Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Base-resolution analysis of deoxyuridine at genome scale based on artificial incorporation modified nucleobase

ABSTRACT: Deoxyuridine (dU) in DNA can result from deamination of cytosine and dUMP misincorporation. The easy single-nucleotide resolution assay for dU are crucial to understanding its role in genome. Herein, we present a new concept of “base substitution” for accurate single-nucleotide resolution profiling of dU. The method termed AI-Seq (Artificial Incorporation of a modified nucleobase for sequencing) was developed using artificial cytosine (N3-C) to replace dU. After the artificial base construction, dU can read as cytosine during polymerase chain reaction assay. AI-seq was validated on synthetic DNA and then applied to the genome of HEK293T cell line. Collectively, the “base substitution” provides a novel approach for generating comprehensive information about the distribution of dU and can be potentially adapted to detect other epigenetic modifications.

ORGANISM(S): Homo sapiens

PROVIDER: GSE142071 | GEO | 2021/03/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA

Project description:Uracil in DNA can be generated as a result of cytosine deamination or dUMP misincorporation. However, its distribution in the human genome is poorly understood, due to the lack of a sensitive detection method. Here we present “dU-seq”, a selective labeling and pull-down technology, to profile uracil in the human genome. dU-seq specifically labels uracil-containing DNA via an in vitro base excision repair reaction and identifies thousands of uracil peaks in the human genome.

2018-05-24 | GSE99011 | GEO

Base-resolution analysis of deoxyuridine at genome scale based on artificial incorporation modified nucleobase

Project description:Base-resolution analysis of deoxyuridine at genome scale based on artificial incorporation modified nucleobase

| PRJNA595860 | ENA

Sperm storage mechanisms in poultry

Project description:Turkey sperm lose viability within 8-18 h when stored as liquid semen using current methods and extenders. In contrast, turkey hens maintain viable, fertile sperm in their sperm storage tubules (SST) for 45 or more days following a single insemination. Our long-term objectives are to identify and characterize differentially expressed genes that may underlie this prolonged sperm storage and then use this information to develop improved methods for storing liquid turkey semen. We employed serial analysis of gene expression (SAGE) to compare gene expression patterns in turkey SST recovered from hens after artificial insemination (AI) with extended semen (sperm AI) or extender alone (control AI). We constructed two separate SAGE libraries with SST RNA obtained from sperm and control AI hens. We used these libraries to generate 95,325 ten-base pair SAGE tags. These 95,325 tags represented 27,430 unique genes. The sperm and control AI libraries contained 47,663 and 47,662 tags representing 18,030 and 19,101 putative unique transcripts, respectively. Approximately 1% of these putative unique genes were differentially expressed (P<0.05) between treatments. Tentative annotations were ascribed to the SAGE tag nucleotide sequences by comparing them against publicly available SAGE tag and cDNA sequence databases. Based on its SAGE tag nucleotide sequence, we cloned a partial turkey avidin cDNA and confirmed its up-regulation in the sperm AI SST. The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems. Keywords: other

2003-03-22 | E-GEOD-351 | biostudies-arrayexpress

Sperm storage mechanisms in poultry

2003-03-23 | GSE351 | GEO

Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells -T cells

Project description:Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.

2024-01-12 | GSE253182 | GEO

Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells-K562 cells

2024-01-12 | GSE253184 | GEO

Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine

Project description:mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. While cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5’UTRs impacts protein synthesis at the level of initiation. 5’UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results, and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed ac4C in the -1-position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.

2022-06-08 | GSE162043 | GEO

Uracil Repair - A Source of DNA Glycosylase Dependent Genome Instability

Project description:Uracil DNA glycosylases (UDGs) excise uracil from DNA arising from dUMP misincorporation during replication or from cytosine deamination. Besides functioning in canonical uracil repair, UDGs cooperate with DNA base modifying enzymes to effect mutagenesis or DNA demethylation. Mammalian cells express four UDGs, the functional dissection of which represents a challenge. Here, we used Schizosaccharomyces pombe with only two UDGs, Ung1 and Thp1, as a simpler model to study functional interactions in uracil repair. We show that despite a predominance of Ung1 activity in cell extracts, both UDGs act redundantly against genomic uracil accumulation and mutations from cytosine deamination in cells. Notably, Thp1 but not Ung1-dependent repair is cytotoxic under genomic uracil stress induced by 5-fluorouracil exposure or AID expression. Also, Thp1- but not Ung1-mediated base excision is recombinogenic, accounting for more than 60% of spontaneous mitotic recombination events in a recombination assay. Hence, the qualitative outcome of uracil repair depends on the initiating UDG; while Ung1 shows expected features of a bona-fide DNA repair enzyme, Thp1-initiated repair appears slow and non-productive, implicating a function beyond canonical DNA repair. Given the epigenetic role of mammalian TDGs, we performed transcriptome analyses and identified a possible function of Thp1 in stabilizing gene expression.

2014-12-31 | GSE64585 | GEO

Oryza sativa isolate:ZhongHua11 | cultivar:Oryza sativa Japonica Group

Project description:Cytosine, but not adenine, base editors induce unexpected genome-wide single nucleotide mutations in rice

| PRJNA522656 | ENA

Effects of fertility on gene expression and function of the bovine endometrium

Project description:To identify heifers of contrasting fertility, serial rounds of artificial insemination (AI) were conducted in 201 synchronized crossbred beef heifers. The heifers were then fertility classified based on number of pregnancies detected on day 35 in the four AI opportunities. The reproductive tracts of a subset of the classified heifers were obtained on day 14 of the estrous cycle. Microarray analysis revealed differences in the endometrial transcriptome based on fertility classification.

2013-04-23 | GSE46274 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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