lncRNA CDKN2B-AS1 regulates collagen expression

Alfeghaly C, Sanchez A, Rouget R, Thuillier Q, Igel-Bourguignon V, Marchand V, Branlant C, Motorin Y, Behm-Ansmant I, Maenner S (2021) Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res 49:4954–4970. https://doi.org/10.1093/nar/gkab245

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ambrosini G, Groux R, Bucher P (2018) PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. Bioinformatics 34:2483–2484. https://doi.org/10.1093/bioinformatics/bty127

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bochenek G, Hasler R, El Mokhtari NE, Konig IR, Loos BG, Jepsen S, Rosenstiel P, Schreiber S, Schaefer AS (2013) The large non-coding RNA ANRIL, which is associated with atherosclerosis, periodontitis and several forms of cancer, regulates ADIPOR1, VAMP3 and C11ORF10. Hum Mol Genet 22:4516–4527. https://doi.org/10.1093/hmg/ddt299

Article  CAS  PubMed  Google Scholar 

Buck M, Houglum K, Chojkier M (1996) Tumor necrosis factor-alpha inhibits collagen alpha1(I) gene expression and wound healing in a murine model of cachexia. Am J Pathol 149:195–204

CAS  PubMed  PubMed Central  Google Scholar 

Burleigh MC, Briggs AD, Lendon CL, Davies MJ, Born GV, Richardson PD (1992) Collagen types I and III, collagen content, GAGs and mechanical strength of human atherosclerotic plaque caps: span-wise variations. Atherosclerosis 96:71–81. https://doi.org/10.1016/0021-9150(92)90039-j

Article  CAS  PubMed  Google Scholar 

Chopra A, Mueller R, Weiner J 3rd, Rosowski J, Dommisch H, Grohmann E, Schaefer AS (2021) BACH1 binding links the genetic risk for severe periodontitis with ST8SIA1. J Dent Res 220345211017510. https://doi.org/10.1177/00220345211017510

Consortium CAD, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J, Goldstein BA, Stirrups K, Konig IR, Cazier JB, Johansson A, Hall AS, Lee JY, Willer CJ, Chambers JC, Esko T, Folkersen L, Goel A, Grundberg E, Havulinna AS, Ho WK, Hopewell JC, Eriksson N, Kleber ME, Kristiansson K, Lundmark P, Lyytikainen LP, Rafelt S, Shungin D, Strawbridge RJ, Thorleifsson G, Tikkanen E, Van Zuydam N, Voight BF, Waite LL, Zhang W, Ziegler A, Absher D, Altshuler D, Balmforth AJ, Barroso I, Braund PS, Burgdorf C, Claudi-Boehm S, Cox D, Dimitriou M, Do R, Consortium D, Consortium C, Doney AS, El Mokhtari N, Eriksson P, Fischer K, Fontanillas P, Franco-Cereceda A, Gigante B, Groop L, Gustafsson S, Hager J, Hallmans G, Han BG, Hunt SE, Kang HM, Illig T, Kessler T, Knowles JW, Kolovou G, Kuusisto J, Langenberg C, Langford C, Leander K, Lokki ML, Lundmark A, McCarthy MI, Meisinger C, Melander O, Mihailov E, Maouche S, Morris AD, Muller-Nurasyid M, Mu TC, Nikus K, Peden JF, Rayner NW, Rasheed A, Rosinger S, Rubin D, Rumpf MP, Schafer A, Sivananthan M, Song C, Stewart AF, Tan ST, Thorgeirsson G, van der Schoot CE, Wagner PJ et al (2013) Large-scale association analysis identifies new risk loci for coronary artery disease. Nat Genet 45:25–33. https://doi.org/10.1038/ng.2480

Article  CAS  Google Scholar 

DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28:1530–1532. https://doi.org/10.1093/bioinformatics/bts196

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

Article  CAS  PubMed  Google Scholar 

Ewels P, Magnusson M, Lundin S, Kaller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048. https://doi.org/10.1093/bioinformatics/btw354

Article  CAS  PubMed  PubMed Central  Google Scholar 

Folkersen L, Kyriakou T, Goel A, Peden J, Malarstig A, Paulsson-Berne G, Hamsten A, Hugh W, Franco-Cereceda A, Gabrielsen A, Eriksson P (2009) consortia P Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PLoS One 4:e7677. https://doi.org/10.1371/journal.pone.0007677

Freitag-Wolf S, Munz M, Wiehe R, Junge O, Graetz C, Jockel-Schneider Y, Staufenbiel I, Bruckmann C, Lieb W, Franke A, Loos BG, Jepsen S, Dommisch H, Schaefer AS (2019) Smoking modifies the genetic risk for early-onset Periodontitis. J Dent Res 98:1332–1339. https://doi.org/10.1177/0022034519875443

Article  CAS  PubMed  Google Scholar 

Garcia-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Gotz S, Tarazona S, Dopazo J, Meyer TF, Conesa A (2012) Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28:2678–2679. https://doi.org/10.1093/bioinformatics/bts503

Article  CAS  PubMed  Google Scholar 

Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA (2011) 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response. Nature 470:264–268. https://doi.org/10.1038/nature09753

Article  CAS  PubMed  PubMed Central  Google Scholar 

Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, Jonasdottir A, Jonasdottir A, Sigurdsson A, Baker A, Palsson A, Masson G, Gudbjartsson DF, Magnusson KP, Andersen K, Levey AI, Backman VM, Matthiasdottir S, Jonsdottir T, Palsson S, Einarsdottir H, Gunnarsdottir S, Gylfason A, Vaccarino V, Hooper WC, Reilly MP, Granger CB, Austin H, Rader DJ, Shah SH, Quyyumi AA, Gulcher JR, Thorgeirsson G, Thorsteinsdottir U, Kong A, Stefansson K (2007a) A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316:1491–1493. https://doi.org/10.1126/science.1142842

Article  CAS  PubMed  Google Scholar 

Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, Jonasdottir A, Sigurdsson A, Baker A, Palsson A, Masson G, Gudbjartsson DF, Magnusson KP, Andersen K, Levey AI, Backman VM, Matthiasdottir S, Jonsdottir T, Palsson S, Einarsdottir H, Gunnarsdottir S, Gylfason A, Vaccarino V, Hooper WC, Reilly MP, Granger CB, Austin H, Rader DJ, Shah SH, Quyyumi AA, Gulcher JR, Thorgeirsson G, Thorsteinsdottir U, Kong A, Stefansson K (2007b) A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316:1491–1493

Article  CAS  PubMed  Google Scholar 

Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gabel G, Bergert H, Bechmann I, Stadler PF, Thiery J, Teupser D (2013) Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet 9:e1003588. https://doi.org/10.1371/journal.pgen.1003588

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hubberten M, Bochenek G, Chen H, Hasler R, Wiehe R, Rosenstiel P, Jepsen S, Dommisch H, Schaefer AS (2019) Linear isoforms of the long noncoding RNA CDKN2B-AS1 regulate the c-myc-enhancer binding factor RBMS1. Eur J Hum Genet 27:80–89. https://doi.org/10.1038/s41431-018-0210-7

Article  CAS  PubMed  Google Scholar 

Ji J, Su L, Liu Z (2016) Critical role of calpain in inflammation. Biomed Rep 5:647–652. https://doi.org/10.3892/br.2016.785

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim DH, Beckett JD, Nagpal V, Seman-Senderos MA, Gould RA, Creamer TJ, MacFarlane EG, Chen Y, Bedja D, Butcher JT, Mitzner W, Rouf R, Hata S, Warren DS, Dietz HC (2019) Calpain 9 as a therapeutic target in TGFbeta-induced mesenchymal transition and fibrosis. Sci Transl Med 11. https://doi.org/10.1126/scitranslmed.aau2814

Lee RT, Libby P (1997) The unstable atheroma. Arterioscler Thromb Vasc Biol 17:1859–1867. https://doi.org/10.1161/01.atv.17.10.1859

Article  CAS  PubMed  Google Scholar 

Letavernier E, Zafrani L, Perez J, Letavernier B, Haymann JP, Baud L (2012) The role of calpains in myocardial remodelling and heart failure. Cardiovasc Res 96:38–45. https://doi.org/10.1093/cvr/cvs099

Article  CAS  PubMed  Google Scholar 

Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P (2015) The Molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst 1:417–425. https://doi.org/10.1016/j.cels.2015.12.004

Article  CAS  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S (2014) Moderated estimation of Fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Machiela MJ, Chanock SJ (2015) LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. Bioinform 31:3555–3557. https://doi.org/10.1093/bioinformatics/btv402

Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155–159. https://doi.org/10.1038/nrg2521

Article  CAS  PubMed  Google Scholar 

Munz M, Richter GM, Loos BG, Jepsen S, Divaris K, Offenbacher S, Teumer A, Holtfreter B, Kocher T, Bruckmann C, Jockel-Schneider Y, Graetz C, Munoz L, Bhandari A, Tennstedt S, Staufenbiel I, van der Velde N, Uitterlinden AG, de Groot L, Wellmann J, Berger K, Krone B, Hoffmann P, Laudes M, Lieb W, Franke A, Dommisch H, Erdmann J, Schaefer AS (2018) Genome-wide association meta-analysis of coronary artery disease and periodontitis reveals a novel shared risk locus. Sci Rep 8:13678. https://doi.org/10.1038/s41598-018-31980-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Munz M, Wohlers I, Simon E, Reinberger T, Busch H, Schaefer AS, Erdmann J (2020) Qtlizer: comprehensive QTL annotation of GWAS results. Sci Rep 10:20417. https://doi.org/10.1038/s41598-020-75770-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Myocardial Infarction Genetics C, Kathiresan S, Voight BF, Purcell S, Musunuru K, Ardissino D, Mannucci PM, Anand S, Engert JC, Samani NJ, Schunkert H, Erdmann J, Reilly MP, Rader DJ, Morgan T, Spertus JA, Stoll M, Girelli D, McKeown PP, Patterson CC, Siscovick DS, O’Donnell CJ, Elosua R, Peltonen L, Salomaa V, Schwartz SM, Melander O, Altshuler D, Ardissino D, Merlini PA, Berzuini C, Bernardinelli L, Peyvandi F, Tubaro M, Celli P, Ferrario M, Fetiveau R, Marziliano N, Casari G, Galli M, Ribichini F, Rossi M, Bernardi F, Zonzin P, Piazza A, Mannucci PM, Schwartz SM, Siscovick DS, Yee J, Friedlander Y, Elosua R, Marrugat J, Lucas G, Subirana I, Sala J, Ramos R, Kathiresan S, Meigs JB, Williams G, Nathan DM, MacRae CA, O’Donnell CJ, Salomaa V, Havulinna AS, Peltonen L, Melander O, Berglund G, Voight BF, Kathiresan S, Hirschhorn JN, Asselta R, Duga S, Spreafico M, Musunuru K, Daly MJ, Purcell S, Voight BF, Purcell S, Nemesh J, Korn JM, McCarroll SA, Schwartz SM, Yee J, Kathiresan S, Lucas G, Subirana I, Elosua R, Surti A, Guiducci C, Gianniny L, Mirel D, Parkin M, Burtt N, Gabriel SB, Samani NJ, Thompson JR, Braund PS, Wright BJ, Balmforth AJ, Ball SG et al (2009) Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. Nat Genet 41:334–341. https://doi.org/10.1038/ng.327

Article  CAS  Google Scholar 

Nikpay M, Goel A, Won HH, Hall LM, Willenborg C, Kanoni S, Saleheen D, Kyriakou T, Nelson CP, Hopewell JC, Webb TR, Zeng L, Dehghan A, Alver M, Armasu SM, Auro K, Bjonnes A, Chasman DI, Chen S, Ford I, Franceschini N, Gieger C, Grace C, Gustafsson S, Huang J, Hwang SJ, Kim YK, Kleber ME

留言 (0)

沒有登入
gif