Computational identification and experimental characterization of preferred downstream positions in human core promoters

PLoS Comput Biol. 2021 Aug 12;17(8):e1009256. doi: 10.1371/journal.pcbi.1009256. eCollection 2021 Aug.

Abstract

Metazoan core promoters, which direct the initiation of transcription by RNA polymerase II (Pol II), may contain short sequence motifs termed core promoter elements/motifs (e.g. the TATA box, initiator (Inr) and downstream core promoter element (DPE)), which recruit Pol II via the general transcription machinery. The DPE was discovered and extensively characterized in Drosophila, where it is strictly dependent on both the presence of an Inr and the precise spacing from it. Since the Drosophila DPE is recognized by the human transcription machinery, it is most likely that some human promoters contain a downstream element that is similar, though not necessarily identical, to the Drosophila DPE. However, only a couple of human promoters were shown to contain a functional DPE, and attempts to computationally detect human DPE-containing promoters have mostly been unsuccessful. Using a newly-designed motif discovery strategy based on Expectation-Maximization probabilistic partitioning algorithms, we discovered preferred downstream positions (PDP) in human promoters that resemble the Drosophila DPE. Available chromatin accessibility footprints revealed that Drosophila and human Inr+DPE promoter classes are not only highly structured, but also similar to each other, particularly in the proximal downstream region. Clustering of the corresponding sequence motifs using a neighbor-joining algorithm strongly suggests that canonical Inr+DPE promoters could be common to metazoan species. Using reporter assays we demonstrate the contribution of the identified downstream positions to the function of multiple human promoters. Furthermore, we show that alteration of the spacing between the Inr and PDP by two nucleotides results in reduced promoter activity, suggesting a spacing dependency of the newly discovered human PDP on the Inr. Taken together, our strategy identified novel functional downstream positions within human core promoters, supporting the existence of DPE-like motifs in human promoters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Base Sequence
  • Computational Biology
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • Gene Expression Regulation
  • Genome, Human*
  • HEK293 Cells
  • Humans
  • Models, Genetic
  • Models, Statistical
  • Promoter Regions, Genetic*
  • RNA Polymerase II / metabolism
  • Species Specificity
  • TATA Box
  • Transcription, Genetic

Substances

  • RNA Polymerase II

Grants and funding

The work was supported by the Swiss Government (to PB) http://www.admin.ch and the Israel Science Foundation (no. 798/10 to TJG) https://isf.org.il. AS was supported by the Nehemia Levzion Scholarship and Bar-Ilan University President’s Scholarship. Research funds available to the TJG from Bar-Ilan University https://www1.biu.ac.il/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.