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).

Chipmodule: Systematic Discovery of Transcription Factors and Their Cofactors From Chip-Seq Data

“…A pair of TFs shares similar motifs if the STAMP p-value of the similarity of the two motifs is less than 1E-5, as in previous studies. [33][34][35] We also noticed that several inserted TF groups were not identified. We hypothesized that these TF groups were missed by ChIPModule because not all TFBSs of the TFs in these TF groups satisfied the required putative TFBS cutoff used in Section 2.3, or TFBSs of different TFs may overlap and some of them were thus discarded.…”

The Chlamydomonas genome project: a decade on

“…Alternatively, the Iomiqs database [29] utilizes MapMan ontologies to provide a visual output that “bins” genes into various metabolic groupings. More specific types of annotation can be found on the Chlamydomonas section of BioCyc, which maps genes onto metabolic pathways, the cis -regulatory element prediction database [30], and PredAlgo [31], providing green algae-specific protein localization predictions (Table 3). …”

Hypoosmotic Expression of Dunaliella bardawil ζ-Carotene Desaturase Is Attributed to a Hypoosmolarity-Responsive Element Different from Other Key Carotenogenic Genes

“…However, the up-regulation or down-regulation responses of the AGC box to stress signals is dependent on the protein factors binding in Arabidopsis (Fujimoto et al, . Anaerobic motif2 (21,718; AGCAGC) is found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway in plants (Mohanty et al, 2005) as well as in C. reinhardtii (Ding et al, 2012). The activation sequence factor1 (ASF1) binding site (21,839; TGACG) is identical to the TGACG motif, which is the binding site of the ASF1 in the cauliflower mosaic virus 35S promoter (Lam et al, 1989).…”