New approaches for the analysis of Arabidopsis thaliana small RNAs

Boccara, M., Sarazin, A., Billoud, B., Jolly, V., Martienssen, R., Baulcombe, D., Colot, V. (October 2007) New approaches for the analysis of Arabidopsis thaliana small RNAs. Biochimie, 89 (10). pp. 1252-6. ISSN 0300-9084 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/17562352
DOI: 10.1016/j.biochi.2007.04.011

Abstract

We are interested in the study of small RNAs (sRNAs) that over-accumulate during the plant hypersensitive response (HR), a form of programmed cell death that occurs in and around the site of infection when plants are challenged by pathogens. For this purpose, we have constructed, by subtractive hybridization, a cDNA library of Arabidopsis sRNAs that are enriched during HR. Sequencing of randomly chosen clones provided evidence for the specific accumulation of several microRNAs as well as previously unidentified sRNAs. In a second approach, we have tested the possibility to hybridize labelled cDNAs derived from sRNAs to a DNA tiling array. We could reproducibly hybridize a custom-made tiling array covering Arabidopsis chromosome 4, with small cDNAs as targets. Furthermore, we have found that the distribution of hybridized fragments with sRNAs extracted from control leaves is in good agreement with the abundance of Arabidopsis sRNAs that correspond to this chromosome as determined by massive parallel sequence signature (MPSS).

Item Type: Paper
Additional Information:
Uncontrolled Keywords: Arabidopsis/*genetics Base Sequence Blotting, Northern Chromosomes, Plant/genetics DNA, Complementary/genetics/metabolism Gene Expression Regulation, Plant Gene Library MicroRNAs/*genetics Oligonucleotide Array Sequence Analysis/methods RNA, Plant/*genetics RNA, Small Interfering/genetics
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: CSHL Librarian
Date: October 2007
Date Deposited: 30 Nov 2011 21:32
Last Modified: 09 Apr 2014 20:23
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22972

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