Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

ABSTRACT: The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

PROVIDER: PRJNA643248 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12120405.fastq.gz	Fastqsanger.gz
	SRR12120406.fastq.gz	Fastqsanger.gz
	SRR12120407.fastq.gz	Fastqsanger.gz
	SRR12120408.fastq.gz	Fastqsanger.gz
	SRR12120409.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 76

Similar Datasets

The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

Project description:Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in S. cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression in vivo and provide additional evidence that it functions as a histone chaperone.

2020-07-01 | GSE153567 | GEO

The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae.

Project description:Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.

| S-EPMC7544207 | biostudies-literature

Multiple direct and indirect roles of the Paf1 Complex in elongation, splicing, and histone post-translational modifications [ChIP-seq]

Project description:Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. Through nascent transcript sequencing, RNAPII profiling, and mechanistic modeling of transcription elongation dynamics, we find evidence for unique roles of Paf1C subunits in regulating RNAPII processivity, elongation rate, mRNA stability, transcript splicing, and repression of antisense transcripts. Through genetic suppression, we attribute increased antisense transcription, but not other defects, of a PAF1 mutant to loss of H3 K36 methylation. This work comprehensively analyzes both the immediate and extended roles of Paf1C subunits in transcription elongation and transcript regulation.

2024-05-15 | GSE255361 | GEO

Multiple direct and indirect roles of the Paf1 Complex in elongation, splicing, and histone post-translational modifications [RNA-seq]

2024-05-15 | GSE255362 | GEO

Multiple direct and indirect roles of the Paf1 Complex in elongation, splicing, and histone post-translational modifications [4tU-seq]

2024-05-15 | GSE255360 | GEO

A Highly Conserved GAD-1 Is Required for Pre-mRNA Splicing and Transcription Elongation by Forming Spliceosome with NineTeen Complex

Project description:Pre-mRNA splicing requires assembly of spliceosome that consists of hundreds of factors forming various dynamic complexes with or without small nuclear RNAs (snRNAs). Systematic identification of the splicing factors remains a significant challenge especially in vivo. In our genetic screening for the factors required for division asynchrony during Caenorhabditis elegans embryogenesis, we identified a highly conserved but uncharacterized essential protein, GAD-1, that is necessary for setting cell cycle length of intestine progenitors, a function that is shared with many other factors involved in transcription, pre-mRNA splicing or polyadenylation, suggesting its potential role in mRNA biogenesis. Co-immunoprecipitation followed by mass spectrometry reveals that GAD-1 mainly interacts with non-snRNP type of splicing complex called NineTeen Complex (NTC). Consistent with this, RNA-seq analysis demonstrates pervasive defects in pre-mRNA splicing in gad-1 mutants. Transgenic reporter assay shows its ubiquitous and nuclear expression across developmental stages. Immunostaining of the C-terminal domain of RNA polymerase II demonstrates a GAD-1’s role in transcription elongation. In agreement with this, depletion of GAD-1 and its interacting partners inhibits expression of both ubiquitous and tissue-specific genes, supporting that both GAD-1 and many of its interacting proteins are novel components of NTC or its associated spliceosome. Taken together, we identify GAD-1 and its multiple interacting partners as novel components of spliceosome in vivo through which they regulate pre-mRNA splicing and transcription elongation.

2017-12-31 | GSE94463 | GEO

Mechanisms of site-specific methylation by a highly conserved elongation factor 1A lysine methyltransferase

Project description:Translation elongation factor 1A (eEF1A) is an essential and highly conserved protein required for protein synthesis in eukaryotes. In both Saccharomyces cerevisiae and human, five different methyltransferase enzymes methylate specific residues on eEF1A, making eEF1A the eukaryotic protein targeted by the highest number of dedicated methyltransferases. eEF1A methyltransferases are highly selective enzymes, only targeting eEF1A and each targeting just one or two specific residues in eEF1A. However, the mechanism of this selectivity remains poorly understood. Here we have used AlphaFold modelling in combination with crosslinking mass spectrometry (XL-MS) and enzyme mutagenesis to reveal how S. cerevisiae elongation factor methyltransferase 4 (Efm4) specifically methylates eEF1A at K316. We find that a unique beta-hairpin motif, which extends out from the core methyltransferase fold, is important for methylation of eEF1A K316 in vitro. An alanine mutation of a single residue on this beta-hairpin, F212, significantly reduces Efm4 activity in vitro and in yeast cells. We show that the equivalent residue in human eEF1A-KMT2 (METTL10), F220, is also important for its activity towards eEF1A in vitro. Lastly, we find that phosphorylation of eEF1A at S314 negatively crosstalks with Efm4-mediated methylation of K316. Our findings demonstrate how protein methyltransferases can be being highly selective towards a single residue on a single protein.

2024-01-03 | PXD042599 | Pride

Greb1 is required for axial elongation and segmentation in vertebrate embryos

Project description:Greb1 is required for axial elongation and segmentation in vertebrate embryos

| PRJNA593776 | ENA

RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

Project description:RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

| PRJNA838484 | ENA

A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans.

Project description:The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.

| S-EPMC4991786 | biostudies-literature

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