Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach

ABSTRACT: 5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow the m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE242724 | GEO | 2024/07/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

rRNA 5-methylcytosine in Arabidopsis thaliana

Project description:Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C.

2015-10-01 | GSE68444 | GEO

tRNA 5-methylcytosine in Arabidopsis thaliana

Project description:Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in transfer RNAs of all three sub-cellular transcriptomes of Arabidopsis thaliana. 5-methylcytosine sites in tRNAs were also determined in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5 and NOP2A.

2015-10-01 | GSE68445 | GEO

Effects of NSUN6 deficiency by systematic transcriptomes and m5C profiles in mice across tissue [RNA-Seq]

Project description:we constructed Nsun6-KO mouse, and observed that the wight and appearance of KO mice didn’t show abnormality. Through Bisulfite sequencing (BS-seq) in wild-type (WT) as well as KO mice and mRNA-seq, we identified high confident Nsun6-dependent m5C sites and performed the transcriptome analysis across five tissues.

2022-06-16 | GSE200952 | GEO

Effects of NSUN6 deficiency by systematic transcriptomes and m5C profiles in mice across tissue [BS-Seq]

2022-06-16 | GSE200951 | GEO

Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases

Project description:Epitranscriptomic RNA modifications can regulate fundamental biological processes, but we lack approaches to map modification sites and probe writer enzymes. Here we present a chemoproteomic strategy to characterize RNA 5-methylcytidine (m5C) dioxygenase enzymes in their native context based upon metabolic labeling and activity-based crosslinking with 5-ethynylcytidine (5-EC), RNA-protein enrichment, and quantitative proteomics. We profile m5C dioxygenases in human cells including ALKBH1 and TET2 and use quantitative nucleoside LC-MS to show that ALKBH1 is the major hm5C and f5C-forming enzyme in RNA, including upon polyadenylated RNA. Further, we map ALKBH1 modification sites transcriptome-wide using 5-EC-based iCLIP analysis to show that ALKBH1 oxidizes m5C in a variety of tRNA anticodon stem loops (ASL), as well as on mRNA and lncRNA, and analyze its substrate specificity using in vitro enzymatic assays. Finally, we apply pyridine borane-mediated sequencing to identify f5C sites in tRNA ASLs. Our work provides powerful chemical approaches for studying RNA m5C dioxygenases and mapping oxidative m5C modifications and reveals the existence of novel epitranscriptomic pathways for regulating RNA function.

2022-07-16 | PXD029955 | Pride

Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution

Project description:We report RBS-Seq, a new RNA bisulfite sequencing method enabling the sensitive and simultaneous detection of m5C, pseudouridine, and m1A at single-base resolution transcriptome-wide. For each, we detect ‘signature’ base mismatches (for m5C and m1A), or 1-2 base deletions (for pseudouridine) structurally explained by ribose ring-opened pseudouridine-mono-bisulfite adducts. Our profiles for pseudouridine reveal clear signatures at known sites in tRNAs and rRNAs, and provide hundreds of new targets in non-coding RNAs and mRNAs. However, our results diverge greatly from prior work, suggesting ~10-fold fewer m5C sites, and the absence of substantial m1A in mRNAs.

2019-03-08 | GSE90963 | GEO

A Quantitative Sequencing Method for 5-Formylcytosine in RNA

Project description:5-Formylcytosine (f5C) modification is present in human mitochondrial methionine tRNA (mt-tRNAMet) and cytosolic leucine tRNA (ct-tRNALeu), with their formation mediated by NSUN3 and ALKBH1. f5C has also been detected in mRNA of yeast and human cells, but its transcriptome-wide distribution has not been studied. Here we report f5C-seq, a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs). We show that f5C in RNA can be reduced to dihydrouracil (DHU) by pico-brane, and DHU can be exclusively read as U during reverse transcription (RT) reaction, allowing the detection and quantification of f5C sites by a unique C-to-U mutation signature. We validated f5C-seq by identifying and quantifying the two known f5C sites in tRNA, in which the f5C modification fractions dropped significantly in ALKBH1-depleted cells. By applying f5C-seq to small RNA, we identified 13 and 11 new f5C sites in HeLa and mESC tRNA, respectively.

2021-08-01 | GSE156933 | GEO

Single-Base Resolution Mapping Reveals Distinct 5-Formylcytidine in Saccharomyces cerevisiae mRNAs

Project description:5-Formylcytidine (f5C) is one type of post-transcriptional RNA modifi-cations, which is known at the wobble position of tRNA in mitochon-dria and essential for mitochondrial protein synthesis. Here, we show a method to detect f5C modifications in RNA and a transcriptome-wide f5C mapping technique, named f5C-seq. It is developed based on the treatment of pyridine borane, which can reduce f5C to 5,6-dihydrouracil (DHU), thus inducing C-to-T transition in f5C sites during PCR to achieve single-base resolution detection. Thousands of f5C sites were identified after mapping in Saccharomyces cerevisiae by f5C-seq. Moreover, codon composition demonstrated a preference for f5C within wobble sites in mRNA, suggesting the potential role in regulation of translation. These findings expand the scope of the understanding of cytosine modifications in mRNA. Reference build: S288C_reference_genome_R64-2-1_20150113

2021-12-01 | GSE133138 | GEO

RNA BS-seq of Nocodazole treated HeLa cells with NSUN family member deficiency

Project description:m5C accumulates on mRNAs in Nocodazole (Noc) treated cells. To figure out which m5C writer is responsible for these m5C sites, we generated three KO cell lines (NSUN2, NSUN5, and NSUN6) with CRISPR induced mutagenesis. We also used siRNA to suppress the expression of Nop2 (NSUN1) in wild-type HeLa cells. Then we performed mRNA BS-seq on the cells harvested after 48 hours Noc-treatment (for siRNA experiments, cells were treated with siRNA for 48 hours first).

2023-08-20 | GSE197650 | GEO

Ultrafast Bisulfite Sequencing for Efficient and Accurate 5-Methylcytosine Detection in DNA and RNA

Project description:We present an ultrafast bisulfite sequencing (UBS-seq) method, which accelerates the bisulfite reaction by about 13-fold, resulting in minimal DNA damage and much lower background in all DNA sequences. This ultrafast BS protocol is also ideal for mapping of RNA 5-methylcytosine (m5C) because of much shorter reaction time and dramatically reduced RNA background. And allowed detection of m5C stoichiometry in highly structured RNA species.

2023-10-13 | GSE225614 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data