Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tracking Epigenetic Modification-Mediated Genome Organization

ABSTRACT: Tracking Epigenetic Modification-Mediated Genome Organization

PROVIDER: PRJNA565701 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10123750_1.fastq.gz	Fastqsanger.gz
	SRR10123750_2.fastq.gz	Fastqsanger.gz
	SRR10123751_1.fastq.gz	Fastqsanger.gz
	SRR10123751_2.fastq.gz	Fastqsanger.gz
	SRR10123752_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Tracking Epigenetic Modification-Mediated Genome Organization

Project description:Spatiotemporal control of chromatin structure and dynamics at sub-kilobase to megabase scales is essential for genome function. Epigenetic modification plays important roles in transcriptional regulation. How histone marks regulate genome organization at different scales remain unclear. Here we introduce an EpiGo (Epigenetic perturbation induced Genome organization) system to modify hundreds of genomic loci with H3K9me3 spanning megabases on human chromosome 19 and simultaneously track their changes of genome organization. EpiGo-mediated H3K9me3 spreads more extensively in transcriptionally inactive regions than active regions. H3K9 trimethylation of active regions trigger local chromatin compaction without substantial gene silencing. H3K9 trimethylated loci or regions associate with HP1a condensates and adjacent loci with H3K9me3 coalesce over time. H3K9 trimethylation of inactive regions reshape local genome compartmentalization. These results reveal that H3K9me3 mediates local chromatin compaction or genome compartmentalization upon distinct transcriptional states.

2020-11-04 | GSE137469 | GEO

Tracking epigenetic changes during human leukemogenesis

Project description:Tracking epigenetic changes during human leukemogenesis

| PRJNA597528 | ENA

PRC2 mediated paternal epigenetic inheritance

Project description:PRC2 mediated paternal epigenetic inheritance - E15.5

| PRJEB24910 | ENA

Deeply hidden genome organization directly mediated by SATB1

Project description:Deeply hidden genome organization directly mediated by SATB1

| PRJNA789873 | ENA

METTL1-mediated m7G tRNA modification drives oncogenic transformation

Project description:METTL1-mediated m7G tRNA modification drives oncogenic transformation

| PRJNA631030 | ENA

The transcriptome, histone modification and chromatin organization of kidney tubule cells

Project description:The transcriptome, histone modification and chromatin organization of kidney tubule cells

| PRJNA615869 | ENA

Function and Mechanism of METTL5-mediated 18S rRNA m6A1832 modification in hepatocellular carcinoma

Project description:Tumor recurrence is main pattern of treatment failure for early-stage hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying disease recurrence remain poorly understood. Here, we showed that 18S rRNA N6-methyladenosine (m6A1832) modification and its methyltransferase complex METTL5/TRMT112 were upregulated in HCC and correlated with poor prognosis. Loss-of-function and gain-of-function assays demonstrated that METTL5/TRMT112 mediated 18S rRNA m6A1832 modification promotes HCC tumorigenesis in vitro and in vivo. Mechanistically, 18S rRNA m6A1832 modification selectively regulated the translation of mRNAs with long 5’UTR and short 3’UTR through affecting the assembly of 80S subunit at translation initiation and its dissociation at translation termination which was executed by weakening the interaction of ABCE1 with eRF1 and eRF3. Moreover, METTL5-mediated 18S rRNA m6A1832 modification regulated β-oxidation of long-chain fatty acid through ACSL4 to promote HCC progression. Our work uncovered a novel layer of mRNA translation regulation mechanism at ribosome 80S subunit assembly and dissociation step mediated by 18S rRNA m6A1832 modification and revealed a new crosslink between RNA epigenetic modification and fatty acid metabolism in HCC.

2021-06-01 | GSE175827 | GEO

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Project description:NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

| PRJNA814692 | ENA

Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression

Project description:Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression

| PRJNA701297 | ENA

Tracking-seq reveals the heterogeneity of off-target effects in CRISPR/Cas9-mediated genome editing

Project description:The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.

2024-05-31 | GSE236360 | 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