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Deep membrane proteome profiling of high-risk human paraganglioma

ABSTRACT: We combined glycopeptide enrichment by N-glyco-FASP (Zielinska et al., 2010), SPEG (Tian et al., 2007) with a hydrophobic segment-oriented hpTC method (Vít et al 2016) and a standard “detergent and trypsin” approach into a tree-pronged “Pitchfork” strategy for the analysis of membrane proteome in high-risk human paraganglioma.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Adrenal Medulla

DISEASE(S): Paraganglioma

SUBMITTER: Ondrej Vit

LAB HEAD: Jiri Petrak

PROVIDER: PXD029344 | Pride | 2021-11-25

REPOSITORIES: Pride

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Project description:Here we exploit the essential process of X-chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome-wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. The DCC binds to two categories of sites on X: rex sites that recruit the DCC in an autonomous, sequence- dependent manner, and dox sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DCC mutants that abolish rex-site binding do not eliminate dox-site binding, but instead reduce it to the level observed at autosomal binding sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex-site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites exhibit similar binding properties. Our data support a model for DCC binding in which low-level DCC binding at dox and autosomal sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then greatly elevates DCC binding to dox sites in cis, which lack intrinsically high DCC affinity on their own. We also show here that the C. elegans DCC achieves dosage compensation through its effects on transcription. ChIP-chip experiments using antibodies against DPY-27, SDC-3, DPY-30, DPY-26, MIX-1, SMC-4, ASH-2 in wild-type embryos. ChIP-chip experiments using antibodies against SDC-3, DPY-27, DPY-30, ASH-2, and IgG in different DCC mutants. ChIP-chip experiments using antibodies against RNA Pol II (hypophosphorylated and S2 and S5) in wild type and sdc-2 partial loss of function mutants.

			Action	DRS
	checksum.txt	Txt
	control_gfasp.raw	Raw
	control_gfasp_peptides.txt	Txt
	control_gfasp_proteinGroups.txt	Txt
	control_hptc.raw	Raw

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Deep membrane proteome profiling of high-risk human paraganglioma

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