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Björk P, Persson JO, Wieslander L. Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo. J Cell Biol 2016; 211:63-75. [PMID: 26459599 PMCID: PMC4602041 DOI: 10.1083/jcb.201412017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The exon junction core complex associates with Balbiani ring (BR) premRNPs during transcription and in relation to splicing, whereas the export factor NXF1 is recruited in the interchromatin, and BR mRNPs become export competent only after passage through the interchromatin. Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-Olov Persson
- Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 2014; 15:819. [PMID: 25261295 PMCID: PMC4192438 DOI: 10.1186/1471-2164-15-819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/22/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes. RESULTS The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations. CONCLUSIONS We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.
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Affiliation(s)
- Alexey Kutsenko
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Thomas Svensson
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Björn Nystedt
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE 752 37 Uppsala, Sweden
| | - Joakim Lundeberg
- />Science for Life Laboratory, KTH, Royal Institute of Technology, Science for Life Laboratory, SE 171 65 Solna, Sweden
| | - Petra Björk
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Erik Sonnhammer
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Stefania Giacomello
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Neus Visa
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Lars Wieslander
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
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