Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

THE HISTONE CHAPERONE SPN1 PRESERVES SUBNUCLEOSOMAL STRUCTURES AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES

ABSTRACT: THE HISTONE CHAPERONE SPN1 PRESERVES SUBNUCLEOSOMAL STRUCTURES AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES

PROVIDER: PRJNA1086537 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

THE HISTONE CHAPERONE SPN1 PRESERVES SUBNUCLEOSOMAL STRUCTURES AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES

Project description:Spn1 is a multifunctional histone chaperone essential for life in eukaryotes. While previous work has elucidated regions of the protein important for its many interactions, it is unknown how these domains contribute to the maintenance of chromatin structure. Here, we employ digestion by micrococcal nuclease followed by single-stranded library preparation and sequencing (MNase-SSP) to characterize chromatin structure in yeast expressing wild-type or mutants of Spn1. We mapped nucleosome and subnucleosomal protections genome-wide, and surprisingly, we observed a genome-wide loss of subnucleosomal protection over nucleosome-depleted regions (NDRs) in the Spn1-K192N-containing strain, indicating critical functions of Spn1 in maintaining normal chromatin architecture in promoter regions. Additionally, alterations in nucleosome and hexasome positioning were observed in markedly different mutant Spn1 strains, demonstrating that multiple functions of Spn1 are required to maintain proper chromatin structure in open reading frames. Moreover, the impact of these functions correlated with gene expression and length. Taken together, our results reveal a previously unknown role of Spn1 in the maintenance of NDR architecture and deepen our understanding of Spn1-dependent chromatin maintenance over transcribed regions.

2025-02-11 | GSE261349 | GEO

THE HISTONE CHAPERONE SPN1 PRESERVES SUBNUCLEOSOMAL STRUCTURES AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES.

Project description:Spn1 is a multifunctional histone chaperone essential for life in eukaryotes. While previous work has elucidated regions of the protein important for its many interactions, it is unknown how these domains contribute to the maintenance of chromatin structure. Here, we employ digestion by micrococcal nuclease followed by single-stranded library preparation and sequencing (MNase-SSP) to characterize chromatin structure in yeast expressing wild-type or mutants of Spn1. We mapped nucleosome and subnucleosomal protections genome-wide, and surprisingly, we observed a genome-wide loss of subnucleosomal protection over nucleosome-depleted regions (NDRs) in the Spn1-K192N-containing strain, indicating critical functions of Spn1 in maintaining normal chromatin architecture in promoter regions. Additionally, alterations in nucleosome and hexasome positioning were observed in markedly different mutant Spn1 strains, demonstrating that multiple functions of Spn1 are required to maintain proper chromatin structure in open reading frames, particularly at higher expressed and longer genes. Taken together, our results reveal a previously unknown role of Spn1 in the maintenance of NDR architecture and deepen our understanding of Spn1-dependent chromatin maintenance over transcribed regions.

| S-EPMC10979989 | biostudies-literature

Pervasive functional translation of noncanonical open reading frames

Project description:Pervasive functional translation of noncanonical open reading frames

| PRJNA544411 | ENA

Identification of translated small open reading frames in lymphocytes

Project description:Identification of translated small open reading frames in lymphocytes

| PRJNA646476 | ENA

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

Project description:We present a genome-wide assessment of small open reading frames (smORF) translation by ribosomal profiling of polysomal fractions in Drosophila S2 cell. In this way, mRNAs bound by multiple ribosomes and hence actively translated can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits. Ribosomal profiling of large and small polysomal fractions in Drosophila S2 cells to assess translation of smORFs

2014-09-11 | E-GEOD-60384 | biostudies-arrayexpress

Accurate annotation of human protein-coding small open reading frames

Project description:Accurate annotation of human protein-coding small open reading frames

| PRJNA515538 | ENA

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

2014-09-11 | GSE60384 | GEO

Pervasive functional translation of noncanonical open reading frames

Project description:Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). Here, we exploit a systematic CRISPR-based screening strategy to identify hundreds of non-canonical CDSs that are essential for cellular growth and whose disruption elicit specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds that are presented by the HLA system. Interestingly, we find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same mRNA, thus revealing the diverse use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

2020-03-14 | GSE131650 | GEO

The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

Project description:The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

| PRJNA494404 | ENA

Identification of translated small open reading frames in lymphocytes

Project description:Open reading frames (ORFs) are the genomic DNA sequences that have the potential to be translated. Genome annotation pipelines dismiss translation products of small ORFs (smORFs) of less than 100 codons (<300 nucleotides) as being unlikely to have a biological function. In this study, we systematically characterized smORFs in mouse B and T cells under different conditions and predicted a total of 5744 unique actively translated smORFs. We then extended our analysis to ORFs of 101-200 codons in length and predicted 945 of such longer translation products. Additionally, our results have suggested the existence of candidate secreted micropeptides. Furthermore, verifying their existence and identifying their functions will be essential and potentially lead to useful applications.

2021-04-28 | GSE154491 | 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