Genome-wide analysis of mRNAs associated with mouse peroxisomes

Abstract

BackgroundRNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.ResultsIn this study we performed the genome wide transcriptome analysis of peroxisome preparations from the mouse liver using microarrays. We demonstrate that RNA is absent inside peroxisomes, however it is associated at their exterior via the noncovalent contacts with the membrane proteins. We detect enrichment of specific sets of transcripts in two preparations of peroxisomes, purified with different degrees of stringency. Importantly, among these were mRNAs encoding bona fide peroxisomal proteins, such as peroxins and peroxisomal matrix enzymes involved in beta-oxidation of fatty acids and bile acid biosynthesis. The top-most enriched mRNA, whose association with peroxisomes we confirm microscopically was Hmgcs1, encoding 3-hydroxy-3-methylglutaryl-CoA synthase, a crucial enzyme of cholesterol biosynthesis pathway. We observed significant representation of mRNAs encoding mitochondrial and secreted proteins in the peroxisomal fractions.ConclusionsThis is a pioneer genome-wide study of localization of mRNAs to peroxisomes that provides foundation for more detailed dissection of mechanisms of RNA targeting to subcellular compartments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3330-x) contains supplementary material, which is available to authorized users.

Local Translation in Axons: When Membraneless RNP Granules Meet Membrane-Bound Organelles

“…By targeting their bound RNAs to specialized organelles or subcellular micro-domains, RBPs may thus favor stimuli-specific spatio-temporal responses. Although a systematic profiling of organelle-associated transcriptomes has not been performed in neuronal cells, distinct RBPs and mRNA populations were found associated with different types of membrane-bound organelles, consistent with such a model (Peter et al, 2011; Todd et al, 2013; Debaisieux et al, 2016; Yarmishyn et al, 2016; Liao et al, 2019). Analysis of mRNAs co-precipitating with COPIa, for example, revealed the presence of more than a thousand of mRNAs, 8 to 10% overlapping with the axonal transcriptome and about the same percentage encoding cytoskeletal components and/or regulators (Todd et al, 2013).…”

Molecular mechanisms behind mRNA localization in axons

“…As other organelles present in axons (e.g. mitochondria, endoplasmic reticulum, peroxisomes) have also been shown to harbour mRNAs on their membrane [ 171 , 186 – 188 ], these results open the possibility that hitchhiking on membranes could be an important regulatory process in axonal mRNA trafficking.…”

Drosophila mRNA Localization During Later Development: Past, Present, and Future

“…It has been proposed that the association of mRNAs encoding cytoplasmic Pex proteins with peroxisomes foster local translation and Insertion incorporation of peroxisomal membrane proteins (Weis et al, 2013 ; Haimovich et al, 2016a ). However, other mRNAs associated with the exterior membrane of peroxisomes isolated from mouse liver were also identified (Yarmishyn et al, 2016 ). This included mRNAs encoding Pex6, Pex11a /b, and Pex19 , and Peroxisomal Membrane Protein 70 kDa (Pmp 70) as well as mRNAs encoding homologs to several peroxisomal localized enzymes including Hmgcs1, Acaa1a / b, Hsd14b4, Paox, Nudt7, Acox, Baat , and Acsl5 as peroxisome associated (Yarmishyn et al, 2016 ).…”

“…However, other mRNAs associated with the exterior membrane of peroxisomes isolated from mouse liver were also identified (Yarmishyn et al, 2016 ). This included mRNAs encoding Pex6, Pex11a /b, and Pex19 , and Peroxisomal Membrane Protein 70 kDa (Pmp 70) as well as mRNAs encoding homologs to several peroxisomal localized enzymes including Hmgcs1, Acaa1a / b, Hsd14b4, Paox, Nudt7, Acox, Baat , and Acsl5 as peroxisome associated (Yarmishyn et al, 2016 ). However, FISH was used to confirm peroxisome localization of only one of these mRNAs, Hmgcs1 (Yarmishyn et al, 2016 ).…”

“…This included mRNAs encoding Pex6, Pex11a /b, and Pex19 , and Peroxisomal Membrane Protein 70 kDa (Pmp 70) as well as mRNAs encoding homologs to several peroxisomal localized enzymes including Hmgcs1, Acaa1a / b, Hsd14b4, Paox, Nudt7, Acox, Baat , and Acsl5 as peroxisome associated (Yarmishyn et al, 2016 ). However, FISH was used to confirm peroxisome localization of only one of these mRNAs, Hmgcs1 (Yarmishyn et al, 2016 ). While the prevalence of mRNA localization of peroxisome mRNAs is striking and suggests a functional role, the localization pattern of these mRNAs encompasses apical and basal restriction, perinuclear patterns and cytoplasmic foci in embryo ectoderm and various larval tissues (Wilk et al, 2016 ).…”