Dataset Information

Blue Native Page based separation of the TNFRSC

ABSTRACT: Separation and relative quantification by targeted mass spectrometry of the TNFRSC members pior and after treatment with a generic deubiquitinating enzyme

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Federico Uliana

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD019847 | Pride | 2022-10-13

REPOSITORIES: Pride

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Publications

Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics.

Ciuffa Rodolfo R Uliana Federico F Uliana Federico F Mannion Jonathan J Mehnert Martin M Tenev Tencho T Marulli Cathy C Satanowski Ari A Keller Lena Maria Leone LML Rodilla Ramírez Pilar Natalia PN Ori Alessandro A Gstaiger Matthias M Meier Pascal P Aebersold Ruedi R

Proceedings of the National Academy of Sciences of the United States of America 20220930 40

Protein-protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes-a goal that remains an unsolved challenge. Here we describ ...[more]

PMID: 36179048

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Project description:Distant enhancer elements are a major source of specificity in mammalian gene expression. Although enhancers that regulate broad developmental decisions and inducible gene expression have been studied extensively, little is known about regulatory elements that govern monogenic and monoallelic expression. Here, using high throughput epigenetic and genetic techniques we identified a plethora of distant enhancers that regulate monoallelic olfactory receptor (OR) gene expression. Potential OR enhancers have unique, cell type specific epigenetic marks that distinguish them from other neuronal enhancers and correlate with enhancer activity in vivo. Using sequence capture to enrich for these sequences we identified Dnase-protected footprints that reveal novel regulatory sequences and transcription factors required for OR gene activation. Our experiments provide insight to the regulation of OR expression, and describe novel principles and methodologies towards the understanding of transcriptional mechanisms that generate cellular diversity. In vivo examination of H3K79me3 enrichment and DNAse protected footprints on olfactory receptor enhancer sequences. We performed ChIP-seq on native chromatin isolated from the mouse olfactory epithelium using antibodies against H3K79me3. To sequence accessible regions of the genome we treated nuclei with limiting amounts of DNAse I to digest accessible chromatin and perform Dnase Hypersensitivity (DHS)-seq. In the olfactory epithelium, the H enhancer – the first described enhancer for olfactory receptors has a well-defined DNAse I hypersensitivity peak and is flanked by high levels of H3K79me3. We find other intergenic sequences nearby olfactory receptor genes that share the same chromatin signature, and test their function in vivo. TO uncover transcription factor footprints on olfactory receptor enhancers we performed sequence capture of the DHS-seq library to enrich for these sequences. We find multiple DNAse-protected sequences and perform motif analysis on transcription factor footprints to reveal factors involved in olfactory receptor gene regulation.

Dataset Information

Blue Native Page based separation of the TNFRSC

Publications

Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics.

Similar Datasets

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