Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

    Authors

    J. Ding; X. M. Li;H. Y. Hu

    Comments

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    Abbreviated Journal Title

    Plant Physiol.

    Keywords

    FACTOR-BINDING SITES; GENE-EXPRESSION; ABSCISIC-ACID; CHROMATIN-IMMUNOPRECIPITATION; TRANSCRIPTIONAL ACTIVATORS; STATISTICAL; SIGNIFICANCE; ARABIDOPSIS-THALIANA; RESPONSIVE ELEMENT; PROTEIN-BINDING; IN-VIVO; Plant Sciences

    Abstract

    Chlamydomonas reinhardtii is one of the most important microalgae model organisms and has been widely studied toward the understanding of chloroplast functions and various cellular processes. Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study, such as global cis-regulatory element (CRE) identification, in C. reinhardtii. Recently, large-scale genomic data in microalgae species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here, we performed in silico CRE identification at the whole genome level in C. reinhardtii using a comparative genomics-based method. We predicted a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple lines of evidence from literature, gene transcriptional profiles, and gene annotation resources support our prediction. The predicted CREs will serve, to our knowledge, as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation. The accompanying software tool and the predictions in C. reinhardtii are also made available through a Web-accessible database (http://hulab.ucf.edu/research/projects/Microalgae/sdcre/motifcomb.html).

    Journal Title

    Plant Physiology

    Volume

    160

    Issue/Number

    2

    Publication Date

    1-1-2012

    Document Type

    Article

    Language

    English

    First Page

    613

    Last Page

    623

    WOS Identifier

    WOS:000309523800005

    ISSN

    0032-0889

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