Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis.

ABSTRACT: In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of '4 bases-a spacer with a flexible length-4 bases'. 8,044 pre-selected bipartite octamers, which had an overrepresentation of specific spacer lengths in promoter sequences and sequences related to core elements removed, were subjected to frequency comparison analysis. Prediction of

SUBMITTER: Yamamoto YY 

PROVIDER: S-EPMC5499772 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature