Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1156013 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30521734.fastq.gz | Fastqsanger.gz | |||
| SRR30521735.fastq.gz | Fastqsanger.gz | |||
| SRR30521736.fastq.gz | Fastqsanger.gz | |||
| SRR30521737.fastq.gz | Fastqsanger.gz | |||
| SRR30521738.fastq.gz | Fastqsanger.gz |
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Project description:Arabidopsis polyadenylation factor PCFS4 functioned in the alternative polyadenylation of FCA. To identify additional genes differetially processed by PCFS4, we compared the transcriptomes of PCFS4 mutant, pcfs4-1 and wild type Col with Arabidopsis tiling array analyses and a newly developed data processing protocol, RADPRE. We found 68 genes were differentially processed and 114 genes differetially expressed in pcfs4-1 mutant. The top 7 of 68 differetially processed genes were further confirmed with real-time RT-PCR analysis.
2011-02-28 | GSE21250 | GEO
Project description:Arabidopsis polyadenylation factor PCFS4 functioned in the alternative polyadenylation of FCA. To identify additional genes differetially processed by PCFS4, we compared the transcriptomes of PCFS4 mutant, pcfs4-1 and wild type Col with Arabidopsis tiling array analyses and a newly developed data processing protocol, RADPRE. We found 68 genes were differentially processed and 114 genes differetially expressed in pcfs4-1 mutant. The top 7 of 68 differetially processed genes were further confirmed with real-time RT-PCR analysis. Arabidopsis plants were grown in a radomized block design with 3 replicates for each of pcfs4-1 and Col. Each block contained one pcfs4-1 and one Col. above ground tissue of 15-day old seedlings was collected 8 hours after dawn. Total RNAs were extracted using Concert Plant RNA reagent (Invitrogen); The double-stranded cDNA targets prepared from total RNA were labeled and hybridized to the Arabidopsis Tiling 1.0R array.
2011-02-28 | E-GEOD-21250 | biostudies-arrayexpress
Project description:Profiling of alternative polyadenylation events in Arabidopsis thaliana
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Project description:Use 3ʹ region extraction and deep sequencing (3'READS) and bioinformatics techniques to profile alternative polyadenylation and gene regulation in plant Arabidopsis thaliana exposed to light and darkness
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Project description:The oxt6 mutant is an oxidative stress-tolerant Arabidopsis mutant that is deficient in a polyadenylation factor subunit. Expression analysis suggests that impaired poly(A) site choice is responsible for the stress-tolerant phenotype. We used microarrays to understand the link between the polyadenylation defect and stress tolerance. Keywords: mutant, wild-type, complemented line comparison
2007-03-07 | GSE7211 | GEO
Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.
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Project description:Circadian clock regulation of alternative splicing and alternative polyadenylation in Arabidopsis thaliana
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Project description:The tumorigenesis of small intestinal neuroendocrine tumors (NETs) is poorly understood. Recent studies have associated alternative polyadenylation with proliferation, cell transformation and cancer. Polyadenylation is the process in which the pre-mRNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo alternative polyadenylation. This produces two or more distinct mRNA isoforms with different 3M-bM-^@M-^Y untranslated regions. Additionally, alternative polyadenylation can also produce mRNAs containing different 3M-bM-^@M-^Y-terminal coding regions. Therefore, alternative polyadenylation alters both the repertoire and the expression level of proteins. Here we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three small intestinal neuroendocrine tumors and a reference sample. In the tumors sixteen genes showed significant changes of alternative polyadenylation pattern, which lead to either the 3M-bM-^@M-^Y truncation of mRNA coding regions or 3M-bM-^@M-^Y untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1 and DACT2. We validated the alternative polyadenylation in 3 out of 3 cases with Q-RT-PCR. Our findings suggest that changes of alternative polyadenylation pattern in these 16 genes could be involved in the tumorigenesis of small intestinal neuroendocrine tumors. Furthermore, they also point to alternative polyadenylation as a new target for both diagnostic and treatment of small intestinal neuroendocrine tumors. The identified genes with alternative polyadenylation specific to the small intestinal neuroendocrine tumors could be further tested as diagnostic markers and drug targets for disease prevention and treatment. PolyA-seq profiling of 3 human neuroendocrine tumors compared and pituitary using Direct RNA Sequencing from Helicos Biosciences Technology
2014-04-10 | E-GEOD-56657 | biostudies-arrayexpress
Project description:Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. AtPRMT10 mutations cause significant proximal-to-distal poly(A) site shifts largely overlapping with those in hlp1-1 mutants. Proximal polyadenylation is maintained by AtPRMT10-directed methylation and is mediated in part by methylation of HLP1 at specific arginine residues. Our findings demonstrate that arginine methylation of an RNA-binding protein adds a novel layer of regulation to widespread alternative polyadenylation.
2019-01-01 | GSE69904 | GEO
Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects.
2016-03-14 | GSE79157 | GEO