GEO DataSets

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

18 Samples

Download data: TSV

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

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL27812 GPL21656

73 Samples

Download data: BIGWIG

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

10 Samples

Download data: TSV

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

18 Samples

Download data: TSV

(Submitter supplied) During meiosis, in Saccharomyces cerevisiae, N6-methyladenosine (m6A) modified transcripts are induced, of which the function is unknown. Here, we uncover the role of the m6A reader Pho92. Cross-linking immunoprecipitation (CLIP) revealed that Pho92 associates with meiotic mRNAs in both m6A dependent and independent manner. Incidentally, Pho92 resides in the nucleus during early meiosis and associates with nascent RNAs, which is mediated through its interaction with Paf1C. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

27 Samples

Download data: BED, BIGWIG

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21656 GPL19756

71 Samples

Download data: BW

(Submitter supplied) We performed CRAC (UV-crosslinking and analysis of cDNA) to identify Ime4-dependent mRNA targets of Pho92 during meiosis at 5 hr in SPO.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

8 Samples

Download data: BW, XLSX

(Submitter supplied) We performed high-throughput mRNA sequencing during a meiotic time course (0, 2, 3, 5, 6, 7 and 9 hr) in WT, pho92 mutant and ime4 mutant cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

63 Samples

Download data: XLSX

(Submitter supplied) Interest in mRNA methylation has exploded in recent years. The sudden interest in a 40 year old discovery was due in part to the recent finding of FTO?s (Fat Mass Obesity) N6-methyl-adenosine (m6A) deaminase activity, thus suggested a link between obesity-associated diseases and the presence of m6A in mRNA. Another catalyst of the sudden rise in mRNA methylation research was the release of mRNA methylomes for human, mouse and Saccharomyces cerevisiae. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae; Saccharomyces cerevisiae SK1

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) The Ydr374c is the only protein that has the YTH domain in Saccharomyces cerevisiae. The YTH domain was identified by comparing all known protein sequences with the YT521-B splicing factor, and it is found only in eukaryotes. Recently, it has been reported that the YTH domain conveys RNA-binding ability to a new class of proteins. However, the roles of most YTH family members lacking common sequence motifs outside the YTH domain are unknown. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7293

2 Samples

Download data: TXT

(Submitter supplied) RNAseq across a time course of meiosis of cells with and without Kfc1p. The overexpression of either IME1 or both IME1 and RIM4 was used to determine how overexpression of the two genes functions to resuce the meiotic defect associated with the loss of Kar4p.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

64 Samples

Download data: XLSX

(Submitter supplied) To investigate the role of METTL3-mediated m6A modification, we performed m6A-sequencing to map the m6A modification in control or METTL3 knockdown BGC823 cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

4 Samples

Download data: BED, XLSX

(Submitter supplied) The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL15263

14 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Abstract: N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/insects/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis and was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19756 GPL27812

215 Samples

Download data: RDS

(Submitter supplied) N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/insects/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis and was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian MTC orthologs. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL27812 GPL19756

76 Samples

Download data: RDS

(Submitter supplied) N6-methyladenosine (m6A), the most abundant mRNA modification, is deposited in mammals/drosophila/plants by m6A methyltransferase complexes (MTC) comprising a catalytic subunit and at least five additional proteins. The yeast MTC is critical for meiosis but was known to comprise three proteins, of which two were conserved. We uncover three novel MTC components (Kar4/Ygl036w-Vir1/Dyn2). All MTC subunits, except for Dyn2, are essential for m6A deposition and have corresponding mammalian MTC orthologs. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

139 Samples

Download data: BED, TAB

(Submitter supplied) Understanding how RNA-binding proteins interact with RNA transcripts for splicing regulation is fundamental to human biology and disease. N6-methyladenosine (m6A), the most abundant and dynamic internal modification of eukaryotic messenger RNA (mRNA), is important for RNA splicing, but its detailed mechanism remains unclear. We find the splicing factor heterogeneous nuclear ribonucleoprotein G (HNRNPG) selectively binds m6A-modified RNA in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

22 Samples

Download data: XLSX

(Submitter supplied) Nascent RNA was tagged with EU, via EC feeding, in targeted cells (neuroblasts or neurons) then purified after the initial pulse labeling or after a chase using media containing excess unmodified uridine

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

16 Samples

Download data: TXT

(Submitter supplied) meRIP_seq and Input total RNA_seq in neuroblast-biases brains, neuron-biased brains, and Mettl3 null brains

Organism:

Drosophila melanogaster

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL25244

12 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we uncover that m6A deposition is not selective. Instead, m6A distribution is exclusion-based: m6A-consensus harboring sites are methylated by default, unless they are within a window of up to ~200 nt from an exon-intron junction. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

250 Samples

Download data: BED, CSV, RDATA, RDS, XLSX