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Co-opted transposons help perpetuate conserved higher-order chromosomal structures

ABSTRACT: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

PROVIDER: PRJNA593858 | ENA |

REPOSITORIES: ENA

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Co-opted transposons help perpetuate conserved higher-order chromosomal structures

Project description:Co-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.

2019-12-08 | GSE141550 | GEO

Co-opted transposons help perpetuate conserved higher-order chromosomal structures.

Project description: Not available

| S-EPMC6979391 | biostudies-literature

Interrogating the higher order structures of snake venom proteins

Project description:Snake venoms contain complex mixtures of proteins that play vital roles in the survival of venomous snakes. In line with their diverse pharmacological activities, the protein compositions of snake venoms can be highly variable, and efforts to characterise the primary structures of such proteins are extensive and ongoing. In addition, a significant knowledge gap exists in terms of higher-order interactionsbetweenproteinsproposedto modulate venom potency, which poses a challenge for treatment of envenomation and development of successful therapeutic applications.Here we use a multifaceted mass spectrometrybased approach to characteriseproteinsfrom the medically significant venomsof Collett’s snake Pseudechis collettiand the puff adder Bitis arietans.Following chromatographic fractionation and bottom-up proteomics identification, native mass spectrometry identified, among other components, a 117 kDa non-covalent L-amino acid oxidase dimer in the P. collettivenom and a 60 kDa C-type lectin tetramer in the B. arietansvenom. Furthermore, a 27.7 kDa covalently-linked phospholipase A2(PLA2) dimer was identified in P. collettivenom, and thePLA2species were shownto adopt a highly compact geometry based on ion mobility measurements. Exploration of the catalytic efficiencies of the monomeric and dimeric forms of PLA2revealed that the dimeric PLA2 possessed greater bioactivity than the monomeric PLA2s.This work contributes to ongoing efforts to catalogue the protein components of snake venoms, and notably,itemphasises the importance of understanding higher-order protein interactions in venomsand the utility of a combined mass spectrometric approachfor this task.

2020-02-17 | PXD016503 | Pride

Higher-Order Organization Principles of Pre-translational mRNPs [RIPPLiT]

Project description:Higher-Order Organization Principles of Pre-translational mRNPs [RIPPLiT]

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DNA methylation maintains integrity of higher order genome architecture

Project description:DNA methylation maintains integrity of higher order genome architecture

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DNA methylation maintains integrity of higher order genome architecture (Nanopore)

Project description:DNA methylation maintains integrity of higher order genome architecture (Nanopore)

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SETMAR regulates gene expression and modulates higher order chromatin structure

Project description:SETMAR regulates gene expression and modulates higher order chromatin structure

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Gamma entrainment binds higher order brain regions and alleviates neurodegeneration

Project description:Gamma entrainment binds higher order brain regions and alleviates neurodegeneration

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DNA methylation maintains integrity of higher order genome architecture (WGBS)

Project description:DNA methylation maintains integrity of higher order genome architecture (WGBS)

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Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin

Project description:Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. We assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions, performed statistical analyses and computer modelling. We found no difference in MNase accessibility, suggesting no difference in fiber folding between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially organized domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.

2018-12-04 | GSE100401 | GEO

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