Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metagenome-assembled genomes of the Roseobacter RCA cluster (Planktomarina)

ABSTRACT: Ecogenomics and diversification of the Roseobacter RCA cluster and global biogeography of sublineages

PROVIDER: PRJEB62088 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Regulatory architecture of the RCA gene cluster captures a novel intragenic boundary and enhancer elements in B cells

Project description:The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes which share functions in the innate immune system. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this important immunomodulatory region. Using 4C-seq, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topological associated domains (TADs). Interestingly, the inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we uncovered an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells simultaneously. Here, we highlight novel, long-range mechanisms whereby SLE susceptibility may be influenced by genetic variants, and the important contribution of chromatin topology to gene regulation and complex genetic disease.

2022-06-09 | GSE140127 | GEO

Roseobacter litoralis

Project description:Roseobacter litoralis overview

| PRJNA36145 | ENA

Roseobacter

Project description:Roseobacter Genome sequencing and assembly

| PRJNA269051 | ENA

Roseobacter

Project description:Pseudogenes in the Roseobacter group

| PRJNA593724 | ENA

Roseobacter

Project description:Roseobacter Genome sequencing and assembly

| PRJNA1023705 | ENA

Transcriptome response to oxygen tension and light irradiation in Roseobacter denitrificans OCh114

Project description:Transcriptome profiles of an aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 grown under different oxygen tension and light irradiation conditions were determined by NimbleGen Prokaryotic Expression array (12x135K).

2021-06-30 | GSE152336 | GEO

Roseobacter denitrificans

Project description:Roseobacter denitrificans Genome sequencing

| PRJNA943617 | ENA

Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray

Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd.

2010-08-05 | GSE21325 | GEO

Roseobacter denitrificans

Project description:Roseobacter denitrificans Raw sequence reads

| PRJNA937784 | ENA

DSMZ-Roseobacter

Project description:Sequencing of eight Roseobacter strains

| PRJEB591 | ENA