Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two paralogous PHD finger proteins participate in Paramecium tetraurelia's natural genome editing

ABSTRACT: The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sexual reproduction, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique Internal Eliminated Sequences (IESs) located throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IESs excision occurs. In DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functionalities, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Paramecium Tetraurelia

SUBMITTER: Lilia Häußermann

LAB HEAD: Estienne Swart

PROVIDER: PXD046704 | Pride | 2024-08-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	P2854_TMT16plex_5prc_ion.tsv	Tabular
	P2854_TMT16plex_5prc_peptide.tsv	Tabular
	P2854_TMT16plex_5prc_protein.tsv	Tabular
	P2854_TMT16plex_5prc_psm.tsv	Tabular
	P2854_TMT16plex_FragPipe_workflow.workflow	Other

Items per page:

1 - 5 of 20

Similar Datasets

The Prion Protein (PrP) is involved in translation via RNA granule-like mRNPs, a connection which is impaired during neurodegenerative diseases

Project description:Cytoplasmic RNA granules have emerged as important elements of posttranscriptional and translational regulation. Stress, germinal and neuronal granules contain RNA-binding proteins capable of self-assembly due to prion-like domains. Hyperassembly mediated by these prion-like domains causes several neurodegenerative diseases. Here, we report a subset of the mammalian prion protein (PrP), also prone to self-assembly, propagation and to cause devastating diseases, is a component of naturally occurring messenger ribonucleoproteins (mRNPs) in adult mouse brains. Biomolecules co-purified with PrP revealed a multitude of diverse RNA granule associated proteins and mRNAs encoding members of the translation machinery, indicating a role in a specialized translation process. Importantly, PrP mutations linked to Creutzfeldt-Jakob disease (CJD) or fatal familial insomnia (FFI) severely impaired recovery of mRNPs from preclinical mice, possibly representing a very early pathological process. Thus, mutant PrP may cause dysfunction in RNA regulation, thereby joining the constantly expanding ranks of disease associated RNP granule proteins. The file Enrichment_analysis.xlsx contains mRNAs (FDR < 0.01) co-purified with PrP in both WT sample pools as identified by DESeq2 and the respective gene counts and log2 fold changes for CJD and FFI PrP:IP sample pools. RIP-Seq analysis of mRNAs co-purified with PrP from murine brain cytoplasmic fractions in wild-type (WT), CJD and FFI mice. Each RIP-Seq and control (input) library represents a pool of 12 to 16 co-immunoprecipitation samples out of 3 to 4 mice. To control for post-homogenization artifacts, we conducted an experiment in which we prepared homogenates from WT and PrP-KO (Prnp-/-) mice of different genetic backgrounds (C57BL/6 and 129S4) and identified SNPs in RIP-Seq and control libraries to finally identify specifically co-purified mRNAs.

2015-11-01 | E-GEOD-57233 | biostudies-arrayexpress

Releasing activity disengages cohesinâs Smc3/Scc1 interface in a process blocked by acetylation

Project description:Sister chromatid cohesion conferred by entrapment of sister DNAs within a tripartite ring formed between cohesinâs Scc1, Smc1, and Smc3 subunits is generated during S and eventually destroyed at anaphase through cleavage of Scc1 by separase. Throughout the cell cycle, cohesinâs association with chromosomes is controlled by opposing activities: loading by the Scc2/4 complex and release by a separase independent releasing activity. Co-entrapment of sister DNAs during replication is accompanied by acetylation of Smc3 by Eco1, which blocks releasing activity and ensures that sisters remain stably connected. Because fusion of Smc3 to Scc1 prevents release and bypasses the requirement for Eco1, we suggested that release is mediated by disengagement of the Smc3/Scc1 interface. We now show that all mutations capable of bypassing Eco1, be they in cohesinâs Smc1, Smc3, Scc1,Wapl, Pds5, or Scc3 subunits, greatly reduce dissociation of N-terminal cleavage fragments of Scc1 (NScc1) from Smc3. We show that this process involves interaction between Smc ATPase heads and is inhibited by Smc3 acetylation Effect of mutations QQ and EQ in Smc3 on cohesin loading onto chromosomes

2016-02-18 | E-GEOD-76890 | biostudies-arrayexpress

Cohesin releases DNA through asymmetric ATPase-driven ring opening

Project description:Cohesin stably holds together the sister chromatids from S phase until mitosis. To do so, cohesin must be protected against its cellular antagonist Wapl. Eco1 acetylates cohesinâs Smc3 subunit, which locks together the sister DNAs. We used yeast genetics to dissect how Wapl drives cohesin from chromatin and identified mutants of cohesin that are impaired in ATPase activity but remarkably confer robust cohesion that bypasses the need for the cohesin protectors Eco1 in yeast and Sororin in human cells. We uncover an unexpected functional asymmetry within the heart of cohesinâs highly conserved ABC-like ATPase machinery and show that an activity associated with one of cohesinâs two ATPase sites drives DNA release from cohesin rings. This key mechanism is conserved from yeast to humans. We propose that Eco1 locks cohesin rings around the sister chromatids by counteracting an asymmetric cohesin-associated ATPase activity. Effect of mutations in Smc1 and Smc3 on cohesin loading onto chromosomes

2016-02-18 | E-GEOD-76891 | biostudies-arrayexpress

Sgt1 interactome analysis under proteostatic stress and steady state conditions

Project description:Buildup of misfolded proteins are prevented by chaperone-assisted refolding and/or proteasome dependent degradation. The coordination of these two protein quality control (PQC) systems is not fully understood. We identified the essential Hsp90 co-chaperone Sgt1 as a new member of a general PQC linking folding and degradation. Upon proteostatic stress, e.g. heat shock, Sgt1 accumulates in an Hsp90- and proteasome dependent manner at an until now unknown spatial PQC compartment in both yeast and human cells. In order to find further components of this new PQC compartment we performed pull down experiments and a protein interaction analysis of cells expressing either GFP tagged Sgt1 (or GFP alone, as a negative control) that were either grown at 30Â°C or under heat shock conditions (42Â°C, 30 minutes).

2021-07-02 | PXD016174 | Pride

Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri

Project description:Recent functional genomics and genome-scale modeling approaches indicated that B12 production in Lactobacillus reuteri could be improved by medium optimization. Here we show that a series of systematic single amino acid omissions could significantly modulate the production of B12 from nearly undetectable levels (by isoleucine omission) to 20-fold higher than previously reported through omission of cysteine. We analyzed by cDNA microarray experiments the transcriptional response of L. reuteri to the medium lacking cysteine. These results supported the observed high B12 production and provided new avenues for future improvement of production of vitamin B12. Keywords: cell type comparison loop design

2010-05-17 | E-GEOD-13391 | biostudies-arrayexpress

Paramecium tetraurelia autogamy series 2 (ND7-silenced and control cells)

Project description:P. tetraurelia, like all ciliates, is a unicellular eukaryote processing two different kinds of nuclei, germline micronuclei (mic) and somatic macronucleus (mac). The diploid micronuclei undergo meiosis during sexual events to transmit the germline genome to the next generation. The highly polyploid mac (~800 n) is responsible for transcription during the life cycle but is lost after fertilisation; the new mic and mac develop from mitotic copies of the zygotic nucleus. During development of the new mac, the germline genome is amplified from 2n to ~800n and is extensively rearranged by two distinct kinds of DNA elimination. The micronuclear 50 to 60 Chromosomes are fragmented into ~200 shorter molecules caped by de novo telomere addition as a result of the imprecise elimination transposons and minisatellites. Moreover, approximately 60,000 short, single-copy elements called internal eliminated sequences (IESs) are precisely removed from coding and non-coding sequences. It was shown that the rearrangements in the developing mac appear to reproduce the rearrangements observed in the old mac, implying the existence of homology dependent cross talk between germline and somatic genomes during sexual event. To understand the molecular mechanisms and the genetic control involved in genome rearrangements, we studied the evolution of the transcriptome during Paramecium tetraurelia sexual reproduction.

2010-07-07 | GSE18002 | GEO

Aerobic cultivation vs Respiratory conditions

Project description:The effect of respiration (aerobic cultivation in the presence of heme and vitamin K2) was compared with unsupplemented aerobic cultivation with Lactobacillus plantarum. Two-condition experiment, aerobic vs respiring cells. Biological replicates: 3 aerobic cultures, 3 respiring cultures, independently grown and harvested. One replicate per array. Respiring cultures are called reactor 1-3; Aerobic cultures are called reactor 4-6 In the subsequent analysis data from reactor 4 were not used. There was likely a mistake made during quenching. This was concluded as new labeling/hybridisation gave same (bad) results (128a); slide 128b was dye-swap.

2010-05-16 | E-GEOD-18432 | biostudies-arrayexpress

Genome-wide analysis of HoxBlinc lncRNA downstream targets in mouse ESC-derived embryonic bodies

Project description:We find a new non-coding transcript associated with active HoxB locus, which we named HoxBlinc lncRNA. We report that HoxBlinc RNA specifies Flk1+ mesoderm and then promotes the development of HS/PCs and cardiomyocytes. To understand the molecular pathways reguated by HoxBlinc, we generate two doxycycline inducible KD ES R1E cell lines, then differentiate these cell lines to day 6 via embryonic bodies stage. RNA-seq analysis were performed for day 6 EBs with or without doxycycline treatment starting at Flk1+ mesodermal stage. RNA from day 6 EBs targeting with 2 invidiual shRNAs with or without doxycycline treatment were combined together for RNA-seq analysis.

2015-11-11 | E-GEOD-74894 | biostudies-arrayexpress

Gene expression in ABHD5-knockdown RAW264.7 cells

Project description:RAW cells or ABHD5-KD RAW cells were subjected to microarray assays. Each group contain 3 samples. To explore the regulatory role of ABHD5 in metabolic pathways, RAW cells or ABHD5-KD RAW cells were subjected to microarray assays.

2016-05-12 | E-GEOD-80066 | biostudies-arrayexpress

Regulation of Histone Acetylation by SUMOylation Through TFAP2C Binding to the Chromatin and Recruitment of HDAC Complex

Project description:Enhancers are fundamental to gene regulation. Post-translational modifications by the small ubiquitin-like modifiers (SUMO) modify chromatin regulation enzymes, including histone acetylases and deacetylases. However, it remains unclear whether SUMOylation regulates enhancer marks, acetylation at the 27th lysine residue of the histone H3 protein (H3K27Ac). We hypothesize that SUMOylation regulates H3K27Ac. To test this hypothesis, we performed genome-wide ChIP-seq analyses. We discovered that knockdown (KD) of the SUMO activating enzyme catalytic subunit UBA2 reduced H3K27Ac at most enhancers. Bioinformatic analysis revealed that TFAP2C-binding sites are enriched in enhancers whose H3K27Ac was reduced by UBA2 KD. ChIP-seq analysis in combination with molecular biological methods showed that TFAP2C binding to enhancers increased upon UBA2 KD or inhibition of SUMOylation by a small molecule SUMOylation inhibitor. However, this is not due to the SUMOylation of TFAP2C itself. Proteomics analysis of TFAP2C interactome on the chromatin identified histone deacetylation (HDAC) machinery. TFAP2C KD reduced HDAC binding to chromatin and increased H3K27Ac marks at enhancer regions, suggesting that TFAP2C is involved in recruiting HDAC. Taken together, our findings provide important insights into regulation of enhancer marks by SUMOylation.

2024-04-13 | PXD045644 | Pride

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