Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

European Heart Journal

Volumn 36, Issue 6, 2015, Pages 353-368

  Ounzain, Samir ^a   Micheletti, Rudi ^a   Beckmann, Tal ^a   Schroen, Blanche ^b   Alexanian, Michael ^a   Pezzuto, Iole ^a   Crippa, Stefania ^a   Nemir, Mohamed ^a   Sarre, Alexandre ^c   Johnson, Rory ^d   Dauvillier, Jérôme ^c   Burdet, Frédéric ^c   Ibberson, Mark ^c   Guigó, Roderic ^d   Xenarios, Ioannis ^c   Heymans, Stephane ^b   Pedrazzini, Thierry ^a  

^a University of Lausanne Medical Center   (Switzerland)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

^d CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

Heart failure; Long non coding RNAs; Myocardial infarction; Next generation sequencing; Transcriptome

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; OLIGONUCLEOTIDE; TRANSCRIPTOME; BIOLOGICAL MARKER; CHROMATIN;

AB INITIO CALCULATION; ANIMAL CELL; ANIMAL MODEL; ANIMAL TISSUE; AORTA STENOSIS; ARTICLE; CALCIUM HOMEOSTASIS; CHROMATIN; CONGESTIVE CARDIOMYOPATHY; CONTROLLED STUDY; DEVELOPMENTAL GENE; GENE EXPRESSION; GENE FUNCTION; GENE ONTOLOGY; GENE SILENCING; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HEART DEVELOPMENT; HEART FUNCTION; HEART INFARCTION; HEART SIZE; HUMAN; HUMAN GENOME; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOLOGY; PRIORITY JOURNAL; RNA SEQUENCE; ANALYSIS OF VARIANCE; ANIMAL; C57BL MOUSE; CELL CULTURE; CELL DIFFERENTIATION; CYTOLOGY; EMBRYONIC STEM CELL; GENE EXPRESSION PROFILING; GENETIC TRANSFECTION; GENETICS; MALE; METABOLISM; PHYSIOLOGY; PROCEDURES; VASCULAR REMODELING;

ANALYSIS OF VARIANCE; ANIMALS; BIOMARKERS; CELL DIFFERENTIATION; CELLS, CULTURED; CHROMATIN; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; HUMANS; MALE; MICE, INBRED C57BL; MYOCARDIAL INFARCTION; RNA, LONG NONCODING; TRANSCRIPTOME; TRANSFECTION; VASCULAR REMODELING;

EID: 84928233559     PISSN: 0195668X     EISSN: 15229645     Source Type: Journal    
DOI: 10.1093/eurheartj/ehu180     Document Type: Article

References (19)

1. Roger VL, Go AS, Lloyd-Jones DM, Benjamin EJ, Berry JD, Borden WB, Bravata DM, Dai S, Ford ES, Fox CS, Fullerton HJ, Gillespie C, Hailpern SM, Heit JA, Howard VJ, Kissela BM, Kittner SJ, Lackland DT, Lichtman JH, Lisabeth LD, Makuc DM, Marcus GM, Marelli A, Matchar DB, Moy CS, Mozaffarian D, Mussolino ME, Nichol G, Paynter NP, Soliman EZ, Sorlie PD, Sotoodehnia N, Turan TN, Virani SS, Wong ND, Woo D, Turner MB, American Heart Association Statistics C, Stroke Statistics S. Heart disease and stroke statistics-2012 update: a report from the American Heart Association. Circulation 2012;125:e2-e220.
2. Hill JA, Olson EN. Cardiac plasticity. N Engl J Med 2008;358:1370-1380.
3. van Berlo JH, Maillet M, Molkentin JD. Signaling effectors underlying pathologic growth and remodeling of the heart. J Clin Invest 2013;123:37-45.
4. Lee TI, Young RA. Transcriptional regulation and its misregulation in disease. Cell 2013;152:1237-1251.
5. Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 2013;20:300-307.
6. Ounzain S, Crippa S, Pedrazzini T. Small and long non-coding RNAs in cardiac homeostasis and regeneration. Biochim Biophys Acta 2013;1833:923-933.
7. Mendell JT, Olson EN. MicroRNAs in stress signaling and human disease. Cell 2012; 148:1172-1187.
8. Kumarswamy R, Thum T. Non-codingRNAs in cardiac remodeling and heart failure. Circ Res 2013;113:676-689.
9. Carninci P, KasukawaT, Katayama S, Gough J, Frith MC, Maeda N, OyamaR, RavasiT, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y, Consortium F, Group RGER, Genome Science G. The transcriptional landscape of the mammalian genome. Science 2005;309:1559-1563.
10. Consortium EP, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassmann T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP,WuW, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigo R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Roder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
11. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009;458:223-227.
12. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008;322:750-756.
13. Latos PA, Pauler FM, Koerner MV, Senergin HB, Hudson QJ, Stocsits RR, AllhoffW, Stricker SH, Klement RM,Warczok KE, AumayrK, Pasierbek P, BarlowDP. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012;338:1469-1472.
14. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, SharmaA, Bubulya PA, Blencowe BJ, Prasanth SG, PrasanthKV. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010;39:925-938.
15. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010;329:689-693.
16. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011;477:295-300.
17. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012;22:1775-1789.
18. Moran I, Akerman I, van de Bunt M, Xie R, Benazra M, Nammo T, Arnes L, Nakic N, Garcia-Hurtado J, Rodriguez-Segui S, Pasquali L, Sauty-Colace C, Beucher A, Scharfmann R, van Arensbergen J, Johnson PR, Berry A, Lee C, Harkins T, Gmyr V, Pattou F, Kerr-Conte J, Piemonti L, Berney T, Hanley N, Gloyn AL, Sussel L, Langman L, Brayman KL, Sander M, McCarthy MI, Ravassard P, Ferrer J. Human beta cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. Cell Metab 2012;16: 435-448.
19. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 2013; 12:616-628.