Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stoichiometric Production of Protein-Complex Components in Eukaryotes Without Widespread Feedback Regulation

ABSTRACT: Stoichiometric Production of Protein-Complex Components in Eukaryotes Without Widespread Feedback Regulation

PROVIDER: PRJNA486442 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7704600.fastq.gz	Fastqsanger.gz
	SRR7704601.fastq.gz	Fastqsanger.gz
	SRR7704602.fastq.gz	Fastqsanger.gz
	SRR7704603.fastq.gz	Fastqsanger.gz
	SRR7704604.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 13

Similar Datasets

Stoichiometric Production of Protein-Complex Components in Eukaryotes Without Widespread Feedback Regulation

Project description:Constituents of multi-protein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here we quantified the production rates of multi-protein complexes in single- and multi-cellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities present in a large fraction of ribosome footprints which often distorts quantitation accuracy in eukaryotes, we found that obligate components of multi-protein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution towards quantitative control at every stage of the central dogma.

2018-12-03 | GSE118676 | GEO

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes

Project description:DNA methylation in the form of 5-methylcytosine (5mC) is widespread in eukaryotes, while the presence of N6-methyladenine (6mA) has sparked considerable debate. Methodological disparities in quantifying and mapping 6mA in genomic DNA have fueled this controversy. Yet, the distantly related early branching fungi, ciliates and the algae Chlamydomonas reinhardtii exhibit robust 6mA methylation patterns, but the origin and evolution of 6mA remain unknown. Here we use Oxford Nanopore modified base calling to profile 6mA at base pair resolution in 18 unicellular eukaryotes spanning all major eukaryotic supergroups. Our results reveal that only species encoding the adenine methyltransferase AMT1 display robust genomic 6mA patterns. Notably, 6mA consistently accumulates downstream of transcriptional start sites, aligning with H3K4me3-enriched nucleosomes, suggesting a conserved role in placing transcriptionally permissive nucleosomes. Intriguingly, the recurrent loss of the 6mA pathway across eukaryotes, particularly in major multicellular lineages, implies a convergent alteration in the dual methylation system of the Last Eukaryotic Common Ancestor, which featured transcription-associated 6mA and repression-associated 5mC.

2025-09-17 | GSE261870 | GEO

Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes.

Project description:Constituents of multiprotein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here, we quantified the production rates of multiprotein complexes in unicellular and multicellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities, which occur for a large fraction of ribosome footprints and distort quantitation accuracy in eukaryotes, we found that obligate components of multiprotein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution toward quantitative control at every step in the central dogma.

| S-EPMC6659121 | biostudies-literature

Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes

Project description:Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes

| PRJNA1089232 | ENA

Sediment eukaryotes

Project description:Sediment eukaryotes Raw sequence reads

| PRJNA1133151 | ENA

Mutant PRPF8 causes widespread splicing changes in spliceosome components in retinitis pigmentosa patient RPE cells

Project description:Mutant PRPF8 causes widespread splicing changes in spliceosome components in retinitis pigmentosa patient RPE cells

| PRJNA694104 | ENA

Diversity in DNA: Identification of methylated deoxyadenosines in higher eukaryotes

Project description:Since the discovery that cytosine deoxynucleotides could be methylated (dC5m), not much is known in higher eukaryotes about modifications affecting other deoxynucleotides. Here, we now report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and human. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, is present in different cell types, but commonly depleted from gene exons. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that such direct DNA modifications might be more widespread than previously thought.

2015-11-16 | MTBLS276 | MetaboLights

Soil eukaryotes in Australia

Project description:Soil eukaryotes in Australia

| PRJNA891465 | ENA

Methylome analysis of deoxyadenosines in higher eukaryotes

Project description:Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, and it is present in different cell types. dA6m is commonly depleted in gene exons, whilst it remains abundant in introns. Finally, we have identified the putative consensus sequence, where there is preferential methylation. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that DNA alterations might be more widespread than previously thought.

2015-11-12 | GSE74184 | GEO

Improving Competency and Metrics for PoLypectomy Skills Using Evaluation Tools and VidEo Feedback (COMPLETE)

Project description:I plan to investigate the value of video-based feedback in endoscopic training - specifically, the role of terminal video feedback as compared to usual concurrent feedback on cold snare polypectomy technique in trainees, using Direct Observation of Polypectomy Skills (DOPyS) competency score. I have focused the study on the competency of cold snare polypectomy for subcentimeter polyps. The majority (>75%) of colon polyps are smaller than one centimeter. Cold snare polypectomy has been shown, and recommended by the American Society for Gastrointestinal Endoscopy (ASGE), to be an effective removal technique. However, its widespread use and moreover, its teaching to trainees is lacking. It takes time and resources to learn and teach endoscopic techniques. Our study will hope to identify a mechanism through video-based feedback that could help to improve the translation of the training of polypectomy skills to its actual performance, and to accelerate the learning curve.

| 2241449 | ecrin-mdr-crc

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