RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2015 
FD December 01 
VO 25 
IS 12 
SP 1812 
OP 1824 
DO 10.1101/gr.191031.115 
UL http://genome.cshlp.org/content/25/12/1812.abstract 
AB 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.