RNA-seq identified a super-long intergenic transcript functioning in adipogenesis

RNA Biology

Volumn 10, Issue 6, 2013, Pages 990-1001

  Yi, Fan ^a   Yang, Feng ^a   Liu, Xiaoqiao ^a   Chen, Hongbo ^a   Ji, Ting ^b   Jiang, Lixiang ^b   Wang, Xiaoxia ^a   Yang, Zhangping ^c   Zhang, Li He ^a   Ding, Xianfeng ^b   Liang, Zicai ^a   Du, Quan ^a  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b ZHEJIANG SCI TECH UNIVERSITY   (China)

^c Hangzhou Center for Disease Control and Prevention   (China)

Author keywords

Adipogenesis; High throughput sequencing; Large intergenic non coding RNA; Obesity; PolyA minus RNA

Indexed keywords

LONG UNTRANSLATED RNA; SMALL INTERFERING RNA; MESSENGER RNA; POLYADENYLIC ACID;

ADIPOGENESIS; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL DIFFERENTIATION; CELLULAR DISTRIBUTION; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE FUNCTION; IN VITRO STUDY; LIPID STORAGE; MALE; MOUSE; NONHUMAN; RNA SEQUENCE; RNA TRANSCRIPTION; UPREGULATION; 3T3 CELL LINE; ADIPOCYTE; ANIMAL; ANTIBODY SPECIFICITY; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; SEQUENCE ANALYSIS;

3T3-L1 CELLS; ADIPOCYTES; ADIPOGENESIS; ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICE; ORGAN SPECIFICITY; POLY A; RNA, LONG NONCODING; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 84894532379     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.24644     Document Type: Article

References (34)

1. Buckle P, Buckle J. Obesity, ergonomics and public health. Perspect Public Health 2011; 131:170-6; PMID:21888119; http://dx.doi.org/10.1177/ 1757913911407267.
2. Guilherme A, Virbasius JV, Puri V, Czech MP. Adipocyte dysfunctions linking obesity to insulin resistance and type 2 diabetes. Nat Rev Mol Cell Biol 2008; 9:367-77; PMID:18401346; http://dx.doi.org/10.1038/nrm2391.
3. Kahn SE, Hull RL, Utzschneider KM. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 2006; 444:840-6; PMID:17167471; http://dx.doi.org/10.1038/nature05482.
4. Haemer M, Cluett S, Hassink SG, Liu L, Mangarelli C, Peterson T, et al. Building capacity for childhood obesity prevention and treatment in the medical community: call to action. Pediatrics 2011; 128(Suppl 2):S71-7; PMID:21885648; http://dx.doi.org/10.1542/peds.2011-0480G.
5. Chawla A, Lazar MA. Peroxisome proliferator and retinoid signaling pathways co-regulate preadipocyte phenotype and survival. Proc Natl Acad Sci USA 1994; 91:1786-90; PMID:8127882; http://dx.doi.org/10.1073/pnas.91.5.1786.
6. Tontonoz P, Hu E, Graves RA, Budavari AI, Spiegelman BM. mPPAR gamma 2: tissue-specific regulator of an adipocyte enhancer. Genes Dev 1994; 8:1224-34; PMID:7926726; http://dx.doi.org/10.1101/gad.8.10.1224.
7. Elbrecht A, Chen Y, Cullinan CA, Hayes N, Leibowitz Md, Moller DE, et al. Molecular cloning, expression and characterization of human peroxisome proliferator activated receptors gamma 1 and gamma 2. Biochem Biophys Res Commun 1996; 224:431-7; PMID:8702406; http://dx.doi.org/10.1006/bbrc.1996.1044.
8. Clarke SL, Robinson CE, Gimble JM. CAAT/enhancer binding proteins directly modulate transcription from the peroxisome proliferator-activated receptor gamma 2 promoter. Biochem Biophys Res Commun 1997; 240:99-103; PMID:9367890; http://dx.doi.org/10.1006/bbrc.1997.7627.
9. Guo X, Liao K. Analysis of gene expression profile during 3T3-L1 preadipocyte differentiation. Gene 2000; 251:45-53; PMID:10863095; http://dx.doi.org/10.1016/S0378-1119(00)00192-X.
10. Ibarrola N, Raghothama C, Pandey A. Proteomic analysis of the adipocyte secretome. In: Berdanier, CD and Moustaid-Moussa, N, eds. Genomics and Proteomics in Nutrition. New York: Marcel Dekker, Inc, 2004: 393-411.
11. Lee HK, Lee BH, Park SA, Kim CW. The proteomic analysis of an adipocyte differentiated from human mesenchymal stem cells using two-dimensional gel electrophoresis. Proteomics 2006; 6:1223-9; PMID:16421933; http://dx.doi.org/10. 1002/pmic.200500385.
12. Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, et al. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 2008; 22:2941-52; PMID:18981473; http://dx.doi.org/10.1101/gad.1709008.
13. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10:155-9; PMID:19188922; http://dx.doi.org/10. 1038/nrg2521.
14. Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010; 143:156-69; PMID:20887899; http://dx.doi.org/10.1016/j.cell.2010.09.006.
15. Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, et al. Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 2008; 22:2953-67; PMID:18981474; http://dx.doi.org/10.1101/gad.501108.
16. Payne VA, Au WS, Gray SL, Nora ED, Rahman SM, Sanders R, et al. Sequential regulation of diacylglycerol acyltransferase 2 expression by CAAT/enhancer-binding protein beta (C/EBPbeta) and C/EBPalpha during adipogenesis. J Biol Chem 2007; 282:21005-14; PMID:17504763; http://dx.doi.org/10.1074/jbc.M702871200.
17. Qiao L, Zou C, Shao P, Schaack J, Johnson PF, Shao J. Transcriptional regulation of fatty acid translocase/CD36 expression by CCAAT/enhancer-binding protein alpha. J Biol Chem 2008; 283:8788-95; PMID:18263877; http://dx.doi.org/10.1074/jbc.M800055200.
18. Rahman A, Kumar SG, Kim SW, Hwang HJ, Baek YM, Lee SH, et al. Proteomic analysis for inhibitory effect of chitosan oligosaccharides on 3T3-L1 adipocyte differentiation. Proteomics 2008; 8:569-81; PMID:18175373; http://dx.doi.org/10. 1002/pmic.200700888.
19. Shao D, Lazar MA. Peroxisome proliferator activated receptor gamma, CCAAT/enhancer-binding protein alpha, and cell cycle status regulate the commitment to adipocyte differentiation. J Biol Chem 1997; 272:21473-8; PMID:9261165; http://dx.doi.org/10.1074/jbc.272.34.21473.
20. Wu Z, Xie Y, Bucher NL, Farmer SR. Conditional ectopic expression of C/EBP beta in NIH-3T3 cells induces PPAR gamma and stimulates adipogenesis. Genes Dev 1995; 9:2350-63; PMID:7557387; http://dx.doi.org/10.1101/gad.9.19. 2350.
21. Yang F, Yi F, Zheng Z, Ling Z, Ding J, Guo J, et al. Characterization of a carcinogenesis-associated long non-coding RNA. RNA Biol 2012; 9:110-6; PMID:22258142; http://dx.doi.org/10.4161/rna.9.1.18332.
22. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-11; PMID:19289445; http://dx.doi.org/10.1093/bioinformatics/btp120.
23. Ji P, Diederichs S, Wang W, Böing S, Metzger R, Schneider PM, et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003; 22:8031-41; PMID:12970751; http://dx.doi.org/10.1038/sj.onc.1206928.
24. Wagner LA, Christensen CJ, Dunn DM, Spangrude GJ, Georgelas A, Kelley L, et al. EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood 2007; 109:5191-8; PMID:17351112; http://dx.doi.org/10.1182/blood-2006-06-027987.
25. Siersbæk R, Nielsen R, John S, Sung MH, Baek S, Loft A, et al. Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. EMBO J 2011; 30:1459-72; PMID:21427703; http://dx.doi.org/10.1038/emboj.2011.65.
26. Soukas A, Socci ND, Saatkamp BD, Novelli S, Friedman JM. Distinct transcriptional profiles of adipogenesis in vivo and in vitro. J Biol Chem 2001; 276:34167-74; PMID:11445576; http://dx.doi.org/10.1074/jbc.M104421200.
27. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7; PMID:19182780; http://dx.doi.org/10. 1038/nature07672.
28. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011; 147:1537-50; PMID:22196729; http://dx.doi.org/10.1016/j.cell.2011.11. 055.
29. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009; 106:11667-72; PMID:19571010; http://dx.doi.org/10.1073/pnas.0904715106.
30. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005; 15:1034-50; PMID:16024819; http://dx.doi.org/10.1101/ gr.3715005.
31. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007; 35(Web Server issue):W345-9; PMID:17631615; http://dx.doi.org/10.1093/nar/gkm391.
32. Zuo Y, Qiang L, Farmer SR. Activation of CCAAT/enhancer-binding protein (C/EBP) alpha expression by C/EBP beta during adipogenesis requires a peroxisome proliferator-activated receptor-gamma-associated repression of HDAC1 at the C/ebp alpha gene promoter. J Biol Chem 2006; 281:7960-7; PMID:16431920; http://dx.doi.org/10.1074/jbc.M510682200.
33. Yazgan O, Krebs JE. Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem Cell Biol 2007; 85:484-96; PMID:17713583; http://dx.doi.org/10.1139/O07-061.
34. Prokesch A, Hackl H, Hakim-Weber R, Bornstein SR, Trajanoski Z. Novel insights into adipogenesis from omics data. Curr Med Chem 2009; 16:2952-64; PMID:19689276; http://dx.doi.org/10.2174/092986709788803132.