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Genome-wide computational identification of biologically significant cis-regulatory elements and associated transcription factors from rice


Ho, Chai Ling and Geisler, Matt (2019) Genome-wide computational identification of biologically significant cis-regulatory elements and associated transcription factors from rice. Plants, 8 (11). art. no. 441. pp. 1-26. ISSN 2223-7747


The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene’s expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some—but not all—CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.

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Official URL or Download Paper: https://www.mdpi.com/2223-7747/8/11/441

Additional Metadata

Item Type: Article
Divisions: Faculty of Biotechnology and Biomolecular Sciences
DOI Number: https://doi.org/10.3390/plants8110441
Publisher: MDPI
Keywords: Bioinformatic prediction; Co-expressed genes; In silico; cDNA microarray; Correlation
Depositing User: Nabilah Mustapa
Date Deposited: 04 May 2020 16:00
Last Modified: 04 May 2020 16:00
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.3390/plants8110441
URI: http://psasir.upm.edu.my/id/eprint/38227
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