A large scale expression study associates uc.283-plus IncRNA with pluripotent stem cells and human glioma

被引：32

作者：

Galasso, Marco ^{[1
]}

Dama, Paola ^{[1
]}

Previati, Maurizio ^{[1
]}

Sandhu, Sukhinder ^{[2
]}

Palatini, Jeff ^{[2
]}

Coppola, Vincenzo ^{[2
]}

Warner, Sarah ^{[2
]}

Sana, Maria E. ^{[1
]}

Zanella, Riccardo ^{[1
]}

Abujarour, Ramzey ^{[5
]}

Desponts, Caroline ^{[6
]}

Teitell, Michael A. ^{[7
]}

Garzon, Ramiro ^{[2
]}

Calin, George ^{[4
]}

Croce, Carlo M. ^{[2
]}

Volinia, Stefano ^{[1
,2
,3
]}

机构：

[1] Univ Ferrara, Dept Morphol Surg & Expt Med, LTTA, I-44123 Ferrara, Italy

[2] Ohio State Univ, Wexner Med Ctr & Biomed Informat, Comprehens Canc Ctr, Columbus, OH 43210 USA

[3] Ohio State Univ, Columbus, OH 43210 USA

[4] Univ Texas Houston, MD Anderson Canc Ctr, Houston, TX 77030 USA

[5] Fate Therapeut, San Diego, CA 92121 USA

[6] Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA

[7] Univ Calif Los Angeles, David Geffen Sch Med, Dept Pathol & Lab Med, Los Angeles, CA 90095 USA

来源：

GENOME MEDICINE | 2014年 / 6卷

关键词：

ULTRACONSERVED ELEMENTS; NONCODING RNAS; ENHANCER; CANCER; TRANSCRIPTION; REGIONS; PREDICTION; SIGNATURE; GENOMICS; TARGETS;

D O I：

10.1186/s13073-014-0076-4

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Background: There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. About half of these UCRs are reported as transcribed and many correspond to long non-coding RNAs (IncRNAs). Methods: We used custom microarrays with 962 probes representing sense and antisense sequences for the 481 UCRs to examine their expression across 374 normal samples from 46 different tissues and 510 samples representing 10 different types of cancer. The expression in embryonic stem cells of selected UCRs was validated by real time PCR. Results: We identified tissue selective UCRs and studied UCRs in embryonic and induced pluripotent stem cells. Among the normal tissues, the uc.283 IncRNA was highly specific for pluripotent stem cells. Intriguingly, the uc.283-plus IncRNA was highly expressed in some solid cancers, particularly in one of the most untreatable types, glioma. Conclusion: Our results suggest that uc.283-plus IncRNA might have a role in pluripotency of stem cells and in the biology of glioma.

引用

页数：8

共 42 条

[1] Ultraconserved elements Genomics, function and disease [J].

Baira, Eirini ;

Greshock, Joel ;

Coukos, George ;

Zhang, Lin .

RNA BIOLOGY, 2008, 5 (03) :132-134

[2] MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries [J].

Bar, Merav ;

Wyman, Stacia K. ;

Fritz, Brian R. ;

Qi, Junlin ;

Garg, Kavita S. ;

Parkin, Rachael K. ;

Kroh, Evan M. ;

Bendoraite, Ausra ;

Mitchell, Patrick S. ;

Nelson, Angelique M. ;

Ruzzo, Walter L. ;

Ware, Carol ;

Radich, Jerald P. ;

Gentleman, Robert ;

Ruohola-Baker, Hannele ;

Tewari, Muneesh .

STEM CELLS, 2008, 26 (10) :2496-2505

[3] A distal enhancer and an ultraconserved exon are derived from a novel retroposon [J].

Bejerano, G ;

Lowe, CB ;

Ahituv, N ;

King, B ;

Siepel, A ;

Salama, SR ;

Rubin, EM ;

Kent, WJ ;

Haussler, D .

NATURE, 2006, 441 (7089) :87-90

[4] Ultraconserved elements in the human genome [J].

Bejerano, G ;

Pheasant, M ;

Makunin, I ;

Stephen, S ;

Kent, WJ ;

Mattick, JS ;

Haussler, D .

SCIENCE, 2004, 304 (5675) :1321-1325

[5] A comparison of normalization methods for high density oligonucleotide array data based on variance and bias [J].

Bolstad, BM ;

Irizarry, RA ;

Åstrand, M ;

Speed, TP .

BIOINFORMATICS, 2003, 19 (02) :185-193

[6] IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions [J].

Busch, Anke ;

Richter, Andreas S. ;

Backofen, Rolf .

BIOINFORMATICS, 2008, 24 (24) :2849-2856

[7] A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia [J].

Calin, GA ;

Ferracin, M ;

Cimmino, A ;

Di Leva, G ;

Shimizu, M ;

Wojcik, SE ;

Iorio, MV ;

Visone, R ;

Sever, NI ;

Fabbri, M ;

Iuliano, R ;

Palumbo, T ;

Pichiorri, F ;

Roldo, C ;

Garzon, R ;

Sevignani, C ;

Rassenti, L ;

Alder, H ;

Volinia, S ;

Liu, CG ;

Kipps, TJ ;

Negrini, M ;

Croce, CM .

NEW ENGLAND JOURNAL OF MEDICINE, 2005, 353 (17) :1793-1801

[8] Ultraconserved regions encoding ncRNAs are, altered in human leukemias and carcinomas [J].

Calin, George A. ;

Liu, Chang-Gong ;

Ferracin, Manuela ;

Hyslop, Terry ;

Spizzo, Riccardo ;

Sevignani, Cinzia ;

Fabbri, Muller ;

Cimmino, Amelia ;

Lee, Eun Joo ;

Wojcik, Sylwia E. ;

Shimizu, Masayoshi ;

Tili, Esmerina ;

Rossi, Simona ;

Taccioli, Cristian ;

Pichiorri, Flavia ;

Liu, Xiuping ;

Zupo, Simona ;

Herlea, Vlad ;

Gramantieri, Laura ;

Lanza, Giovanni ;

Alder, Hansjuerg ;

Rassenti, Laura ;

Volinia, Stefano ;

Schmittgen, Thomas D. ;

Kipps, Thomas J. ;

Negrini, Massimo ;

Croce, Carlo M. .

CANCER CELL, 2007, 12 (03) :215-229

[9] An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs [J].

Chang, Tzu-Hao ;

Huang, Hsi-Yuan ;

Hsu, Justin Bo-Kai ;

Weng, Shun-Long ;

Horng, Jorng-Tzong ;

Huang, Hsien-Da .

BMC BIOINFORMATICS, 2013, 14

[10] Mapping and analysis of chromatin state dynamics in nine human cell types [J].

Ernst, Jason ;

Kheradpour, Pouya ;

Mikkelsen, Tarjei S. ;

Shoresh, Noam ;

Ward, Lucas D. ;

Epstein, Charles B. ;

Zhang, Xiaolan ;

Wang, Li ;

Issner, Robbyn ;

Coyne, Michael ;

Ku, Manching ;

Durham, Timothy ;

Kellis, Manolis ;

Bernstein, Bradley E. .

NATURE, 2011, 473 (7345) :43-U52

← 1 2 3 4 5 →