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S. pombe LC-MS G4-binding proteins_2

ABSTRACT: Affinity-purification study of G-quadruplex binding proteins from the S. pombe proteomics.

INSTRUMENT(S):

ORGANISM(S): Schizosaccharomyces Pombe 927

TISSUE(S): Bile

SUBMITTER: Nasim Sabouri

LAB HEAD: Nasim Sabouri

PROVIDER: PXD020921 | Pride | 2021-09-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	2016_10_14_gel_band_05_rDNA_wholecellextract.raw.zip	Raw
	2016_10_14_gel_band_06_rDNA_scr_wholecellextract.raw.zip	Raw
	2016_10_14_gel_band_07_rDNA_m4_wholecellextract.raw.zip	Raw
	2016_10_14_gel_band_08_biotin_wholecellextract.raw.zip	Raw
	2016_10_17_Gel_band_05_Sprot_S_pombe_data_20161017_F112359.csv	Csv

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Publications

The RGG domain in the C-terminus of the DEAD box helicases Dbp2 and Ded1 is necessary for G-quadruplex destabilization.

Yan Kevin Kok-Phen KK Obi Ikenna I Sabouri Nasim N

Nucleic acids research 20210801 14

The identification of G-quadruplex (G4) binding proteins and insights into their mechanism of action are important for understanding the regulatory functions of G4 structures. Here, we performed an unbiased affinity-purification assay coupled with mass spectrometry and identified 30 putative G4 binding proteins from the fission yeast Schizosaccharomyces pombe. Gene ontology analysis of the molecular functions enriched in this pull-down assay included mRNA binding, RNA helicase activity, and tran ...[more]

PMID: 34302476

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S. pombe LC-MS G4-binding proteins

Project description:Affinity-purification study of G-quadruplex binding proteins from the S. pombe proteomics.

2021-09-07 | PXD020907 | Pride

G4 Quadruplex Binding Proteins

Project description:In this study we discover proteins that bind to G4 quadruplex DNA structure. We use modified c-myc quadruplex as a bait, and compare it to the control bait - T15 oligo. We use spectral counts and G-test to determine significant binders. T15 and G4 datafiles are uploaded

2016-07-07 | PXD003501 | Pride

Identification of human proteins interacting with locked G4 structures

Project description:G4 are noncanonical secondary structures consist in stacked tetrads of Hoogsteen hydrogen-bonded guanines bases. An essential feature of G-quadruplexes is their intrinsic polymorphic nature. Indeed, depending on the length and the composition of the sequence, as well as the environmental conditions (including the nature and concentration of metal cations, and local molecular crowding), a G-quadruplex-forming sequence can adopt different topologies in which the strands are in parallel or antiparallel conformations, with the co-existence of different types of loops (lateral, diagonal or propeller) with variable lengths. The impact of G4 on cellular metabolism is associated with protein or enzymatic factors that promote, inhibits or resolve these structures. Thus, the major impact of G4 on the human cell metabolism is associated with genetic defects affecting proteins that counteract their formation. Although a large number of proteins able to bind and/or "to resolve" G-quadruplex structures have been identified in vitro, less is known about their mode of interaction with G-quadruplex, their specificity versus the topology and finally their specificity for G4 structures relatively to G-rich single-stranded sequences. In this study we aimed to identify and characterize human proteins interacting with locked G4 structures.

2021-07-16 | PXD021003 | Pride

G4-RNA binding proteins from K562

Project description:G-quadruplex RNA pulldown followed by mass spectrometry. G4A4 oligoribonucleotide (5’-AAAAAAGGGGAAAAGGGGAAAAGGGGAAAAGGGGAAAAAA-3’) was biotinylated and folded in either K+ or Li+ containing buffers, causing folding of G-quadruplex (K+) or destabilization of the secondary structure (Li+). G4A4 pulldown was used to identify G4-RNA binding proteins from K562 human cell line nuclear extracts, interacting in structure-dependent manner.

2024-02-20 | PXD041154 | Pride

Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq

Project description:The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.

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Bloom syndrome protein modulates protein-coding gene and miRNA expression as a function of G4 DNA content

Project description:Bloom syndrome is a rare autosomal recessive genetic instability and cancer predisposition syndrome caused by loss of function mutations in the BLM RECQ helicase gene. To ask if some of the distinctive pathological features of Bloom syndrome might reflect altered gene expression, we analyzed global mRNA and miRNA expression in fibroblasts from 16 patients and 15 matched normal controls, and in control primary diploid fibroblasts depleted of the BLM protein. We document significant differential expression of both protein-coding genes and miRNAs with well-characterized cancer associations in BLM-deficient cells. Differences in expression correlated significantly with G4 motifs, which are associated with potential to form G-quadruplex structures. These results indicate that BLM helicase may modulate gene expression by regulating the in vivo stability of G-quadruplex structures, and identify sets of genes and miRNAs whose expression, when altered, may drive the pathogenesis of Bloom syndrome and associated cancers. Global profiling of mRNA and miRNA expression was analyzed in primary fibroblasts from 16 patients and 15 matched normal controls, and in 9 primary diploid fibroblasts depleted of BLM protein by BLM-specific (3), control (3) and scrambled (3) shRNA.

2014-06-12 | E-GEOD-54502 | biostudies-arrayexpress

G4 quadruplex landscape and its regulation revealed by a new antibody capture method

Project description:Currently, the identification of G4 quadruplexes in vivo depends on a published and widely used G4-ChIP protocol (PMID: 29470465) that uses the anti-G4 antibody to captures the quadruplexes like regular chromatin. This method is challenged by some false positives and false negatives in G4-quadruplex capture. We have developed an antibody capture G4-ChIP (AbC G4-ChIP) method to overcome these challenges. The AbC G4-ChIP achieves (i) minimized in vitro artifacts during the incubation steps, and (ii) capture of G4-quadruplexes which are not protein-bound. We have applied the AbC G4-ChIP to study the regulatory effect of a CGG-repeat binding protein CGGBP1 on G4-quadruplex formation. The AbC G4-ChIP identifies inter-strand G/C-skew as a sequence property associated with CGGBP1-regulated G4-quadruplexes.

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Nucleosome Mapping in S. pombe Centromeres

Project description:A key element for defining the centromere identity is the incorporation of a specific histone H3, CENP-A, known as Cnp1p in S. pombe. Previous studies have suggested that functional S. pombe centromeres lack nucleosome arrays and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are in fact positioned in regular intervals in the core of centromere 2, providing the first high resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore proteins cnp1, mis18, mis12, nuf2, mal2, overexpression of Cnp1p, or deletion of ams2. Bioinformatic analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence-bias in nucleosome positioning. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites for the GATA-like protein Ams2p, which participates in CENP-A incorporation. Keywords: Nucleosome Mapping Study Entire cnt regions and histone-related genes were tiled at 1-5 bp spacing using 60-mer probes.

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