Ahlgren-Berg A, Egan JB, Dodd IB and Shearwin KE (2009) Potent Transcriptional Interference by Pausing of RNA Polymerases over a Downstream Promoter. Mol Cell 34, 545-555   DOI
91 Pelechano V and Steinmetz LM (2013) NON-CODING RNA Gene regulation by antisense transcription. Nat Rev Genet 14, 880-893   DOI
92 Latos PA, Pauler FM, Koerner MV et al (2012) Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing. Science 338, 1469-1472   DOI
93 Zhao XY, Li SM, Wang GX, Yu Q and Lin JD (2014) A Long Noncoding RNA Transcriptional Regulatory Circuit Drives Thermogenic Adipocyte Differentiation. Mol Cell 55, 372-382   DOI