Unknown,Transcriptomics,Genomics,Proteomics

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Development of gene expression profiles for pearl oyster Pinctada fucata exposed in near-future ocean warming and acidification.

ABSTRACT: To elucidate how does the gene expression profiles of whole transcriptome of P.fucata response to acute and gradual seawater acidification and warming, and which genes or functional gene clusters are involved in the stress response to enviromental stressors, we have employed microarray as a tool to identify genes in these stress. For acute temperature and acidity stress treatment, oysters were added into the tanks immediately with the maintaining conditions of temperature 25M-BM-11 M-BM-0C and 31M-BM-11 M-BM-0C, acidity pH7.8M-BM-10.05 and pH7.5M-BM-10.05, salinity 33M-BM-11M-bM-^@M-0 in recirculating seawater. The temperatures and pH values in the studies were near future levels and predicted for 2100 and 2300. The pallial zone of mantle were collected and preserved on the hours of 72 after treatment for subsequent studies. All the collected mantles above were snap-frozen in liquid nitrogen, and stored at -80M-BM-0C. The conditions of salinity 33M-BM-11M-bM-^@M-0, 19M-BM-11 M-BM-0C and pH8.1M-BM-10.05 (~380 ppm CO2) in pre-culture tanks was as a control. In total, 15 mantle tissue samples from 15 individuals were used for the microarray analysis and 3 samples were used as control .Three biological replicates were employed in each treatment.

ORGANISM(S): Pinctada fucata

SUBMITTER: Shiguo Li

PROVIDER: E-GEOD-57171 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Development of gene expression profiles for pearl oyster Pinctada fucata exposed in near-future ocean warming and acidification.

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