GEO DataSets

(Submitter supplied) We aimed to examine the gene expression changes responding to a depletion of intracellular S-adenosylmethionine (SAM). The mouse plasma cell line X63/0 was treated with the SAM-synthetase inhibitor cycloleucine (cLEU), and the total RNA was isolated and analyzed by RNA-sequencing. As a result, we idntified 27 genes, including the ubiquitous SAM-synthetase MAT2A, whose expssions were up-regulated by two-fold or more.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18635

2 Samples

Download data: TXT

(Submitter supplied) Maintenance of the intracellular levels of the methyl donor S-adenosylmethionine (SAM) is essential for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of MAT2A, which encodes the only SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: XLS

(Submitter supplied) The only S-adenosymethionine (SAM) synthetase expressed in most human cells, MAT2A, is regulated by intron detention. Using a GFP fusion reporter, we conducted a CRISPR screen to identify regulators of this alternative splicing event. The screen identified METTL16, a known regulator of this process, and NUDT21. NUDT21 encodes the CFIm25 protein a member of the CFIm complex involved in alternative polyadenylation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) NUDT21 encodes the CFIm25 protein, a component of the CFIm complex that regulates alternative polyadenylation (APA). Our data suggest that the CFIm complex also induces splicing of a detained intron in the the S-adenosylmethionine (SAM) synthetase MAT2A to control intracellular levels of SAM. To genetically separate these functions, we used poly(A) Click-seq (PAC-seq) to determine the changes in poly(A) site selection in two cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: BED, TXT

(Submitter supplied) m6A RNA immunoprecipitation was performed according to published procedure (Dominissini et al., 2012). Human m6A-seq data from DTSC2 HeLa cells were aligned to the hg19 transcriptome. To locate m6A peaks, the hg19 transcriptome was divided into 25 nucleotide-wide tiles. The number of reads in the m6A immunoprecipitation (IP) and non-IP (control) sample was counted in each tile, and a p-value was calculated using Fisher’s exact test and adjusted for multiple testing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved and widely used means of gene expression control. METTL16 is an m6A writer but how it recognizes its RNA targets and its physiological roles remain unknown. Here we describe the crystal structure of human METTL16 to reveal a classical methyltransferase domain but with an extra N-terminal module that is essential for catalysis. more...

Organism:

Mus musculus; synthetic RNA

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24911

74 Samples

Download data: CSV

(Submitter supplied) Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor of methylation of DNA, RNA and proteins, SAM amount affects gene expression by changing their methylation. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells. However, how MAT2A promotes cell proliferation is largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

8 Samples

Download data: TXT

(Submitter supplied) OThe N6-methyladenosine (m6A) RNA modification is widely used to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (orthologue of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the SAM synthetase pre-mRNA which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet, and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. more...

Organism:

Caenorhabditis elegans; Bombyx mori; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22765 GPL19757 GPL28266

42 Samples

Download data: BW, CSV, XLSX

(Submitter supplied) N6-methyladenosine (m6A) is a highly dynamic RNA modification that has recently emerged as a key regulator of gene expression. While many m6A modifications are installed by the METTL3-METTL14 complex, others appear to be introduced independently, implying that additional human m6A methyltransferases remain to be identified. Using crosslinking and analysis of cDNA (CRAC), we reveal that the putative human m6A “writer” protein METTL16 binds to the U6 snRNA and other ncRNAs as well as numerous lncRNAs and pre-mRNAs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is the most common internal modification in eukaryotic messenger RNA (mRNA). The effects of this reversible cheimcal modification are mediated in part by methyl-specific RNA binding protein 'readers' of the YTH family. In this study we present the function of YTHDC1 (YT521) in promoting the export of mRNA from the nucleus to the cytoplasm. Additionally, we identify a role for YTHDC1 in exon retention in mouse embryonic stem cells (mESCs).

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL13112

38 Samples

Download data: BED, DIFF, TXT, XLSX

(Submitter supplied) MAT2A inhibitor is dosed to MTAP null cell lines, samples are collected for transcriptome profiling

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: PY, R, XLSX

(Submitter supplied) Gene expression was compared from adult C. elegans after RNAi

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL19230

9 Samples

Download data: CEL

(Submitter supplied) The goal of this project is to understand the role of SIRT1, the most conserved mammalian NAD+-dependent protein deacetylase, in methionine metabolism and pluripotency of mESCs. Our recent studies indicate that SIRT1 deficient mESCs are hypersensitive to methionine restriction-induced differentiation and apoptosis, primarily due to a reduced conversion of methionine to S-adenosylmethionine. This reduction leads to marked decrease in methylation levels of histones in SIRT1 deficient mESCs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

36 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is the most common internal modification in eukaryotic messenger RNAs (mRNAs) and plays essential roles in mammals. The function of this chemical modification is deciphered by m6A-specific binding proteins of the YTH family. Recent studies indicated that m6A methyltransferase METTL3 ('writer') and demethylase FTO ('eraser') play critical roles in cardiovascular diseases. However, function of m6A 'reader' proteins in the heart is still largely unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

18 Samples

Download data: BW

(Submitter supplied) RTqPCR results suggested a relevant role for Pdrg1 in rat hepatoma H35 cells, where its expression was dramatically enhanced. Hence, these cells were chosen as a suitable model for stable Pdrg1 silencing. For this purpose, H35 cells were transfected with appropriate shRNA plasmids against Pdrg1 and stable clones isolated. Among those exhibiting reproducible behavior, clones CN-10 (negative control), 3-44 (shRNA3) and 4-18 (shRNA4) were selected for further analysis. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14745

16 Samples

Download data: TXT

(Submitter supplied) To identify the directly bound transcripts of Flag antibody (the backgroud control for our METTL16 RIP-seq), RNA immunoprecipitation sequencing (RIP-seq) was conducted HEK293T. Briefly, HEK293T cells were infected with pmiRNA1-empty vector. Only the GFP-positive cells were used for study and expanded in DMEM medium.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) All the three enzymes, METTL3, METTL14, and METTL16, belong to methyltransferase like (METTL) family and possess the ability to deposit N6-methyladenosine (m6A) in mRNA. Via immunofluorescence staining and wertern blotting, we discovered either METTL3 or METTL14 mainly localize in nuclear, but METTL16 localizes in both cytosol and nuclei. To compare the m6A methyltransferase activities of the three m6A 'writers' and better understand their differences, MeRIP-seq (m6A-seq) was conducted with poly(A) RNAs isolaed from HEK293T cells with METTL3, 14 and 16 knockout.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

51 Samples

Download data

(Submitter supplied) To identify the directly bound transcripts of METTL3, METTL14, and METTL16, RNA immunoprecipitation sequencing (RIP-seq) was conducted HEK293T stablely expressing METTL3, METTL14, and METTL16, respectively. Briefly, HEK293T cells were infected with lentivirus, pmiRNA1-3 x Flag-METTL3, pmiRNA1-3 x Flag-METTL14, and pmiRNA1-3 x Flag-METTL14, to overexpress the three METTL family members with 3 x Flag fused in the N-terminal. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

11 Samples

Download data: TXT

(Submitter supplied) METTL16 is a member of methyltransferase like (METTL) family. Unlike well-studied METTL3 and METTL14, we found a much higher percentage of METTL16 is localized in the cytosol. The subcellular distribution holds the ability to potentiate translation efficiency. Via Far-western blotting and Co-Immunoprecipitation (Co-IP) assays, we have identified the direct interactions between METTL16 and eukaryotic initiation factor 3 (eIF3) a and b. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT