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1.
  • Bustamante, Mariona, et al. (författare)
  • A genome-wide association meta-analysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways.
  • 2016
  • Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 25:18, s. 4127-4142
  • Tidskriftsartikel (refereegranskat)abstract
    • More than a million childhood diarrhoeal episodes occur worldwide each year, and in developed countries a considerable part of them are caused by viral infections. In this study, we aimed to search for genetic variants associated with diarrhoeal disease in young children by meta-analyzing genome-wide association studies, and to elucidate plausible biological mechanisms. The study was conducted in the context of the Early Genetics and Lifecourse Epidemiology (EAGLE) consortium. Data about diarrhoeal disease in two time windows (around 1 year of age and around 2 years of age) was obtained via parental questionnaires, doctor interviews or medical records. Standard quality control and statistical tests were applied to the 1000 Genomes imputed genotypic data. The meta-analysis (N = 5758) followed by replication (N = 3784) identified a genome-wide significant association between rs8111874 and diarrhoea at age 1 year. Conditional analysis suggested that the causal variant could be rs601338 (W154X) in the FUT2 gene. Children with the A allele, which results in a truncated FUT2 protein, had lower risk of diarrhoea. FUT2 participates in the production of histo-blood group antigens and has previously been implicated in the susceptibility to infections, including Rotavirus and Norovirus Gene-set enrichment analysis suggested pathways related to the histo-blood group antigen production, and the regulation of ion transport and blood pressure. Among others, the gastrointestinal tract, and the immune and neuro-secretory systems were detected as relevant organs. In summary, this genome-wide association meta-analysis suggests the implication of the FUT2 gene in diarrhoeal disease in young children from the general population.
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2.
  • Bonilla, Carolina (författare)
  • Studies of histone modification systems in Schizosaccharomyces pombe
  • 2010
  • Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The genetic information in every cell is carried in the DNA. In eukaryotes the DNA is wrapped twice around proteins called histones forming a repeating unit called the nucleosome, in fibers known as chromatin. Nucleosomes are folded into higher order structures forming the chromosomes. The chromatin can be more or less compacted, controlling the accessibility of the DNA to ensure correct gene expression. Histones have long N-terminal tails, which can be covalently modified by different modifying enzymes. Different types of histone modifications are linked to the different functional properties of chromatin. In this thesis we have studied three histone modification systems in the model organism Schizosaccharomyces pombe (fission yeast). In paper I, the Rpb7 subunit of the RNA Pol II polymerase function is analyzed in cells with a missense mutation in the rpb7 gene (rpb7-G150D). Chromatin Immunoprecipitation showed decreased levels of methylation of histone H3 at lysine 9 (H3K9me2), heterochromatin protein Swi6 and cohesin Rad21, which is the cause of lagging chromosomes and defects in chromosome segregation in rpb7-G150D. Analysis of centromeric forward and reverse pre-siRNA transcripts showed accumulation in the dcr1delta mutant. In rpb7-G150D the reverse transcripts decreased to 25% of wild type levels. In the double mutant dcr1delta/rpb7-G150D the reverse transcript levels remained low indicating that Rpb7 functions upstream of Dcr1 in the RNAi pathway that maintains the H3K9me2 in heterochromatin. More specifically, we show that Rpb7 is required for initiation of pre-siRNA transcription in this pathway. In paper II, we show that the amino-oxidase family demethylases Lsd1 and Lsd2 from fission yeast are able to demethylate H3K9 but not H3K4 in vitro. Microarray studies showed increased H3K9me2 in 8,2% of the genes both in promoter and coding regions in the lsd1delta knock-out and 3,8% of the genes also showed increased H3K4me2 in promoter regions. These genes also tend to become upregulated in lsd1delta. Conversely, the down-regulated genes in lsd1delta showed increased levels of H3K9me2, consistent with the notion that H3K9me2 is needed for gene repression and silencing. Our data also suggest that Lsd1 and the HDAC Clr6 cooperate to repression of genes. Thus, Lsd1 seems to have demethylase activity at both H3K4 and K9 in vivo but in vitro only K9me activity was detected, suggesting that additional factors are directing Lsd1 specificity in vivo. In paper III, we found that Pst3, one of the three Sin3 homologs in fission yeast, is localized to the entire nuclear space, including the nucleolar core. The deletion of the pst3+ gene affects genome stability, and causes sporulation defects, altered nucleolar structure and chomosome mis-segregation. Our data indicate that genome stability requires an established heterochromatic environment at rDNA repeats maintained by the Clr6 HDAC and Pst3. Pst3 co-purifies with two different Clr6 multi-protein complexes, suggesting that Clr6 HDAC complexes are dynamic. We show that Pst3 is associated with rDNA chromatin and is involved in rDNA silencing. Interestingly, Pst3 is specifically required for repression of endogenous Pol II mediated non-coding RNA transcripts within the rDNA spacer region.
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3.
  • Djupedal, Ingela, et al. (författare)
  • RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing
  • 2005
  • Ingår i: Genes & Development. - : Cold Spring Harbor Laboratory. - 0890-9369 .- 1549-5477. ; 19:19, s. 2301-2306
  • Tidskriftsartikel (refereegranskat)abstract
    • Fission yeast centromeric repeats are transcribed into small interfering RNA (siRNA) precursors (pre-siRNAs), which are processed by Dicer to direct heterochromatin formation. Recently, Rpb1 and Rpb2 subunits of RNA polymerase II (RNA Pol II) were shown to mediate RNA interference (RNAi)-directed chromatin modification but did not affect pre-siRNA levels. Here we show that another Pol II subunit, Rpb7 has a specific role in presiRNA transcription. We define a centromeric presiRNA promoter from which initiation is exquisitely sensitive to the rpb7-G150D mutation. In contrast to other Pol II subunits, Rpb7 promotes pre-siRNA transcription required for RNAi-directed chromatin silencing.
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4.
  • Dunleavy, Elaine M., et al. (författare)
  • A NASP (N1/N2)-related protein, Sim3, binds CENP-A and is required for its deposition at fission yeast Centromeres
  • 2007
  • Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 28:6, s. 1029-1044
  • Tidskriftsartikel (refereegranskat)abstract
    • A defining feature of centromeres is the presence of the histone H3 variant CENP-A(Cnp1). It is not known how CENP-A(Cnp1) is specifically delivered to, and assembled into, centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast, we identified Sim3. Sim3 is homologous to known histone binding proteins NASP(Human) and N1/N2(Xenopus) and aligns with Hif1(S. cerevisiae), defining the SHNi-TPR family. Sim3 is distributed throughout the nucleoplasm, yet it associates with CENP-A(Cnp1) and also binds H3. Cells defective in Sim3 function have reduced levels of CENP-A(CnP1) at centromeres (and increased H3) and display chromosome segregation defects. Sim3 is required to allow newly synthesized CENP-A(Cnp1) to accumulate at centromeres in S and G2 phase-arrested cells in a replication-independent mechanism. We propose that one function of Sim3 is to act as an escort that hands off CENP-A(Cnp1) to chromatin assembly factors, allowing its incorporation into centromeric chromatin.
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5.
  • Durand-Dubief, Mickael, et al. (författare)
  • Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing
  • 2007
  • Ingår i: EMBO Journal. - : Wiley. - 0261-4189 .- 1460-2075. ; 26:10, s. 2477-2488
  • Tidskriftsartikel (refereegranskat)abstract
    • Expression profiling, ChiP-CHIP and phenotypic analysis were used to investigate the functional relationships of class III NAD(+)-dependent HDACs (Sirtuins) in fission yeast. We detected significant histone acetylation increases in Sirtuin mutants at their specific genomic binding targets and were thus able to identify an in vivo substrate preference for each Sirtuin. At heterochromatic loci, we demonstrate that although Hst2 is mainly cytoplasmic, a nuclear pool of Hst2 colocalizes with the other Sirtuins at silent regions (cen, mat, tel, rDNA), and that like the other Sirtuins, Hst2 is required for rDNA and centromeric silencing. Interestingly we found specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation. Hst2 directly represses genes involved in transport and membrane function, whereas Hst4 represses amino-acid biosynthesis genes and Tf2 retrotransposons. A specific role for Hst4 in Tf2 50 mRNA processing was revealed. Thus, Sirtuins share functions at many genomic targets, but Hst2 and Hst4 have also evolved unique functions in gene regulation.
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6.
  • Greenhalgh, David G., et al. (författare)
  • Surviving Sepsis After Burn Campaign
  • 2023
  • Ingår i: Burns. - : Elsevier. - 0305-4179 .- 1879-1409. ; 49:7, s. 1487-1524
  • Tidskriftsartikel (refereegranskat)abstract
    • Introduction: The Surviving Sepsis Campaign was developed to improve outcomes for all patients with sepsis. Despite sepsis being the primary cause of death after thermal injury, burns have always been excluded from the Surviving Sepsis efforts. To improve sepsis outcomes in burn patients, an international group of burn experts developed the Surviving Sepsis After Burn Campaign (SSABC) as a testable guideline to improve burn sepsis outcomes. Methods: The International Society for Burn Injuries (ISBI) reached out to regional or na-tional burn organizations to recommend members to participate in the program. Two members of the ISBI developed specific "patient/population, intervention, comparison and out-come" (PICO) questions that paralleled the 2021 Surviving Sepsis Campaign [1]. SSABC parti-cipants were asked to search the current literature and rate its quality for each topic. At the Congress of the ISBI, in Guadalajara, Mexico, August 28, 2022, a majority of the participants met to create "statements" based on the literature. The "summary statements" were then sent to all members for comment with the hope of developing an 80% consensus. After four reviews, a consensus statement for each topic was created or "no consensus" was reported. Results: The committee developed sixty statements within fourteen topics that provide guidance for the early treatment of sepsis in burn patients. These statements should be used to improve the care of sepsis in burn patients. The statements should not be considered as "static" comments but should rather be used as guidelines for future testing of the best treatments for in burn should be on a basis. Conclusion: Members of the burn community from the around the world have developed the Surviving Sepsis After Burn Campaign guidelines with the goal of improving the outcome of sepsis in burn patients. (c) 2023 Elsevier Ltd and ISBI. All rights reserved.
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7.
  • Opel, Michael, et al. (författare)
  • Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1
  • 2007
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 2:4
  • Tidskriftsartikel (refereegranskat)abstract
    • In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up-and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1(+) gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1 Delta strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression.
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8.
  • Schramke, V, et al. (författare)
  • RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription
  • 2005
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 435:7046, s. 1275-1279
  • Tidskriftsartikel (refereegranskat)abstract
    • RNA interference (RNAi) acts on long double-stranded RNAs (dsRNAs) in a variety of eukaryotes to generate small interfering RNAs that target homologous messenger RNA, resulting in their destruction. This process is widely used to 'knock-down' the expression of genes of interest to explore phenotypes(1-3). In plants(3-5), fission yeast(6-8), ciliates(9,10), flies(11) and mammalian cells(12,13), short interfering RNAs (siRNAs) also induce DNA or chromatin modifications at the homologous genomic locus, which can result in transcriptional silencing or sequence elimination(14). siRNAs may direct DNA or chromatin modification by siRNA - DNA interactions at the homologous locus(4,5). Alternatively, they may act by interactions between siRNA and nascent transcript(15,16). Here we show that in fission yeast ( Schizosaccharomyces pombe), chromatin modifications are only directed by RNAi if the homologous DNA sequences are transcribed. Furthermore, transcription by exogenous T7 polymerase is not sufficient. Ago1, a component of the RNAi effector RISC/RITS complex, associates with target transcripts and RNA polymerase II. Truncation of the regulatory carboxy-terminal domain (CTD) of RNApol II disrupts transcriptional silencing, indicating that, like other RNA processing events(17-19), RNAi-directed chromatin modification is coupled to transcription.
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9.
  • Sinha, Indranil, et al. (författare)
  • Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast
  • 2010
  • Ingår i: Epigenomics. - 1750-1911. ; 2:3, s. 377-393
  • Tidskriftsartikel (refereegranskat)abstract
    • To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. Using clustering analysis and gene ontology search tools, we identified promoter histone modification patterns that characterize several classes of gene function. For example, gene promoters of genes involved in cytokinesis have high H3K36me2 and low H3K4me2, whereas the converse pattern is found ar promoters of gene involved in positive regulation of the cell cycle. We detected acetylation of H4 preferentially at lysine 16 followed by lysine 12, 8 and 5. Our analysis shows that this H4 acetylation bias in the coding regions is dependent upon gene length and linked to gene expression. Our analysis also reveals a role for H3K36 methylation at gene promoters where it functions in a crosstalk between the histone methyltransferase Set2(KMT3) and the histone deacetylase Clr6, which removes H3K27ac leading to repression of transcription. Conclusion: Histone modification patterns could be linked to gene expression in fission yeast.
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