Bioinformatics | Plant Genomes & Evolution
FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation
David Urbina-Gómez*, Flavia Vishi Winck, Bernd Müller-Röber, Diego Riaño-Pachón
*Corresponding author: David Urbina-Gómez
Group of Computational and Evolutionary Biology, Biological Sciences Department, Universidad de los Andes, Bogotá, Colombia
F1000Posters 2012, 3: 385 (poster) [English]
Poster [2.29 MB]
International Society for Computational Biology - Latin America 2012, 17 - 21 Mar 2012, P42
For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyzed an available set of data from an assay of formaldehyde assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding gene-ontology (GO), for an evaluation of over-represented GO categories.
From our results, we can conclude that the genes related to the nucleosome depleted regions link with functions, specific biological processes, and are associated with locations that have been previously described in C.reinhardtii under the same conditions.
Future analysis are needed for a more specific identification of motifs of the putative regulatory elements present in the identified depleted regions.
Figure 1 was reproduced with kind permission from Moroney JV et al (2007) Eukaryot Cell 6(8): 1251-1259
No relevant competing interests disclosed.
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