Title
Systematic Prediction Of Cis-Regulatory Elements In The Chlamydomonas Reinhardtii Genome Using Comparative Genomics
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). © 2012 American Society of Plant Biologists. All Rights Reserved.
Publication Date
1-1-2012
Publication Title
Plant Physiology
Volume
160
Issue
2
Number of Pages
613-623
Document Type
Article
Personal Identifier
scopus
DOI Link
https://doi.org/10.1104/pp.112.200840
Copyright Status
Unknown
Socpus ID
84867119166 (Scopus)
Source API URL
https://api.elsevier.com/content/abstract/scopus_id/84867119166
STARS Citation
Ding, Jun; Li, Xiaoman; and Hu, Haiyan, "Systematic Prediction Of Cis-Regulatory Elements In The Chlamydomonas Reinhardtii Genome Using Comparative Genomics" (2012). Scopus Export 2010-2014. 5531.
https://stars.library.ucf.edu/scopus2010/5531