Genome-wide analysis of mRNAs associated with mouse peroxisomes.
RNA 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.



In 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.



This 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.
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, 138671, Singapore.
Aliaksandr A
AA
Yarmishyn
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, 138671, Singapore.
Maksym
M
Kremenskoy
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, 138671, Singapore.
Arsen O
AO
Batagov
Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, 138673, Singapore.
Axel
A
Preuss
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, 138671, Singapore.
Jin Huei
JH
Wong
Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, 138671, Singapore. Kurochkin.Igor@sysmex.co.jp.|, Present address: Sysmex Corporation, 4-4-4 Takatsukadai, Nishi-ku, Kobe, 651-2271, Japan. Kurochkin.Igor@sysmex.co.jp.
Igor V
IV
Kurochkin
D000818:Animals; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D042541:Intracellular Space; D013058:Mass Spectrometry; D051379:Mice; D020675:Peroxisomes / Q000378:metabolism*; D034443:RNA Transport; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome
D012333:RNA, Messenger
Cholesterol biosynthesis; DNA microarrays; Peroxisomes; RNA localization; Subcellular localization; Translation