DEVELOPMENT OF A PIPELINE FOR PROMOTER REGION ANALYSIS IN SUGARCANE

Alicia Lie de Melo; Alan Durham; Glaucia Souza Mendes

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Paper Title

DEVELOPMENT OF A PIPELINE FOR PROMOTER REGION ANALYSIS IN SUGARCANE

Authors

Alicia Lie de Melo
Alan Durham
Glaucia Souza Mendes

Modality

Xpress presentation

Subject area

Omics

Publishing Date

26/04/2022

Country of Publishing

Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeetingxp2021/421858-development-of-a-pipeline-for-promoter-region-analysis-in-sugarcane

ISBN

978-65-5941-645-5

Keywords

TFBS, motif discovery, gene regulation

Summary

The promoter region of the genes can be characterized by the composition of the transcription factor binding sites present in it. Such characterization can be performed in silico, and it depends on the correct screening of the regions of the genome where these elements are located and on the identification of characteristic and recurrent motifs in these regions, which are detected from a set of related sequences. This type of study can be divided into two approaches: i) detection of binding sites of transcription factors with known biding motifs, and ii) de novo motif discovery. These two approaches were combined into a promoter region analysis pipeline, in which the promoter is defined as a region of 800 bp upstream of the TSS and sequences were masked for low complexity regions. The software FIMO with modified parameters was used to detect known motifs described in the JASPAR database. The de novo motif discovery analysis was based on a previous work developed in our group and was improved with additional filtering steps to ensure more reliable results. To test the combined pipeline, a dataset composed of 14 groups of orthologous genes from sugarcane SP80-3280, Saccharum spontaneum, sorghum, rice and Brachypodium was chosen. To help interpret the results obtained by this pipeline, we developed an illustrative panel containing the motifs found in each of the target sequences, the expression data associated to those genes, as well as information about their differential expression and co-expression, if available. Considering the challenge of relating gene expression to promoter architecture only by the visualization of the data, a relationship between the presence/absence of motifs and gene expression was established by Pearson’s correlation coefficient. In addition, the promoter regions were clustered based on the expression of their associated genes. The proposed pipeline was able to considerably lower the massive number of candidate motifs found in earlier versions of the analysis and has the potential to be extended to characterize a greater number of genes.

Title of the Event: X-Meeting XPerience 2021
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

MELO, Alicia Lie de; DURHAM, Alan; MENDES, Glaucia Souza. DEVELOPMENT OF A PIPELINE FOR PROMOTER REGION ANALYSIS IN SUGARCANE.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/421858-DEVELOPMENT-OF-A-PIPELINE-FOR-PROMOTER-REGION-ANALYSIS-IN-SUGARCANE. Access in: 08/05/2025