Nucleosome Organization around Pseudogenes in the Human Genome

Abstract EN

Pseudogene, disabled copy of functional gene, plays a subtle role in geneexpression and genome evolution.

The first step in deciphering RNA-level regulationof pseudogenes is to understand their transcriptional activity.

So far, there has been noreport on possible roles of nucleosome organization in pseudogene transcription.

Inthis paper, we investigated the effect of nucleosome positioning on pseudogenetranscription.

For transcribed pseudogenes, the experimental nucleosome occupancyshows a prominent depletion at the regions both upstream of pseudogene startpositions and downstream of pseudogene end positions.

Intriguingly, the samedepletion is also observed for nontranscribed pseudogenes, which is unexpectedsince nucleosome depletion in those regions is thought to be unnecessary in light of thenontranscriptional property of those pseudogenes.

The sequence-dependentprediction of nucleosome occupancy shows a consistent pattern with the experimentaldata-based analysis.

Our results indicate that nucleosome positioning may playimportant roles in both the transcription initiation and termination of pseudogenes.