GEO DataSets

(Submitter supplied) Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3’ end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9302 GPL13222

8 Samples

Download data: BED, WIG

(Submitter supplied) In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5’s function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10272

2 Samples

Download data: BEDGRAPH

(Submitter supplied) We have analyzed the poly(A) usage between Arabidopsis control and fip1-2 mutant seedlings grown in normal medium. FIP1 is a subunit of the polyadenalation machinary and loss of function of FIP1 affects plant development and response to salt, ABA and cadmium.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: PDF, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL9052

22 Samples

Download data: BED, WIG

(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

18 Samples

Download data: WIG

(Submitter supplied) Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding sites of 3' end processing factors CPSF‐160, CPSF‐100, CPSF‐73, CPSF‐30, Fip1, CstF‐64, CstF-64tau, CF Im25, CF Im59, and CF Im68 and 3' end processing sites in HEK293 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

4 Samples

Download data: BED

(Submitter supplied) 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. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10298

6 Samples

Download data: CEL, TXT

(Submitter supplied) In eukaryotes, the 3' ends of RNA polymerase II-generated transcripts are made in the majority of cases by site-specific endonucleolytic cleavage, followed by the addition of a poly(A) tail. By alternative polyadenylation, a gene can give rise to multiple mRNA isoforms that differ in the length of their 3' UTRs and hence in their susceptibility to post-transcriptional regulatory factors such as microRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13970

8 Samples

Download data: PAIR

(Submitter supplied) Analysis of loss-of-function mutants of JUMONJI30 (JMJ30) and JMJ32 in Arabidopsis thaliana (Col). JMJ30 and JMJ32 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13970

4 Samples

Download data: PAIR

(Submitter supplied) Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL13970

4 Samples

Download data: PAIR

(Submitter supplied) In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL17639

14 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) As the most ubiquitous internal modification of eukaryotic mRNA, m6A (N6-methyladenosine) modification plays a vital role in almost every aspect of mRNA metabolism. However, the evidence of m6A in regulating the alternative polyadenylation (APA) is limited. APA is controlled by a large protein-RNA complex with many components including CPSF30. Arabidopsis CPSF30 has two isoforms, the longer one named CPSF30-L containing an additional YTH (YT512-B Homology)-domain in the C terminus, which is unique in plant. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19580 GPL26208

24 Samples

Download data: BW

(Submitter supplied) This experimental series concerns the position bias and extent of 3'-end choice in MCF7 cells after knock-down of the CFII subunits PCF11 and CLP1 in MCF7. Loss of either subunit results in 3'-lengthening by APA. Importantly this lengthening is toward a more 'normal-like' distribution. MCF7 cells show a native 3'-end distribution favoring short internal adenylation sites compared to MDAMD231 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

11 Samples

Download data: CSV

(Submitter supplied) We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17970 GPL19580

10 Samples

Download data: BED, TXT

(Submitter supplied) The Arabidopsis RNA-binding proteins FCA and FPA were initially identified based on their suppression of the flowering time regulator FLC. Recently, however, they have been found to influence expression of a wide range of targets in the Arabidopsis genome. Here, we use whole-genome tiling arrays to determine the extent of their targets at two stages of seedling development. A wide range of genes and transposable elements were mis-expressed in the fcafpa double mutant with a significant bias for mis-regulated genomic segments mapping to the 3’ region of genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

12 Samples

Download data: CEL, TXT

(Submitter supplied) RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19580

18 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) The goal of this study is to investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription in A.thaliana. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. The FACT histone chaperone complex is required for this repression mechanism by co-transcriptionally enforcing elevated levels of H3K4me1 at repressed intragenic promoters;

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19580

9 Samples

Download data: BW

(Submitter supplied) We mapped CstF64-RNA interactions at the transcriptome level and studied CstF64-mediated regulation of global mRNA alternative polyadenylation by using iCLIP-seq and direct RNA sequencing analyses.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL14761 GPL11154

6 Samples

Download data: BED

(Submitter supplied) Alternative cleavage and polyadenylation (APA) of pre-mRNAs yields multiple transcripts differing in their 3' end and its regulation is often aberrant in human cancers, including prostate cancer (PC). In this study, we have uncovered a novel mechanism of APA regulation which impinges on the functional interaction between the 5'-3' exonuclease XRN2 and the A/U-rich motif RNA binding protein Sam68 in PC cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX