Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice

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 T...

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Main Authors: Chai-Ling Ho, Matt Geisler
Format: Article
Language:English
Published: MDPI AG 2019-10-01
Series:Plants
Subjects:
Online Access:https://www.mdpi.com/2223-7747/8/11/441
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spelling doaj-777d849a50034b1486318c980e6952852020-11-25T02:26:58ZengMDPI AGPlants2223-77472019-10-0181144110.3390/plants8110441plants8110441Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from RiceChai-Ling Ho0Matt Geisler1Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, MalaysiaDivision of Plant Biology, School of Biological Science, Southern Illinois University Carbondale, 1125 Lincoln Ave., Life Science II, Carbondale, IL 62901-6509, USAThe 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.https://www.mdpi.com/2223-7747/8/11/441bioinformatic predictionco-expressed genesin silicocdna microarraycorrelation
collection DOAJ
language English
format Article
sources DOAJ
author Chai-Ling Ho
Matt Geisler
spellingShingle Chai-Ling Ho
Matt Geisler
Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
Plants
bioinformatic prediction
co-expressed genes
in silico
cdna microarray
correlation
author_facet Chai-Ling Ho
Matt Geisler
author_sort Chai-Ling Ho
title Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
title_short Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
title_full Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
title_fullStr Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
title_full_unstemmed Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice
title_sort genome-wide computational identification of biologically significant cis-regulatory elements and associated transcription factors from rice
publisher MDPI AG
series Plants
issn 2223-7747
publishDate 2019-10-01
description 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.
topic bioinformatic prediction
co-expressed genes
in silico
cdna microarray
correlation
url https://www.mdpi.com/2223-7747/8/11/441
work_keys_str_mv AT chailingho genomewidecomputationalidentificationofbiologicallysignificantcisregulatoryelementsandassociatedtranscriptionfactorsfromrice
AT mattgeisler genomewidecomputationalidentificationofbiologicallysignificantcisregulatoryelementsandassociatedtranscriptionfactorsfromrice
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