Dataset Information

Proteomic analysis of Psmd9 knockdown in the liver

ABSTRACT: We have shown that decreasing psmd9 expression effects lipid metabolism in vivo and were interested in investigating the pathways by which psmd9 elicited these changes. To investigate these mechanisms, we performed proteomic analyses on the livers from C57 and DBA mice that had been treated with antisense oligonucleotides targeted to psmd9.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Liver

SUBMITTER: Benjamin Parker

LAB HEAD: Benjamin Parker

PROVIDER: PXD010759 | Pride | 2019-03-14

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	20180725_QEHF_BenP_PSM9ASO_10.raw	Raw
	20180725_QEHF_BenP_PSM9ASO_12.raw	Raw
	20180725_QEHF_BenP_PSM9ASO_13.raw	Raw
	20180725_QEHF_BenP_PSM9ASO_14.raw	Raw
	20180725_QEHF_BenP_PSM9ASO_15.raw	Raw

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Publications

An integrative systems genetic analysis of mammalian lipid metabolism.

Parker Benjamin L BL Calkin Anna C AC Seldin Marcus M MM Keating Michael F MF Tarling Elizabeth J EJ Yang Pengyi P Moody Sarah C SC Liu Yingying Y Zerenturk Eser J EJ Needham Elise J EJ Miller Matthew L ML Clifford Bethan L BL Morand Pauline P Watt Matthew J MJ Meex Ruth C R RCR Peng Kang-Yu KY Lee Richard R Jayawardana Kaushala K Pan Calvin C Mellett Natalie A NA Weir Jacquelyn M JM Lazarus Ross R Lusis Aldons J AJ Meikle Peter J PJ James David E DE de Aguiar Vallim Thomas Q TQ Drew Brian G BG

Nature 20190227 7747

Dysregulation of lipid homeostasis is a precipitating event in the pathogenesis and progression of hepatosteatosis and metabolic syndrome. These conditions are highly prevalent in developed societies and currently have limited options for diagnostic and therapeutic intervention. Here, using a proteomic and lipidomic-wide systems genetic approach, we interrogated lipid regulatory networks in 107 genetically distinct mouse strains to reveal key insights into the control and network structure of ma ...[more]

PMID: 30814737

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Project description:Strand specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3’ termination and bi-directional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent “horsetail” stage of meiosis. Antisense production had no impact at any of these loci when the RNAi machinery was removed. Thus, far from being simply ‘genome chatter’, this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe. Thorough interrogation of the Schizosaccharomyces pombe transcriptome during sexual differentiation using strand-specific total RNA sequencing (AB SOLiD 3.0 and 3.0+). A total of 19 samples were analysed by two separate machine runs (henceforth first and second runs, respectively). In the first machine run the following 5 samples were processed (on a single sequencing slide): Vegetative haploid (strain IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following temperature shift from 25ºC to 32ºC to induce meiosis by Pat1 inactivation. In the second machine run the following 14 samples were processed (on two sequencing slides): Vegetative haploid (IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift (a biological replicate of the first machine run). In addition, asynchronous IH3365 (wild type diploid) was also sequenced to enable a series of pair-wise haploid/diploid comparisons between itself, asynchronous haploid (IH5974) and pat1.114 diploid (IH2912) at vegetative growth. Finally, to find putative targets of the two bzip transcription factors atf21 and atf31, we sequenced RNA extracts from IH8832 (atf21.delta diploid) and IH8814 (atf31.delta diploid) before (0), and 3, 5, and 10 hours after the temperature shift, while the pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift were used as reference for this analysis.