Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterisation of nuclear and sub-nuclear proteomes of Saccharomyces cerevisiae

ABSTRACT: This study concerns characterisation of the nuclear, chromatin and nuclear non-chromatin proteomes of the yeast Saccharomyces cerevisiae. We performed nuclear and chromatin enrichments from exponentially growing cells using differential centrifugation and analysed the nuclear and chromatin pellets, along with their accompanying supernatants, by LC-MS/MS on two different platforms. We inferred relative quantitation of proteins using emPAI and compared the relative amounts of proteins in each of our samples which enabled us to infer probable residents of the nuclear and chromatin proteomes.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Suspension Culture, Fungal Cell

SUBMITTER: Daniel Nightingale

LAB HEAD: Kathryn Susan Lilley

PROVIDER: PXD007525 | Pride | 2019-11-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae.

Dikicioglu Duygu D Nightingale Daniel J H DJH Wood Valerie V Lilley Kathryn S KS Oliver Stephen G SG

FEMS yeast research 20190301 2

Topological analysis of large networks, which focus on a specific biological process or on related biological processes, where functional coherence exists among the interacting members, may provide a wealth of insight into cellular functionality. This work presents an unbiased systems approach to analyze genetic, transcriptional regulatory and physical interaction networks of yeast genes possessing such functional coherence to gain novel biological insight. The present analysis identified only a ...[more]

PMID: 30753445

Similar Datasets

Identification of the SS18-SSX interacting proteins

Project description:Using affinity purification determine changes in SS18 BAF complex upon fusion to SSX1. Using soluble nuclear fraction (nuclear extract NE) and nuclease digested chromatin fraction (CHR) we performed affinity capture of proteins bound to wild type SS18 and synovial sarcoma SS18-SSX1 fusion from NE and CHR of 293T cells.

2020-08-09 | PXD018715 | Pride

ChIP-seq for ZEB1 in the human breast cancer cell line MDA-MB-231

Project description:Identification of DNA binding sites of the transcription factor ZEB1 in the human breast cancer cell line MDA-MB-231 by chromatin-immunoprecipitation followed by sequencing (ChIP-seq).

2020-07-22 | E-MTAB-8258 | biostudies-arrayexpress

Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

Project description:Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse H2A.Bbd-like histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated Examination of 2 different histone variants in mouse spermatids.

2012-01-20 | E-GEOD-29913 | biostudies-arrayexpress

Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

Project description:Mitogen-activated protein kinases constitute essential signaling mechanisms linking external signal perception to gene expression in all eukaryotes. In Arabidopsis, MAPKs are found in the cytoplasmic and nuclear compartments, but no nuclear phosphoproteomic studies of mapk mutants were performed so far. In this work, we report a panel of nuclear and chromatin-associated targets by performing phosphoproteome analyses of wild-type and mpk3, mpk4, and mpk6 mutant plants. Since the three MAPKs play a role in cell division, development and innate immunity, we also analyzed the phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. A total of 165 proteins were identified to be differentially phosphorylated when compared between genotypes and in response to MAMP treatment. Using different criteria, including different biochemical and interaction assays, a number of the putative MAPK substrates were validated as true substrates for different MAPKs. Signaling networks for the three MAPKs revealed their common role in RNA transcription, RNA processing and chromatin organization, but also specific roles in development and organelle organization. Overall, this study unravels a set of chromatin-associated targets for these three MAPKs and promises novel insights into yet undiscovered domains linking MAPK signaling to a number of chromatin-related events.

2021-01-07 | PXD009823 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening 293T cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from 293T cells.

2021-09-27 | PXD028660 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening K562 cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from K562 cells.

2021-09-27 | PXD028668 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening THP-1 cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from THP-1 cells.

2021-09-27 | PXD028787 | Pride

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

Project description:Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock.M-BM- We have determined the underlyingM-BM- mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of eRNAs that cluster in specific circadian phasesM-BM- identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomicM-BM- analysesM-BM- also revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ. Nascent RNA transcripts in mouse liver were profiled at 8 time points of the 24 hour light-dark cycle. Static state mRNAs in WT and Rev-erbA -/- mice were profiled using microarray (GSE59460).

2014-11-21 | E-GEOD-59486 | biostudies-arrayexpress

Lamin binding profiles in the ENCODE regions

Project description:A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes including gene expression, nuclear organization, centromere function and chromosomal stability, and mutations in SWI/SNF components have been linked to several types of cancer. To better understand the biological processes in which chromatin remodeling proteins participate we globally mapped binding regions for several components of the SWI/SNF complex throughout the human genome using ChIP-Seq. SWI/SNF components were found to lie near regulatory elements integral to transcription (e.g. 5’ ends, RNA Polymerases II and III and enhancers) as well as regions critical for chromosome organization (e.g. CTCF, lamins and DNA replication origins). To further elucidate the association of SWI/SNF subunits with each other as well as with other nuclear proteins we also analyzed SWI/SNF immunoprecipitated complexes by mass spectrometry. Individual SWI/SNF factors are associated with their own family members as well as with cellular constituents such as nuclear matrix proteins, key transcription factors and centromere components implying a ubiquitous role in gene regulation and nuclear function. We find an overrepresentation of both SWI/SNF-associated regions and proteins in cell cycle and chromosome organization. Taken together the results from our ChIP and immunoprecipitation experiments suggest that SWI/SNF facilitates gene regulation and genome function more broadly and through a greater diversity of interactions than previously appreciated. ChIP-chip analysis of lamin A/C and lamin B in HeLa S3 cells

2011-01-10 | E-GEOD-24382 | biostudies-arrayexpress

Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

Project description:One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the Cohesin in chromatin and identified transcription factors, RNA-binding proteins, and chromatin regulators associated with Cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to Cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with Cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in Cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of Cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with Cohesin that warrant further investigation.

2023-06-05 | PXD036004 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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