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RNA-seq and ChIP-seq as complementary approaches for comprehension of plant transcriptional regulatory mechanism


Muhammad, Isiaka Ibrahim and Kong, Sze Ling and Abdullah, Siti Nor Akmar and Munusamy, Umaiyal (2020) RNA-seq and ChIP-seq as complementary approaches for comprehension of plant transcriptional regulatory mechanism. International Journal of Molecular Sciences, 21 (1). art. no. 167. pp. 1-30. ISSN 1661-6596; ESSN: 1422-0067


The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.

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Official URL or Download Paper: https://www.mdpi.com/1422-0067/21/1/167

Additional Metadata

Item Type: Article
Divisions: Faculty of Agriculture
Institute of Plantation Studies
DOI Number: https://doi.org/10.3390/ijms21010167
Publisher: MDPI
Keywords: RNA-sequencing; ChIP-sequencing; Transcriptome; Transcriptional regulatory mechanism; Data integration
Depositing User: Nabilah Mustapa
Date Deposited: 04 May 2020 15:52
Last Modified: 04 May 2020 15:52
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.3390/ijms21010167
URI: http://psasir.upm.edu.my/id/eprint/38197
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