Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of 5-hydroxymethyluracil in eukaryote parasite Leishmania

ABSTRACT: Genome-wide mapping of 5-hydroxymethyluracil in eukaryote parasite Leishmania

PROVIDER: PRJNA325744 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3670010.fastq.gz	Fastqsanger.gz
	SRR3670020.fastq.gz	Fastqsanger.gz
	SRR3670011.fastq.gz	Fastqsanger.gz
	SRR3670021.fastq.gz	Fastqsanger.gz
	SRR3670002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 29

Similar Datasets

Genome-wide mapping of 5-hydroxymethyluracil in eukaryote parasite Leishmania

Project description:5-hydroxymethyluracil (5hmU) is a thymine base modification found in genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we developed a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. We applied the method to generate genome-wide maps of 5hmU in parasitic protozoan Leishmania, where 5hmU forms enzymatically via hydroxylation of thymine. In the genus, another thymine modification 5-(β-glucopyranosyl) hydroxymethyluracil (base J) plays key roles during transcription. To elucidate relationships between 5hmU and base J, we also mapped base J loci by introducing a chemical tagging strategy for the glucopyranoside residue. Results: Observed 5hmU peaks were highly consistent among technical replicates, confirming the robustness of the method. 5hmU were particularly enriched in strand switch regions, telomeric regions and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurred mostly within strand switch regions. We also identified loci comprising 5hmU but not base J. These 5hmU-specific loci were enriched with motifs consisting of a stretch of thymine bases and associated with higher RNA levels. Conclusions: By chemically detecting 5hmU we provide the first genome-wide map of 5hmU, which will help addressing the emerging interest in the role of 5hmU. The presence of 5hmU-specific loci may suggest that 5hmU has unique roles.

2016-12-15 | GSE83384 | GEO

Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

Project description:Some T's in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J (β-D-glucosyl-hydroxymethyluracil). In Leishmania about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA Polymerase II termination sites. Both this internal J and telomeric J can be reduced by a knockout of J-binding protein 2 (JBP2), an enzyme involved in the first step of J biosynthesis. J levels are further reduced by growing Leishmania JBP2 knockout cells in BrdU-containing medium, resulting in cell death. The loss of internal J is accompanied by massive read-through at RNA Polymerase II termination sites. The degree of read-through varies between transcription units, but may extend over 100 kb. We conclude that J is required for proper transcription termination and infer that the absence of internal J kills Leishmania by massive read-through of transcriptional stops.

2011-10-15 | GSE32976 | GEO

Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

Project description:Some T's in nuclear DNA of trypanosomes and Leishmania are hydroxylated and glucosylated to yield base J (?-D-glucosyl-hydroxymethyluracil). In Leishmania about 99% of J is located in telomeric repeats. We show here that most of the remaining J is located at chromosome-internal RNA Polymerase II termination sites. Both this internal J and telomeric J can be reduced by a knockout of J-binding protein 2 (JBP2), an enzyme involved in the first step of J biosynthesis. J levels are further reduced by growing Leishmania JBP2 knockout cells in BrdU-containing medium, resulting in cell death. The loss of internal J is accompanied by massive read-through at RNA Polymerase II termination sites. The degree of read-through varies between transcription units, but may extend over 100 kb. We conclude that J is required for proper transcription termination and infer that the absence of internal J kills Leishmania by massive read-through of transcriptional stops. We determined the exact location of base J in the genome of Leishmania by high-throughput sequencing of J containing DNA fragments. Samples were enriched for J-containing fragments by two independent methods: ChIP using an anti-J DNA antibody or by binding to a the J-binding protein JBP1. We studied the effect of loss of J on transcription using WT, JBP2 knockout (30-37% of WT level J), and JBP2 knockout cells grown in BrdU containing medium (13-16% of WT level of J). We used 6 RNA-seq libraries (three samples & two replica each) containing processed RNA products (transspliced and poly-adenylated) and 3 small RNA libraries representing the entire transcriptome.

2011-10-15 | E-GEOD-32976 | biostudies-arrayexpress

Leishmania major strain:LV39 | breed:Eukaryote

Project description:Leishmania major strain:LV39 | breed:Eukaryote Raw sequence reads

| PRJNA504783 | ENA

In vitro infection of murine osteoclast by the parasite Leishmania infantum

Project description:To investigate the effect of infection of osteoclast by Leishmania infantum, we infected diffentiating bone marrow derived osteoclast with the parasite at day 2 of differentiation We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cultures of cells infected for 24 hours compared to 4 control cultures.

2022-10-26 | GSE216141 | GEO

Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

Project description:Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

| PRJNA146423 | ENA

Genome-wide mapping of 5-hydroxymethyluracil in Trypanosoma brucei

Project description:Genome-wide mapping of 5-hydroxymethyluracil in Trypanosoma brucei

| PRJNA745154 | ENA

Leishmania major strain:hybrid FV1xLV39 | breed:Eukaryote

Project description:Leishmania major strain:hybrid FV1xLV39 | breed:Eukaryote Raw sequence reads

| PRJNA504788 | ENA

Leishmania major strain:hybrid FV1xLV39 | breed:Eukaryote

Project description:Leishmania major strain:hybrid FV1xLV39 | breed:Eukaryote Raw sequence reads