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Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

ABSTRACT: Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

PROVIDER: PRJNA812862 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18220721.fastq.gz	Fastqsanger.gz
	SRR18220722.fastq.gz	Fastqsanger.gz
	SRR18220723.fastq.gz	Fastqsanger.gz
	SRR18220724.fastq.gz	Fastqsanger.gz
	SRR18220725.fastq.gz	Fastqsanger.gz

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Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

Project description:The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides in metabolism—insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1)—microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B a metabolic regulator and part of the brain-adipose axis. Furthermore, we showed that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 25 from mouse serum. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that serum levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

2022-12-13 | GSE197909 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

Project description:Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

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Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

2022-12-13 | GSE198107 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

Project description:Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

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Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins.

Project description:Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.

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Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-13 | GSE198109 | GEO

Improved Super-Resolution Ribosome Profiling Reveals Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.

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DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts [Ribo-Seq]

Project description:To investigate the effect of Decitabine and SB939 treatment on the expression of endoretroviral elements. We treated NCI-H1299 cells with DMSO or a combination of Decitabine and SB939 and performed Ribo-seq. This data was used to identify novel ORFs expressed from endoretroviral elements derived transcripts.

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Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli (Ribo-Seq Caco2)

Project description:Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Here, we examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells (PBMCs), and then used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. This approach reveals a number of new microproteins worthy of additional functional characterization, and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.

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Accurate detection of short and long active ORFs using Ribo-seq data.

Project description:MotivationRibo-seq, a technique for deep-sequencing ribosome-protected mRNA fragments, has enabled transcriptome-wide monitoring of translation in vivo. It has opened avenues for re-evaluating the coding potential of open reading frames (ORFs), including many short ORFs that were previously presumed to be non-translating. However, the detection of translating ORFs, specifically short ORFs, from Ribo-seq data, remains challenging due to its high heterogeneity and noise.ResultsWe present ribotricer, a method for detecting actively translating ORFs by directly leveraging the three-nucleotide periodicity of Ribo-seq data. Ribotricer demonstrates higher accuracy and robustness compared with other methods at detecting actively translating ORFs including short ORFs on multiple published datasets across species inclusive of Arabidopsis, Caenorhabditis elegans, Drosophila, human, mouse, rat, yeast and zebrafish.Availability and implementationRibotricer is available at https://github.com/smithlabcode/ribotricer. All analysis scripts and results are available at https://github.com/smithlabcode/ribotricer-results.Supplementary informationSupplementary data are available at Bioinformatics online.

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