Computational protocol: Identification and Characterization of a cis-Regulatory Element for Zygotic Gene Expression in Chlamydomonas reinhardtii

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Protocol publication

[…] Gene models used for sequence retrieval were downloaded from Phytozome 10 (v5.5, DOE Joint Genome Institute; http://phytozome.jgi.doe.gov; ; ) using the BioMart platform (). Individual portions of genes [500 bp upstream of start codons for gene models, upstream regions to transcription start sites (TSSs), 5′-/3′-UTRs, whole gene models and coding sequences (CDSs)] were retrieved using BioMart. MEME (Multiple Expectation maximization for Motif Elicitation; ) was used to find enriched motifs in the 500 bp regions upstream of CDSs for the 300 most highly upregulated zygotic genes identified in our earlier study () with the background null hypothesis third order Markov model constructed from corresponding regions of all C. reinhardtii genes. FIMO (Find Individual Motif Occurrences; ) was used to count occurrences of the ZYRE motif in different sequence sets. Segmented FIMO frequencies were tested statistically using Student’s t-test to assess enrichment in zygotic genes vs. a background null model composed of sequences from all gene models. […]

Pipeline specifications

Software tools BioMart, MEME, MEME Suite
Databases Phytozome
Application Genome annotation
Organisms Chlamydomonas reinhardtii