Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome of lsm8-1 mutant using whole genome tiling arrays

ABSTRACT: Characterization of gene expression and intron retention in lsm8-1 mutants. Pooled 2 week old rosettes of Col-0 (3 biological replicates) and lsm8-1 mutants (3 biological replicates).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Tamara HernÃ¡ndez-Verdeja

PROVIDER: E-GEOD-39617 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

LSM proteins provide accurate splicing and decay of selected transcripts to ensure normal Arabidopsis development.

Perea-Resa Carlos C Hernández-Verdeja Tamara T López-Cobollo Rosa R del Mar Castellano María M Salinas Julio J

The Plant cell 20121207 12

In yeast and animals, SM-like (LSM) proteins typically exist as heptameric complexes and are involved in different aspects of RNA metabolism. Eight LSM proteins, LSM1 to 8, are highly conserved and form two distinct heteroheptameric complexes, LSM1-7 and LSM2-8,that function in mRNA decay and splicing, respectively. A search of the Arabidopsis thaliana genome identifies 11 genes encoding proteins related to the eight conserved LSMs, the genes encoding the putative LSM1, LSM3, and LSM6 proteins b ...[more]

PMID: 23221597

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Project description:In Arabidopsis thaliana, four different DICER-LIKE (DCL) proteins have distinct, but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs) from longer, non-coding precursor RNAs. To analyze the impact of different components of the small RNA (sRNA) biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in sRNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. We discovered distinct effects of dcl1, hyl1 and se mutations on the transcriptome, as well as a number of common genes affected in dcl1 and dcl2 dcl3 dcl4 triple mutants. Our results furthermore suggest that the DCL1 is not only involved in miRNA action, but can also contribute to silencing of certain transposons, apparently through an effect on DNA methylation. Together, our findings contribute to the knowledge of both specialization and overlap between different RNA silencing pathways. Wild type and dcl1-100, se-3, hyl1-2, rdr6-15 ans dcl2,3,4 mutants were grown on MS or soil at 23M-BM-0C and LL. 7 day old seedlings (grown on MS plates) and inflorescences from 28 (>40) day old plants (dcl1) were used for RNA extraction. For stress treatments, seedlings had been grown for 10 days on solid MS medium at 21M-BM-0C, they were transferred to liquid MS medium containing no additives (mock control), 200 mM NaCl (salt stress), 300 mM mannitol (osmotic stress) or 100 M-NM-<M ABA. For cold and heat stress, seedlings were transferred to pre-chilled or pre-warmed liquid MS medium and incubated at 8M-BM-0C and 30M-BM-0C, respectively. Samples were taken after 1 h and 12 h of continuous stress treatment. RNA was extracted from whole seedlings. All RNA samples were converted into double stranded DNA targets that were hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0RM-BM-.). All hybridizations were performed with 3 biological replicates.

Dataset Information

Transcriptome of lsm8-1 mutant using whole genome tiling arrays

Publications

LSM proteins provide accurate splicing and decay of selected transcripts to ensure normal Arabidopsis development.

Similar Datasets

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