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| 2. |
- Arvestad, Lars, et al.
(author)
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Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans : annotation, bioinformatic classification of unknown transcripts and analysis of expression levels
- 2005
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In: Insect molecular biology (Print). - : Wiley. - 0962-1075 .- 1365-2583. ; 14:6, s. 689-695
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Journal article (peer-reviewed)abstract
- Expressed sequence tags (ESTs) were generated from two Chironomus tentans cDNA libraries, constructed from an embryo epithelial cell line and from larva midgut tissue. 8584 5'-end ESTs were generated and assembled into 3110 tentative unique transcripts, providing the largest contribution of C. tentans sequences to public databases to date. Annotation using BLAST gave 1975 (63.5%) transcripts with a significant match in the major gene/protein databases, 1170 with a best match to Anopheles gambiae and 480 to Drosophila melanogaster. 1091 transcripts (35.1%) had no match to any database. Studies of open reading frames suggest that at least 323 of these contain a coding sequence, indicating that a large proportion of the genes in C. tentans belong to previously unknown gene families.
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| 3. |
- Aspegren, Anders
(author)
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Nuclear Organization of Gene Expression in Adenovirus Infected Cells
- 2001
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Doctoral thesis (other academic/artistic)abstract
- Adenovirus infected cells provide a good model system for studying nuclear organization during RNA production and transport. This thesis is focused on the dynamic organization of splicing factors during the late phase of Adenovirus infection in HeLa cells, the nuclear localization of viral RNA, and the pathway used for viral RNA transport to the cytoplasm.Splicing factors are relocalized from interchromatin granule clusters to sites of transcription in Adenovirus infected cells at intermediate times of infection. Later, splicing factors and viral RNA accumulate posttranscriptionally in interchromatin granule clusters. The release of the splicing factors from transcription sites was energy dependent or preceded by energy requiring mechanisms. Our data indicated that phosphorylation events inhibited by staurosporine, and 3' cleavage of the transcript are two possible mechanisms involved prior to the release of the RNP complex from transcription sites.A viral protein derived from orf6 of early region 4, 34K, is important for the nuclear stability and transport of late viral mRNA derived from the major late transcription unit. A viral mutant lacking this region is defective for posttranscriptional accumulation of viral mRNA in interchromatin granule clusters, and for the accumulation of viral RNA in the cytoplasm. These results suggest that posttranscriptional accumulation of viral RNA in interchromatin granule clusters may contribute to the maturation of the RNP complex or sorting of RNAs and proteins, to prepare the final RNP complex for transport to the cytoplasm.A previous model suggested that adenoviral late mRNA is transported to the cytoplasm by utilizing the CRM-1 pathway. This pathway can be blocked by the drug leptomycin B. The data presented in paper IV suggests that this model might not be applicable, since leptomycin B did not inhibit adenoviral late gene expression.
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| 4. |
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| 5. |
- Björk, Petra, et al.
(author)
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A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis
- 2002
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In: Molecular Biology of the Cell. - 1059-1524 .- 1939-4586. ; 13:10, s. 3683-3695
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Journal article (peer-reviewed)abstract
- Synthesis of the ribosomal subunits from pre-rRNA requires a large number of trans-acting proteins and small nucleolar ribonucleoprotein particles to execute base modifications, RNA cleavages, and structural rearrangements. We have characterized a novel protein, RNA-binding domain-1 (RBD-1), that is involved in ribosome biogenesis. This protein contains six consensus RNA-binding domains and is conserved as to sequence, domain organization, and cellular location from yeast to human. RBD-1 is essential in Caenorhabditis elegans. In the dipteran Chironomus tentans, RBD-1 (Ct-RBD-1) binds pre-rRNA in vitro and anti-Ct-RBD-1 antibodies repress pre-rRNA processing in vivo. Ct-RBD-1 is mainly located in the nucleolus in an RNA polymerase I transcription-dependent manner, but it is also present in discrete foci in the interchromatin and in the cytoplasm. In cytoplasmic extracts, 20-30% of Ct-RBD-1 is associated with ribosomes and, preferentially, with the 40S ribosomal subunit. Our data suggest that RBD-1 plays a role in structurally coordinating pre-rRNA during ribosome biogenesis and that this function is conserved in all eukaryotes.
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| 6. |
- Björk, Petra, et al.
(author)
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Gene Expression in Polytene Nuclei
- 2009. - 2
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In: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 9781603274609 ; , s. 29-53
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Book chapter (other academic/artistic)abstract
- Gene expression in eukaryotic cells is a multi-step process. Many of the steps are both co-ordinated and quality controlled. For example, transcription is closely coupled to pre-messenger RNA (mRNA)-protein assembly, pre-mRNA processing, surveillance of the correct synthesis of messenger ribonucleoprotein (mRNP), and export. The coordination appears to be exerted through dynamic interactions between components of the transcription, processing, surveillance, and export machineries. Our knowledge is so far incomplete about these molecular interactions and where in the nucleus they take place. It is therefore essential to analyze the intranuclear steps of gene expression in vivo. Polytene nuclei are exceptionally large and contain chromosomes and individual genes that can be structurally analyzed in situ during ongoing transcription. Furthermore, they contain gene-specific pre-mRNPs/mRNPs that can be visualised and analyzed as they are synthesised on the gene and then followed on their path to the cytoplasm. We describe methods for investigating the structure and composition of active chromatin and gene-specific pre-mRNPs/mRNPs in the context of analyses of gene expression processes in the nuclei of polytene cells.
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| 7. |
- Björk, Petra, et al.
(author)
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Integration of mRNP formation and export
- 2017
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In: Cellular and Molecular Life Sciences (CMLS). - : Springer Science and Business Media LLC. - 1420-682X .- 1420-9071. ; 74:16, s. 2875-2897
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Research review (peer-reviewed)abstract
- Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA-protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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| 8. |
- Björk, Petra, et al.
(author)
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Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo
- 2015
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In: Journal of Cell Biology. - : Rockefeller University Press. - 0021-9525 .- 1540-8140. ; 211:1, s. 63-75
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Journal article (peer-reviewed)abstract
- 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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| 9. |
- Björk, Petra, et al.
(author)
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Mechanisms of mRNA export
- 2014
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In: Seminars in Cell and Developmental Biology. - : Elsevier BV. - 1084-9521 .- 1096-3634. ; 32, s. 47-54
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Research review (peer-reviewed)abstract
- Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license
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| 10. |
- Björk, Petra, et al.
(author)
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Specific combinations of SR proteins associate with single pre-messenger RNAs in vivo and contribute different functions
- 2009
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In: Journal of Cell Biology. - : Rockefeller University Press. - 0021-9525 .- 1540-8140. ; 184:4, s. 555-568
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Journal article (peer-reviewed)abstract
- Serine/arginine-rich (SR) proteins are required for messenger RNA (mRNA) processing, export, surveillance, and translation. We show that in Chironomus tentans, nascent transcripts associate with multiple types of SR proteins in specific combinations. Alternative splicing factor (ASF)/SF2, SC35, 9G8, and hrp45/SRp55 are all present in Balbiani ring (BR) pre-messenger ribonucleoproteins (mRNPs) preferentially when introns appear in the pre-mRNA and when cotranscriptional splicing takes place. However, hrp45/SRp55 is distributed differently in the pre-mRNPs along the gene compared with ASF/SF2, SC35, and 9G8, suggesting functional differences. All four SR proteins are associated with the BR mRNPs during export to the cytoplasm. Interference with SC35 indicates that SC35 is important for the coordination of splicing, transcription, and 3' end processing and also for nucleocytoplasmic export. ASF/SF2 is associated with polyribosomes, whereas SC35, 9G8, and hrp45/SRp55 cosediment with mono-ribosomes. Thus, individual endogenous pre-mRNPs/mRNPs bind multiple types of SR proteins during transcription, and these SR proteins accompany the mRNA and play different roles during the gene expression pathway in vivo.
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