5' Cap-Isolated RNA Pol II Transcripts and ENCODE Tiling Arrays to Identify Gene Expression Changes in Hepatitis C Liver

ABSTRACT: Recent studies of the human transcriptome suggest that many transcripts have short or lack 3' poly(A) ends. In addition, the length of 3' poly(A) ends may vary for some transcript to regulate mRNA translation. Heterogeneous lengths of poly(A) ends may introduce variations in measuring RNA transcripts using current approaches. We hypothesized that affinity purifying Pol II RNAs by their unique 5' m7GpppN cap regardless of their polyadenylation status would add additional information to genomic expression analyses and possibly overcome the variation in signals sometimes observed with analysis of poly(A) selected mRNA. 5' capped and 3' poly(A) RNA were isolated from normal and hepatitis C cirrhotic (HCV) human liver using a high-affinity variant of eIF4E and standard oligo(dT) methods, respectively. Both populations of RNA were analyzed using ENCODE tiling arrays representing 1% of the genome. A total of 64 annotated genes were significantly increased in HCV as compared to normal liver; 27 of these genes were identified by analyzing 5' capped RNA. A total of 31 annotated genes were significantly decreased; 16 of these were identified by analyzing 5' capped RNA. Bioinformatic analysis showed that 5' capped RNA provided a more extensive expression profile of intronic regions and identified Pol II transcriptionally active regions in unannotated regions of the genome that were differentially expressed in normal and disease states. The analysis of 5' capped RNA isolated from biospecimens provides additional gene expression information and identifies novel Pol II transcripts that are differentially expressed. This approach may also be useful in studying of RNAs regulated by 3' polyadenylation or RNA degradation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE18904 | GEO | 2011/03/29

SECONDARY ACCESSION(S): PRJNA121313

REPOSITORIES: GEO