Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm

PeerJ. 2023 Jun 22:11:e15597. doi: 10.7717/peerj.15597. eCollection 2023.

Abstract

The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 and 5 in the initiator. Incorporating this information in an expanded MARZ algorithm improves predictive performance for the identification of the initiator element. Overall our results demonstrate the need to carefully consider detailed sequence composition features in core promoter elements in order to make more robust and accurate bioinformatic predictions.

Keywords: DNA binding; Initiator; Promoter; TATA box; Transcription.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Animals
  • Base Sequence
  • Drosophila melanogaster* / genetics
  • Drosophila* / genetics
  • Nucleotides

Substances

  • Nucleotides

Grants and funding

This work was funded by National Institutes of Health grants (GM110571 and GM137250) to Robert Drewell and Jacqueline Dresch. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.