Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability

ABSTRACT: Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability

PROVIDER: PRJNA842375 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [pacBio WGS]

Project description:Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [pacBio WGS]

| PRJNA842381 | ENA

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

Project description:Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

| PRJNA841652 | ENA

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [pacBio WGS]

Project description:Numerous indirect, genetic approaches in various experimental systems have implicated dynamic alternative non-B DNA structures in human physiology and disease. Nevertheless, direct detection of dynamic DNA structures in vivo remains a challenge. To address this problem, we developed a new methods to visualize ssDNA containing alternative DNA structures. We described an uncharted landscape of dynamic alternative DNA structures formed by DNA cruciform and DNA triplexes (H-DNA) that contribute to genome instability.

2022-09-01 | GSE204806 | GEO

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

2022-09-01 | GSE203632 | GEO

Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-01 | GSE204808 | GEO

Chromatin immunoprecipitation for genome-wide mapping of endogenous G-quadruplex DNA structures

Project description:G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer and other diseases. Here, we describe a detailed G4 ChIP-seq method that robustly enables the determination of G4 structure formation genome-wide in chromatin. This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific phage display antibody with refinements in chromatin immunoprecipitation followed by high-throughput sequencing. Beginning with chromatin isolation and antibody preparation the entire protocol can be completed in less than 1 week including computational analysis.

2017-11-15 | GSE99205 | GEO

In vivo atlas of RNA secondary structures recognized by ADARs

Project description:In vivo atlas of RNA secondary structures recognized by ADARs

| PRJNA562274 | ENA

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

Project description:By using a novel high-throughput method, named chemical inference of RNA structures (CIRS-seq), that uses dimethyl sulfate (DMS), and N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) to modify RNA residues in single-stranded conformation within native RNA secondary structures, we investigated the structural features of mouse embryonic stem cell (ESC) transcripts. Our analysis revealed an unexpected higher structuring of the 5' and 3' untranslated regions (UTRs) compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observed that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we found that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation. Transcritome-wide mapping of RNA secondary structures in mouse embryonic stem cells (mESC)

2014-10-01 | E-GEOD-54106 | biostudies-arrayexpress

ssDNA-seq mapping of DNA secondary structures in mouse ES cells

Project description:ssDNA-seq mapping of DNA secondary structures in mouse ES cells

| PRJNA520919 | ENA

Transcription dynamics prevents RNA-mediated genomic instability through SRPK2-dependent DDX23 phosphorylation

Project description:Genomic instability is frequently caused by nucleic acids structures formed during transcription termed R-loops. Despite their harmful potential, mechanisms that sense, signal and suppress these structures remain elusive. Here we report that oscillations in transcription dynamics are a major sensor of R-loops. We show that pausing of RNA polymerase II (RNA Pol II) initiates a signaling cascade whereby the serine/arginine protein kinase 2 (SRPK2) phosphorylates the DDX23 helicase culminating in the suppression of R-loops. We show that in the absence of either SRPK2 or DDX23, accumulation of R-loops leads to massive genomic instability revealed by high levels of DNA double-strand breaks (DSBs). Importantly, we found DDX23 mutations in several cancers and detected homozygous deletions of the entire DDX23 locus in 10 (17%) adenoid cystic carcinoma samples. Our results unravel molecular details of a novel link between transcription dynamics and RNA-mediated genomic instability that may play important roles in cancer development.

2016-12-22 | GSE76777 | 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