TY  - JOUR
A1  - Hashimoto, Kosuke
A1  - Suzuki, Ana Maria
A1  - Dos Santos, Alexandre
A1  - Desterke, Christophe
A1  - Collino, Agnese
A1  - Ghisletti, Serena
A1  - Braun, Emilie
A1  - Bonetti, Alessandro
A1  - Fort, Alexandre
A1  - Qin, Xian-Yang
A1  - Radaelli, Enrico
A1  - Kaczkowski, Bogumil
A1  - Forrest, Alistair R.R.
A1  - Kojima, Soichi
A1  - Samuel, Didier
A1  - Natoli, Gioacchino
A1  - Buendia, Marie Annick
A1  - Faivre, Jamila
A1  - Carninci, Piero
T1  - CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
Y1  - 2015/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1812 
EP  - 1824 
DO  - 10.1101/gr.191031.115 
VL  - 25 
IS  - 12 
UR  - http://genome.cshlp.org/content/25/12/1812.abstract 
N2  - An increasing number of noncoding RNAs (ncRNAs) have been implicated in various human diseases including cancer; however, the ncRNA transcriptome of hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to map transcription start sites across various types of human and mouse HCCs with emphasis on ncRNAs distant from protein-coding genes. Here, we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in liver tumors. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated, and showed higher risk of recurrence. ChIP-seq data show that MYC and MAX are associated with ncRNA deregulation. Globally, CAGE enabled us to build a mammalian promoter map for HCC, which uncovers a new layer of complexity in HCC genomics. 
ER  -