
Role of lncRNAs related to NRs in the regulation of gene expression
- Authors:
- Katerina Pierouli
- Louis Papageorgiou
- George P. Chrousos
- Elias Eliopoulos
- Dimitrios Vlachakis
-
Affiliations: Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens 11855, Greece - Published online on: April 22, 2025 https://doi.org/10.3892/ije.2025.26
- Article Number: 3
-
Copyright : © Pierouli et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY 4.0].
This article is mentioned in:
Abstract
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al: The transcriptional landscape of the mammalian genome. Science. 309:1559–1563. 2005.PubMed/NCBI View Article : Google Scholar | |
Mattick JS: RNA regulation: A new genetics? Nat Rev Genet. 5:316–323. 2004.PubMed/NCBI View Article : Google Scholar | |
Frith MC, Pheasant M and Mattick JS: The amazing complexity of the human transcriptome. Eur J Hum Genet. 13:894–897. 2005.PubMed/NCBI View Article : Google Scholar | |
Kaikkonen MU, Lam MTY and Glass CK: Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res. 90:430–440. 2011.PubMed/NCBI View Article : Google Scholar | |
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al: GENCODE: The reference human genome annotation for The ENCODE project. Genome Res. 22:1760–1774. 2012.PubMed/NCBI View Article : Google Scholar | |
Salviano-Silva A, Lobo-Alves SC, Almeida RC, Malheiros D and Petzl-Erler ML: Besides pathology: Long non-coding RNA in cell and tissue homeostasis. Noncoding RNA. 4(3)2018.PubMed/NCBI View Article : Google Scholar | |
Ma L, Bajic VB and Zhang Z: On the classification of long non-coding RNAs. RNA Biol. 10:925–933. 2013.PubMed/NCBI View Article : Google Scholar | |
Wang KC and Chang HY: Molecular mechanisms of long noncoding RNAs. Mol Cell. 43:904–914. 2011.PubMed/NCBI View Article : Google Scholar | |
Hombach S and Kretz M: Non-coding RNAs: Classification, biology and functioning. Adv Exp Med Biol. 937:3–17. 2016.PubMed/NCBI View Article : Google Scholar | |
Rinn JL and Chang HY: Genome regulation by long noncoding RNAs. Annu Rev Biochem. 81:145–166. 2012.PubMed/NCBI View Article : Google Scholar | |
Francis GA, Fayard E, Picard F and Auwerx J: Nuclear receptors and the control of metabolism. Annu Rev Physiol. 65:261–311. 2003.PubMed/NCBI View Article : Google Scholar | |
Olivares AM, Moreno-Ramos OA and Haider NB: Role of nuclear receptors in central nervous system development and associated diseases. J Exp Neurosci. 9 (Suppl 2):S93–S121. 2016.PubMed/NCBI View Article : Google Scholar | |
Foulds CE, Panigrahi AK, Coarfa C, Lanz RB and O'Malley BW: Long noncoding RNAs as targets and regulators of nuclear receptors. Curr Top Microbiol Immunol. 394:143–176. 2016.PubMed/NCBI View Article : Google Scholar | |
Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J and Mestdagh P: LNCipedia: A database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 41 (Database Issue):D246–D251. 2013.PubMed/NCBI View Article : Google Scholar | |
Bailey TL, Williams N, Misleh C and Li WW: MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34 (Web Server Issue):W369–W373. 2006.PubMed/NCBI View Article : Google Scholar | |
Liu W and Wang X: Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biol. 20(18)2019.PubMed/NCBI View Article : Google Scholar | |
Agarwal V, Bell GW, Nam JW and Bartel DP: Predicting effective microRNA target sites in mammalian mRNAs. Elife. 4(e05005)2015.PubMed/NCBI View Article : Google Scholar | |
Garcia DM, Baek D, Shin C, Bell GW, Grimson A and Bartel DP: Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol. 18:1139–1146. 2011.PubMed/NCBI View Article : Google Scholar | |
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP and Bartel DP: MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell. 27:91–105. 2007.PubMed/NCBI View Article : Google Scholar | |
Goecks J, Nekrutenko A and Taylor J: Galaxy Team. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11(R86)2010.PubMed/NCBI View Article : Google Scholar | |
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, et al: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44 (W1):W3–W10. 2016.PubMed/NCBI View Article : Google Scholar | |
Durbin R, Eddy SR, Krogh A and Mitchison G: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998. | |
Ha M and Kim VN: Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol. 15:509–524. 2014.PubMed/NCBI View Article : Google Scholar | |
Broughton JP, Lovci MT, Huang JL, Yeo GW and Pasquinelli AE: Pairing beyond the seed supports microRNA targeting specificity. Mol Cell. 64:320–333. 2016.PubMed/NCBI View Article : Google Scholar | |
John B, Enright AJ, Aravin A, Tuschl T, Sander C and Marks DS: Human MicroRNA targets. PLoS Biol. 2(e363)2004.PubMed/NCBI View Article : Google Scholar | |
Betel D, Koppal A, Agius P, Sander C and Leslie C: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 11(R90)2010.PubMed/NCBI View Article : Google Scholar | |
Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M and Rajewsky N: Combinatorial microRNA target predictions. Nat Genet. 37:495–500. 2005.PubMed/NCBI View Article : Google Scholar | |
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP and Burge CB: Prediction of mammalian microRNA targets. Cell. 115:787–798. 2003.PubMed/NCBI View Article : Google Scholar | |
Lewis BP, Burge CB and Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120:15–20. 2005.PubMed/NCBI View Article : Google Scholar | |
Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B and Rigoutsos I: A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell. 126:1203–1217. 2006.PubMed/NCBI View Article : Google Scholar | |
Kertesz M, Iovino N, Unnerstall U, Gaul U and Segal E: The role of site accessibility in microRNA target recognition. Nat Genet. 39:1278–1284. 2007.PubMed/NCBI View Article : Google Scholar | |
Rehmsmeier M, Steffen P, Hochsmann M and Giegerich R: Fast and effective prediction of microRNA/target duplexes. RNA. 10:1507–1517. 2004.PubMed/NCBI View Article : Google Scholar | |
Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, et al: Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics. 10(295)2009.PubMed/NCBI View Article : Google Scholar | |
Karagkouni D, Paraskevopoulou MD, Chatzopoulos S, Vlachos IS, Tastsoglou S, Kanellos I, Papadimitriou D, Kavakiotis I, Maniou S, Skoufos G, et al: DIANA-TarBase v8: A decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res. 46 (D1):D239–D245. 2018.PubMed/NCBI View Article : Google Scholar | |
McGeary SE, Lin KS, Shi CY, Pham TM, Bisaria N, Kelley GM and Bartel DP: The biochemical basis of microRNA targeting efficacy. Science. 366(eaav1741)2019.PubMed/NCBI View Article : Google Scholar | |
Yang L, Shi CM, Chen L, Pang LX, Xu GF, Gu N, Zhu LJ, Guo XR, Ni YH and Ji CB: The biological effects of hsa-miR-1908 in human adipocytes. Mol Biol Rep. 42:927–935. 2015.PubMed/NCBI View Article : Google Scholar | |
Kuang Q, Li J, You L, Shi C, Ji C, Guo X, Xu M and Ni Y: Identification and characterization of NF-kappaB binding sites in human miR-1908 promoter. Biomed Pharmacother. 74:158–163. 2015.PubMed/NCBI View Article : Google Scholar | |
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, et al: MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells. 26:2496–2505. 2008.PubMed/NCBI View Article : Google Scholar | |
Pencheva N, Tran H, Buss C, Huh D, Drobnjak M, Busam K and Tavazoie SF: Convergent multi-miRNA targeting of ApoE drives LRP1/LRP8-dependent melanoma metastasis and angiogenesis. Cell. 151:1068–1082. 2012.PubMed/NCBI View Article : Google Scholar | |
Xia X, Li Y, Wang W, Tang F, Tan J, Sun L, Li Q, Sun L, Tang B and He S: MicroRNA-1908 functions as a glioblastoma oncogene by suppressing PTEN tumor suppressor pathway. Mol Cancer. 14(154)2015.PubMed/NCBI View Article : Google Scholar | |
Chai Z, Fan H, Li Y, Song L, Jin X, Yu J, Li Y, Ma C and Zhou R: miR-1908 as a novel prognosis marker of glioma via promoting malignant phenotype and modulating SPRY4/RAF1 axis. Oncol Rep. 38:2717–2726. 2017.PubMed/NCBI View Article : Google Scholar | |
Jiang X, Yang L, Pang L, Chen L, Guo X, Ji C, Shi C and Ni Y: Expression of obesity-related miR-1908 in human adipocytes is regulated by adipokines, free fatty acids and hormones. Mol Med Rep. 10:1164–1169. 2014.PubMed/NCBI View Article : Google Scholar | |
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, et al: The DNA sequence and biology of human chromosome 19. Nature. 428:529–535. 2004.PubMed/NCBI View Article : Google Scholar | |
Kumar S, Stecher G, Suleski M and Hedges SB: TimeTree: A resource for timelines, timetrees, and divergence times. Mol Biol Evol. 34:1812–1819. 2017.PubMed/NCBI View Article : Google Scholar | |
Kim SH, Elango N, Warden C, Vigoda E and Yi SV: Heterogeneous genomic molecular clocks in primates. PLoS Genet. 2(e163)2006.PubMed/NCBI View Article : Google Scholar | |
Kotin RM, Menninger JC, Ward DC and Berns KI: Mapping and direct visualization of a region-specific viral DNA integration site on chromosome 19q13-qter. Genomics. 10:831–834. 1991.PubMed/NCBI View Article : Google Scholar | |
Samulski RJ, Zhu X, Xiao X, Brook JD, Housman DE, Epstein N and Hunter LA: Targeted integration of adeno-associated virus (AAV) into human chromosome 19. EMBO J. 10:3941–3950. 1991.PubMed/NCBI View Article : Google Scholar | |
Kotin RM, Linden RM and Berns KI: Characterization of a preferred site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO J. 11:5071–5078. 1992.PubMed/NCBI View Article : Google Scholar | |
Aslanidis C, Jansen G, Amemiya C, Shutler G, Mahadevan M, Tsilfidis C, Chen C, Alleman J, Wormskamp NG, Vooijs M, et al: Cloning of the essential myotonic dystrophy region and mapping of the putative defect. Nature. 355:548–551. 1992.PubMed/NCBI View Article : Google Scholar | |
Feichtinger W and Schmid M: Increased frequencies of sister chromatid exchanges at common fragile sites (1)(q42) and (19)(q13). Hum Genet. 83:145–147. 1989.PubMed/NCBI View Article : Google Scholar | |
Sievers F and Higgins DG: Clustal Omega for making accurate alignments of many protein sequences. Protein Sci. 27:135–145. 2018.PubMed/NCBI View Article : Google Scholar | |
Waterhouse AM, Procter JB, Martin DMA, Clamp M and Barton GJ: Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 25:1189–1191. 2009.PubMed/NCBI View Article : Google Scholar | |
Deaton AM and Bird A: CpG islands and the regulation of transcription. Genes Dev. 25:1010–1022. 2011.PubMed/NCBI View Article : Google Scholar | |
Larsen F, Gundersen G, Lopez R and Prydz H: CpG islands as gene markers in the human genome. Genomics. 13:1095–1107. 1992.PubMed/NCBI View Article : Google Scholar | |
Yamashita R, Suzuki Y, Sugano S and Nakai K: Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene. 350:129–136. 2005.PubMed/NCBI View Article : Google Scholar | |
Lamartina S, Sporeno E, Fattori E and Toniatti C: Characteristics of the adeno-associated virus preintegration site in human chromosome 19: Open chromatin conformation and transcription-competent environment. J Virol. 74:7671–7677. 2000.PubMed/NCBI View Article : Google Scholar | |
Bhagwan JR, Collins E, Mosqueira D, Bakar M, Johnson BB, Thompson A, Smith JGW and Denning C: Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour. F1000Res. 8(1911)2019.PubMed/NCBI View Article : Google Scholar | |
Ogata T, Kozuka T and Kanda T: Identification of an insulator in AAVS1, a preferred region for integration of adeno-associated virus DNA. J Virol. 77:9000–9007. 2003.PubMed/NCBI View Article : Google Scholar | |
Gaspar HB, Cooray S, Gilmour KC, Parsley KL, Zhang F, Adams S, Bjorkegren E, Bayford J, Brown L, Davies EG, et al: Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction. Sci Transl Med. 3(97ra80)2011.PubMed/NCBI View Article : Google Scholar | |
Cartier N, Hacein-Bey-Abina S, Bartholomae CC, Veres G, Schmidt M, Kutschera I, Vidaud M, Abel U, Dal-Cortivo L, Caccavelli L, et al: Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy. Science. 326:818–823. 2009.PubMed/NCBI View Article : Google Scholar | |
Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry CC, Blanche S, Bleesing J, Blondeau J, de Boer H, Buckland KF, et al: A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. N Engl J Med. 371:1407–1417. 2014.PubMed/NCBI View Article : Google Scholar | |
Martin DIK and Whitelaw E: The vagaries of variegating transgenes. Bioessays. 18:919–923. 1996.PubMed/NCBI View Article : Google Scholar | |
Bestor TH: Gene silencing as a threat to the success of gene therapy. J Clin Invest. 105:409–411. 2000.PubMed/NCBI View Article : Google Scholar | |
Papapetrou EP and Schambach A: Gene insertion into genomic safe harbors for human gene therapy. Mol Ther. 24:678–684. 2016.PubMed/NCBI View Article : Google Scholar | |
Wu C and Dunbar CE: Stem cell gene therapy: The risks of insertional mutagenesis and approaches to minimize genotoxicity. Front Med. 5:356–371. 2011.PubMed/NCBI View Article : Google Scholar | |
Lombardo A, Cesana D, Genovese P, Di Stefano B, Provasi E, Colombo DF, Neri M, Magnani Z, Cantore A, Lo Riso P, et al: Site-specific integration and tailoring of cassette design for sustainable gene transfer. Nat Methods. 8:861–869. 2011.PubMed/NCBI View Article : Google Scholar | |
Klatt D, Cheng E, Hoffmann D, Santilli G, Thrasher AJ, Brendel C and Schambach A: Differential transgene silencing of myeloid-specific promoters in the AAVS1 safe harbor locus of induced pluripotent stem cell-derived myeloid cells. Hum Gene Ther. 31:199–210. 2019.PubMed/NCBI View Article : Google Scholar | |
Papapetrou EP, Lee G, Malani N, Setty M, Riviere I, Tirunagari LM, Kadota K, Roth SL, Giardina P, Viale A, et al: Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol. 29:73–78. 2011.PubMed/NCBI View Article : Google Scholar | |
Sadelain M, Papapetrou EP and Bushman FD: Safe harbours for the integration of new DNA in the human genome. Nat Rev Cancer. 12:51–58. 2011.PubMed/NCBI View Article : Google Scholar | |
Smith SD, Morgan R, Gemmell R, Amylon MD, Link MP, Linker C, Hecht BK, Warnke R, Glader BE and Hecht F: Clinical and biologic characterization of T-cell neoplasias with rearrangements of chromosome 7 band q34. Blood. 71:395–402. 1988.PubMed/NCBI | |
Maes OC, Chertkow HM, Wang E and Schipper HM: MicroRNA: Implications for alzheimer disease and other human CNS disorders. Curr Genomics. 10:154–168. 2009.PubMed/NCBI View Article : Google Scholar | |
Garofalo M, Condorelli G and Croce CM: MicroRNAs in diseases and drug response. Curr Opin Pharmacol. 8:661–667. 2008.PubMed/NCBI View Article : Google Scholar | |
Juźwik CA, S Drake S, Zhang Y, Paradis-Isler N, Sylvester A, Amar-Zifkin A, Douglas C, Morquette B, Moore CS and Fournier AE: microRNA dysregulation in neurodegenerative diseases: A systematic review. Prog Neurobiol. 182(101664)2019.PubMed/NCBI View Article : Google Scholar | |
Venneri M and Passantino A: MiRNA: What clinicians need to know. Eur J Intern Med. 113:6–9. 2023.PubMed/NCBI View Article : Google Scholar | |
Zhang B, Pan X, Cobb GP and Anderson TA: microRNAs as oncogenes and tumor suppressors. Dev Biol. 302:1–12. 2007.PubMed/NCBI View Article : Google Scholar | |
Small EM and Olson EN: Pervasive roles of microRNAs in cardiovascular biology. Nature. 469:336–342. 2011.PubMed/NCBI View Article : Google Scholar | |
Romaine SPR, Tomaszewski M, Condorelli G and Samani NJ: MicroRNAs in cardiovascular disease: An introduction for clinicians. Heart. 101:921–928. 2015.PubMed/NCBI View Article : Google Scholar | |
Bailey TL and Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 2:28–36. 1994.PubMed/NCBI | |
Tirosh I and Barkai N: Two strategies for gene regulation by promoter nucleosomes. Genome Res. 18:1084–1091. 2008.PubMed/NCBI View Article : Google Scholar | |
Bird A: DNA methylation patterns and epigenetic memory. Genes Dev. 16:6–21. 2002.PubMed/NCBI View Article : Google Scholar | |
Li E, Bestor TH and Jaenisch R: Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 69:915–926. 1992.PubMed/NCBI View Article : Google Scholar | |
Ulitsky I, Shkumatava A, Jan CH, Sive H and Bartel DP: Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 147:1537–1550. 2011.PubMed/NCBI View Article : Google Scholar | |
Liu L, Wang Z, Jia J, Shi Y, Lian T and Han X: Linc01230, transcriptionally regulated by PPARγ, is identified as a novel modifier in endothelial function. Biochem Biophys Res Commun. 507:369–376. 2018.PubMed/NCBI View Article : Google Scholar | |
Cunningham TJ, Kumar S, Yamaguchi TP and Duester G: Wnt8a and Wnt3a cooperate in the axial stem cell niche to promote mammalian body axis extension. Dev Dyn. 244:797–807. 2015.PubMed/NCBI View Article : Google Scholar | |
Okubo Y, Sugawara T, Abe-Koduka N, Kanno J, Kimura A and Saga Y: Lfng regulates the synchronized oscillation of the mouse segmentation clock via trans-repression of Notch signalling. Nat Commun. 3(1141)2012.PubMed/NCBI View Article : Google Scholar | |
Pai SG, Carneiro BA, Mota JM, Costa R, Leite CA, Barroso-Sousa R, Kaplan JB, Chae YK and Giles FJ: Wnt/beta-catenin pathway: Modulating anticancer immune response. J Hematol Oncol. 10(101)2017.PubMed/NCBI View Article : Google Scholar | |
Amsellem V, Dryden NH, Martinelli R, Gavins F, Almagro LO, Birdsey GM, Haskard DO, Mason JC, Turowski P and Randi AM: ICAM-2 regulates vascular permeability and N-cadherin localization through ezrin-radixin-moesin (ERM) proteins and Rac-1 signalling. Cell Commun Signal. 12(12)2014.PubMed/NCBI View Article : Google Scholar | |
Overton HA, Fyfe MCT and Reynet C: GPR119, a novel G protein-coupled receptor target for the treatment of type 2 diabetes and obesity. Br J Pharmacol. 153 (Suppl 1):S76–S81. 2008.PubMed/NCBI View Article : Google Scholar | |
Shang R, Wang M, Dai B, Du J, Wang J, Liu Z, Qu S, Yang X, Liu J, Xia C, et al: Long noncoding RNA SLC2A1-AS1 regulates aerobic glycolysis and progression in hepatocellular carcinoma via inhibiting the STAT3/FOXM1/GLUT1 pathway. Mol Oncol. 14:1381–1396. 2020.PubMed/NCBI View Article : Google Scholar | |
Kim JJ, Lee SB, Jang J, Yi SY, Kim SH, Han SA, Lee JM, Tong SY, Vincelette ND, Gao B, et al: WSB1 promotes tumor metastasis by inducing pVHL degradation. Genes Dev. 29:2244–2257. 2015.PubMed/NCBI View Article : Google Scholar | |
Shao X, Zhao T, Xi L, Zhang Y, He J, Zeng J and Deng L: LINC00565 promotes the progression of colorectal cancer by upregulating EZH2. Oncol Lett. 21(53)2021.PubMed/NCBI View Article : Google Scholar | |
Chen C, Feng Y, Wang J, Liang Y and Zou W: Long non-coding RNA SNHG15 in various cancers: A meta and bioinformatic analysis. BMC Cancer. 20(1156)2020.PubMed/NCBI View Article : Google Scholar | |
Qian C, Li H, Chang D, Wei B and Wang Y: Identification of functional lncRNAs in atrial fibrillation by integrative analysis of the lncRNA-mRNA network based on competing endogenous RNAs hypothesis. J Cell Physiol. 234:11620–11630. 2019.PubMed/NCBI View Article : Google Scholar | |
Liu J, Xu R, Mai SJ, Ma YS, Zhang MY, Cao PS, Weng NQ, Wang RQ, Cao D, Wei W, et al: LncRNA CSMD1-1 promotes the progression of hepatocellular carcinoma by activating MYC signaling. Theranostics. 10:7527–7544. 2020.PubMed/NCBI View Article : Google Scholar | |
Talwar D and Hammer MF: SCN8A epilepsy, developmental encephalopathy, and related disorders. Pediatr Neurol. 122:76–83. 2021.PubMed/NCBI View Article : Google Scholar | |
Chen XW, Feng YQ, Hao CJ, Guo XL, He X, Zhou ZY, Guo N, Huang HP, Xiong W, Zheng H, et al: DTNBP1, a schizophrenia susceptibility gene, affects kinetics of transmitter release. J Cell Biol. 181:791–801. 2008.PubMed/NCBI View Article : Google Scholar | |
Chen CL, Ke Q, Luo M, Gao ZY, Li ZJ, Luo ZG and Liu DB: Loss of LINC01939 expression predicts progression and poor survival in gastric cancer. Pathol Res Pract. 214:1539–1543. 2018.PubMed/NCBI View Article : Google Scholar | |
Dosil M and Bustelo XR: Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90 S pre-ribosomal particle. J Biol Chem. 279:37385–37397. 2004.PubMed/NCBI View Article : Google Scholar | |
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, et al: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 148:84–98. 2012.PubMed/NCBI View Article : Google Scholar | |
Li Z, Li X, Jian W, Xue Q and Liu Z: Roles of long non-coding RNAs in the development of chronic pain. Front Mol Neurosci. 14(760964)2021.PubMed/NCBI View Article : Google Scholar | |
Luo L, Martin SC, Parkington J, Cadena SM, Zhu J, Ibebunjo C, Summermatter S, Londraville N, Patora-Komisarska K, Widler L, et al: HDAC4 controls muscle homeostasis through deacetylation of myosin heavy chain, PGC-1α, and Hsc70. Cell Rep. 29:749–763.e12. 2019.PubMed/NCBI View Article : Google Scholar | |
Mortison JD, Schenone M, Myers JA, Zhang Z, Chen L, Ciarlo C, Comer E, Natchiar SK, Carr SA, Klaholz BP and Myers AG: Tetracyclines modify translation by targeting key human rRNA substructures. Cell Chem Biol. 25:1506–1518.e13. 2018.PubMed/NCBI View Article : Google Scholar | |
Nelson JK, Koenis DS, Scheij S, Cook EC, Moeton M, Santos A, Lobaccaro JA, Baron S and Zelcer N: EEPD1 is a novel LXR target gene in macrophages which regulates ABCA1 abundance and cholesterol efflux. Arterioscler Thromb Vasc Biol. 37:423–432. 2017.PubMed/NCBI View Article : Google Scholar | |
Zhang T, Xia W, Song X, Mao Q, Huang X, Chen B, Liang Y, Wang H, Chen Y, Yu X, et al: Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway. J Hematol Oncol. 15(114)2022.PubMed/NCBI View Article : Google Scholar | |
Zeng J, Sun W, Chang J, Yi D, Zhu L, Zhang Y, Pan X, Zhou Y, Lai M, Bian G, et al: HOXC4 up-regulates NF-κB signaling and promotes the cell proliferation to drive development of human hematopoiesis, especially CD43+ cells. Blood Sci. 2:117–128. 2020.PubMed/NCBI View Article : Google Scholar | |
Gao Y, Wang F, Zhang L, Kang M, Zhu L, Xu L, Liang W and Zhang W: LINC00311 promotes cancer stem-like properties by targeting miR-330-5p/TLR4 pathway in human papillary thyroid cancer. Cancer Med. 9:1515–1528. 2020.PubMed/NCBI View Article : Google Scholar | |
Flosbach M, Oberle SG, Scherer S, Zecha J, von Hoesslin M, Wiede F, Chennupati V, Cullen JG, List M, Pauling JK, et al: PTPN2 deficiency enhances programmed T cell expansion and survival capacity of activated T cells. Cell Rep. 32(107957)2020.PubMed/NCBI View Article : Google Scholar | |
Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC and Rana TM: The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL. Proc Natl Acad Sci USA. 111:1002–1007. 2014.PubMed/NCBI View Article : Google Scholar | |
Xu LB, Bo BX, Xiong J, Ren YJ, Han D, Wei SH and Ren XP: Long non-coding RNA LINC00887 promotes progression of lung carcinoma by targeting the microRNA-206/NRP1 axis. Oncol Lett. 21(87)2021.PubMed/NCBI View Article : Google Scholar | |
Byun S, Affolter KE, Snow AK, Curtin K, Cannon AR, Cannon-Albright LA, Thota R and Neklason DW: Differential methylation of G-protein coupled receptor signaling genes in gastrointestinal neuroendocrine tumors. Sci Rep. 11(12303)2021.PubMed/NCBI View Article : Google Scholar | |
Fang Z, Zhong M, Zhou L, Le Y, Wang H and Fang Z: Low-density lipoprotein receptor-related protein 8 facilitates the proliferation and invasion of non-small cell lung cancer cells by regulating the Wnt/β-catenin signaling pathway. Bioengineered. 13:6807–6818. 2022.PubMed/NCBI View Article : Google Scholar | |
Huang R, Liu J, Chen X, Zhi Y, Ding S, Ming J, Li Y, Wang Y and Na J: A long non-coding RNA LncSync regulates mouse cardiomyocyte homeostasis and cardiac hypertrophy through coordination of miRNA actions. Protein Cell. 14:153–157. 2023.PubMed/NCBI View Article : Google Scholar | |
Li N and Zhan X and Zhan X: The lncRNA SNHG3 regulates energy metabolism of ovarian cancer by an analysis of mitochondrial proteomes. Gynecol Oncol. 150:343–354. 2018.PubMed/NCBI View Article : Google Scholar | |
Zhen H, Du P, Yi Q, Tang X and Wang T: LINC00958 promotes bladder cancer carcinogenesis by targeting miR-490-3p and AURKA. BMC Cancer. 21(1145)2021.PubMed/NCBI View Article : Google Scholar | |
Majumdar R, Bandyopadhyay A, Deng H and Maitra U: Phosphorylation of mammalian translation initiation factor 5 (eIF5) in vitro and in vivo. Nucleic Acids Res. 30:1154–1162. 2002.PubMed/NCBI View Article : Google Scholar | |
Xu L, Wu Q, Yan H, Shu C, Fan W, Tong X and Li Q: Long noncoding RNA KB-1460A1.5 inhibits glioma tumorigenesis via miR-130a-3p/TSC1/mTOR/YY1 feedback loop. Cancer Lett. 525:33–45. 2022.PubMed/NCBI View Article : Google Scholar | |
Wang F, Peters R, Jia J, Mudd M, Salemi M, Allers L, Javed R, Duque TLA, Paddar MA, Trosdal ES, et al: ATG5 provides host protection acting as a switch in the atg8ylation cascade between autophagy and secretion. Dev Cell. 58:866–884.e8. 2023.PubMed/NCBI View Article : Google Scholar | |
Cruickshank BM, Wasson MD, Brown JM, Fernando W, Venkatesh J, Walker OL, Morales-Quintanilla F, Dahn ML, Vidovic D, Dean CA, et al: LncRNA PART1 promotes proliferation and migration, is associated with cancer stem cells, and alters the miRNA landscape in triple-negative breast cancer. Cancers (Basel). 13(2644)2021.PubMed/NCBI View Article : Google Scholar | |
Vogler M: BCL2A1: The underdog in the BCL2 family. Cell Death Differ. 19:67–74. 2012.PubMed/NCBI View Article : Google Scholar | |
Barriocanal M, Carnero E, Segura V and Fortes P: Long non-coding RNA BST2/BISPR is induced by IFN and regulates the expression of the antiviral factor tetherin. Front Immunol. 5(655)2015.PubMed/NCBI View Article : Google Scholar | |
Mohamed Haroon M, Lakshmanan V, Sarkar SR, Lei K, Vemula PK and Palakodeti D: Mitochondrial state determines functionally divergent stem cell population in planaria. Stem Cell Reports. 16:1302–1316. 2021.PubMed/NCBI View Article : Google Scholar | |
Zhu W, Zhou BL, Rong LJ, Ye L, Xu HJ, Zhou Y, Yan XJ, Liu WD, Zhu B, Wang L, et al: Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis. J Zhejiang Univ Sci B. 21:122–136. 2020.PubMed/NCBI View Article : Google Scholar | |
Lee MY, Sumpter R Jr, Zou Z, Sirasanagandla S, Wei Y, Mishra P, Rosewich H, Crane DI and Levine B: Peroxisomal protein PEX13 functions in selective autophagy. EMBO Rep. 18:48–60. 2017.PubMed/NCBI View Article : Google Scholar | |
L'Abbate A, Tolomeo D, De Astis F, Lonoce A, Lo Cunsolo C, Mühlematter D, Schoumans J, Vandenberghe P, Van Hoof A, Palumbo O, et al: t(15;21) translocations leading to the concurrent downregulation of RUNX1 and its transcription factor partner genes SIN3A and TCF12 in myeloid disorders. Mol Cancer. 14(211)2015.PubMed/NCBI View Article : Google Scholar | |
Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein TI, Nudel R, Lieder I, Mazor Y, et al: The GeneCards suite: From gene data mining to disease genome sequence analyses. Curr Protoc Bioinformatics. 54:1.30.1–1.30.33. 2016.PubMed/NCBI View Article : Google Scholar | |
Laudet V: Evolution of the nuclear receptor superfamily: Early diversification from an ancestral orphan receptor. J Mol Endocrinol. 19:207–226. 1997.PubMed/NCBI View Article : Google Scholar | |
Letunic I and Bork P: Interactive tree of life (iTOL) v4: Recent updates and new developments. Nucleic Acids Res. 47 (W1):W256–W259. 2019.PubMed/NCBI View Article : Google Scholar | |
Mouse Genome Sequencing Consortium. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, et al: Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520–562. 2002.PubMed/NCBI View Article : Google Scholar | |
Castoe TA, de Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, et al: The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci USA. 110:20645–20650. 2013.PubMed/NCBI View Article : Google Scholar | |
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, et al: The zebrafish reference genome sequence and its relationship to the human genome. Nature. 496:498–503. 2013.PubMed/NCBI View Article : Google Scholar | |
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al: The genome sequence of Drosophila melanogaster. Science. 287:2185–2195. 2000.PubMed/NCBI View Article : Google Scholar | |
Hodgkin J, Plasterk RH and Waterston RH: The nematode Caenorhabditis elegans and its genome. Science. 270:410–414. 1995.PubMed/NCBI View Article : Google Scholar | |
Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al: The complete genome sequence of Escherichia coli K-12. Science. 277:1453–1462. 1997.PubMed/NCBI View Article : Google Scholar | |
Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, et al: Saccharomyces genome database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 31:216–218. 2003.PubMed/NCBI View Article : Google Scholar | |
Petersohn A, Brigulla M, Haas S, Hoheisel JD, Völker U and Hecker M: Global analysis of the general stress response of Bacillus subtilis. J Bacteriol. 183:5617–5631. 2001.PubMed/NCBI View Article : Google Scholar | |
Ebenezer TE, Carrington M, Lebert M, Kelly S and Field MC: Euglena gracilis genome and transcriptome: Organelles, nuclear genome assembly strategies and initial features. Adv Exp Med Biol. 979:125–140. 2017.PubMed/NCBI View Article : Google Scholar | |
Owen GI and Zelent A: Origins and evolutionary diversification of the nuclear receptor superfamily. Cell Mol Life Sci. 57:809–827. 2000.PubMed/NCBI View Article : Google Scholar | |
Holzer G, Markov GV and Laudet V: Evolution of nuclear receptors and ligand signaling: Toward a soft key-lock model? Curr Top Dev Biol. 125:1–38. 2017.PubMed/NCBI View Article : Google Scholar | |
Penvose A, Keenan JL, Bray D, Ramlall V and Siggers T: Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. Nat Commun. 10(2514)2019.PubMed/NCBI View Article : Google Scholar | |
Cotnoir-White D, Laperrière D and Mader S: Evolution of the repertoire of nuclear receptor binding sites in genomes. Mol Cell Endocrinol. 334:76–82. 2011.PubMed/NCBI View Article : Google Scholar | |
Hanly D, Esteller M and Berdasco M: Altered long non-coding RNA expression in cancer: Potential biomarkers and therapeutic targets? In: Chemical Epigenetics. Mai A (ed). Topics in Medicinal Chemistry. Vol. 33. Springer, Cham, pp401-428, 2019. | |
Fu D, Shi Y, Liu JB, Wu TM, Jia CY, Yang HQ, Zhang DD, Yang XL, Wang HM and Ma YS: Targeting long non-coding RNA to therapeutically regulate gene expression in cancer. Mol Ther Nucleic Acids. 21:712–724. 2020.PubMed/NCBI View Article : Google Scholar | |
Zhang L, Peng D, Sood AK, Dang CV and Zhong X: Shedding light on the dark cancer genomes: Long noncoding RNAs as novel biomarkers and potential therapeutic targets for cancer. Mol Cancer Ther. 17:1816–1823. 2018.PubMed/NCBI View Article : Google Scholar | |
Fatima R, Akhade VS, Pal D and Rao SM: Long noncoding RNAs in development and cancer: Potential biomarkers and therapeutic targets. Mol Cell Ther. 3(5)2015.PubMed/NCBI View Article : Google Scholar |