Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

R-loop landscapes in Arabidopsis

ABSTRACT: The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas during Arabidopsis development and in response to various environmental factors.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE116232 | GEO | 2020/02/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

R-loop landscapes in Rice (Oryza sativa) [DRIP-seq]

Project description:The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP-seq method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas of Rice (Oryza sativa) at different developmental stages.

2022-12-10 | GSE120922 | GEO

R-loop in soybean

2022-12-10 | GSE216385 | GEO

R-loop landscapes during parental-to-zygotic transition in zebrafish

Project description:The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

2024-05-29 | GSE183453 | GEO

R-loop landscapes in Arabidopsis

Project description:R-loop landscapes in Arabidopsis

| PRJNA477830 | ENA

R-loop landscapes in yeast meiosis

Project description:R-loop landscapes in yeast meiosis

| PRJNA705491 | ENA

ssDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment

Project description:ssDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment

| PRJNA906982 | ENA

ssDRIP-seq analysis of R-loop level in shCTRL, shMETTL3 and shDDX21 HeLa cells

Project description:ssDRIP-seq analysis of R-loop level in shCTRL, shMETTL3 and shDDX21 HeLa cells

| PRJNA553774 | ENA

R-loop landscapes in yeast meiosis

Project description:Meiotic recombination is initiated by the Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions known as hotspots, but the factor(s) which specify the positions for meiotic DSB hotspots remain unclear. Here, we show that the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, change dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage, and found they co-localize with meiotic DSB hotspots. We further show that transcription-replication head-on collisions could promote R-loop formation during meiosis, and apparently direct the initiation of meiotic DSB formation. Furthermore, the hotspots can be eliminated by reverse the direction of either transcription or replication, and reconstituted by reverse both of their direction. Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.

2023-05-14 | GSE167915 | GEO

Sister chromatid cohesion halts DNA loop expansion

Project description:Eukaryotic genomes are folded into DNA loops mediated by SMC complexes, like cohesin, condensin and Smc5/6. This organization regulates different DNA related processes along the cell cycle such as transcription, recombination, segregation and DNA repair. During G2/M phases, SMC complexes mediated DNA loops coexist with cohesin complexes involved in sister chromatid cohesion (SCC). It remains unknown whether SCC and DNA loop expansion influence each other and if they cooperate to regulate DNA-related processes. Here we show that SCC is indeed a barrier to DNA loop expansion mediated by cohesin in G2.

2024-01-30 | GSE237031 | GEO

R-loop landscapes in Rice (Oryza sativa) [DRIP-seq]

Project description:R-loop landscapes in Rice (Oryza sativa) [DRIP-seq]

| PRJNA495027 | ENA