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  • 1.
    Bjerling, Pernilla
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Uppsala University / University of Copenhagen, Denmark .
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Egel, R
    Thon, G
    A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe2004In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 32, no 15, p. 4421-4428Article in journal (Refereed)
    Abstract [en]

    The mating-type region of the fission yeast Schizosaccharomyces pombe comprises three loci: mat1, mat2-P and mat3-M. mat1 is expressed and determines the mating type of the cell. mat2-P and mat3-M are two storage cassettes located in a 17 kb heterochromatic region with features identical to those of mammalian heterochromatin. Mutations in the swi6(+), clr1(+), clr2(+), clr3(+), clr4(+) and clr6(+) genes were obtained in screens for factors necessary for silencing the mat2-P-mat3-M region. swi6(+) encodes a chromodomain protein, clr3(+) and clr6(+) histone deacetylases, and clr4(+) a histone methyltransferase. Here, we describe the cloning and characterization of clr2(+). The clr2(+) gene encodes a 62 kDa protein with no obvious sequence homologs. Deletion of clr2(+) not only affects transcriptional repression in the mating-type region, but also centromeric silencing and silencing of a PolII-transcribed gene inserted in the rDNA repeats. Using chromatin immunoprecipitation, we show that Clr2 is necessary for histone hypoacetylation in the mating-type region, suggesting that Clr2 acts upstream of histone deacetylases to promote transcriptional silencing.

  • 2. Bratic, Ivana
    et al.
    Hench, Jürgen
    Södertörn University, School of Life Sciences.
    Henriksson, Johan
    Södertörn University, School of Life Sciences, Molecular biology.
    Antebi, Adam
    Bürglin, Thomas R.
    Trifunovic, Aleksandra
    Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development2009In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, no 6, p. 1817-1828Article in journal (Refereed)
    Abstract [en]

    A number of studies showed that the development and the lifespan of Caenorhabditis elegans is dependent on mitochondrial function. In this study, we addressed the role of mitochondrial DNA levels and mtDNA maintenance in development of C. elegans by analyzing deletion mutants for mitochondrial polymerase gamma (polg-1(ok1548)). Surprisingly, even though previous studies in other model organisms showed necessity of polymerase gamma for embryonic development, homozygous polg-1(ok1548) mutants had normal development and reached adulthood without any morphological defects. However, polg-1 deficient animals have a seriously compromised gonadal function as a result of severe mitochondrial depletion, leading to sterility and shortened lifespan. Our results indicate that the gonad is the primary site of mtDNA replication, whilst the mtDNA of adult somatic tissues mainly stems from the developing embryo. Furthermore, we show that the mtDNA copy number shows great plasticity as it can be almost tripled as a response to the environmental stimuli. Finally, we show that the mtDNA copy number is an essential limiting factor for the worm development and therefore, a number of mechanisms set to maintain mtDNA levels exist, ensuring a normal development of C. elegans even in the absence of the mitochondrial replicase.

  • 3. Haas, S A
    et al.
    Hild, M
    Wright, Anthony P H
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Hain, T
    Talibi, D
    Vingron, M
    Genome-scale design of PCR primers and long oligomers for DNA microarrays2003In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 31, no 19, p. 5576-5581Article in journal (Refereed)
    Abstract [en]

    During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40-70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.

  • 4. Ivanova, Natalia
    et al.
    Pavlov, Michael Y
    Bouakaz, Elli
    Ehrenberg, Måns
    Holmberg Schiavone, Lovisa
    Södertörn University, School of Life Sciences.
    Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA2005In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 33, no 11, p. 3529-3539Article in journal (Refereed)
    Abstract [en]

    In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the ribosome but there is uncertainty about the number of participating SmpB molecules as well as their ribosomal location. Here, the interaction of SmpB with ribosomal subunits and ribosomes was studied by isolation of SmpB containing complexes followed by chemical modification of ribosomal RNA with dimethyl sulfate, kethoxal and hydroxyl radicals. The results show that SmpB binds 30S and 50S subunits with 1:1 molar ratios and the 70S ribosome with 2:1 molar ratio. SmpB-footprints are similar on subunits and the ribosome. In the 30S subunit, SmpB footprints nucleotides that are in the vicinity of the P-site facing the E-site, and in the 50S subunit SmpB footprints nucleotides that are located below the L7/L12 stalk in the 3D structure of the ribosome. Based on these results, we suggest a mechanism where two molecules of SmpB interact with tmRNA and the ribosome during trans-translation. The first SmpB molecule binds near the factor-binding site on the 50S subunit helping tmRNA accommodation on the ribosome, whereas the second SmpB molecule may functionally substitute for a missing anticodon stem-loop in tmRNA during later steps of trans-translation.

  • 5.
    Walfridsson, Julian
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Bjerling, Pernilla
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Thalen, Maria
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Yoo, Eung-Jae
    Seoul National University, Seoul, Korea.
    Park, Sang Dai
    Seoul national University, Seoul, Korea.
    Ekwall, Karl
    Södertörn University, School of Life Sciences. Karolinska Institute.
    The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres2005In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 33, no 9, p. 2868-2879Article in journal (Refereed)
    Abstract [en]

    Centromeres of fission yeast are arranged with a central core DNA sequence flanked by repeated sequences. The centromere-associated histone H3 variant Cnp1 ( SpCENP-A) binds exclusively to central core DNA, while the heterochromatin proteins and cohesins bind the surrounding outer repeats. CHD (chromo-helicase/ ATPase DNA binding) chromatin remodeling factors were recently shown to affect chromatin assembly in vitro. Here, we report that the CHD protein Hrp1 plays a key role at fission yeast centromeres. The hrp1&UDelta; mutant disrupts silencing of the outer repeats and central core regions of the centromere and displays chromosome segregation defects characteristic for dysfunction of both regions. Importantly, Hrp1 is required to maintain high levels of Cnp1 and low levels of histone H3 and H4 acetylation at the central core region. Hrp1 interacts directly with the centromere in early S-phase when centromeres are replicated, suggesting that Hrp1 plays a direct role in chromatin assembly during DNA replication.

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  • harvard-anglia-ruskin-university
  • apa-old-doi-prefix.csl
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