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  • 1
    Language: English
    In: Nature communications, 2014-06-09, Vol.5 (1), p.4091-4091
    Description: DNA double-strand break (DSB) repair is a highly regulated process performed predominantly by non-homologous end joining (NHEJ) or homologous recombination (HR) pathways. How these pathways are coordinated in the context of chromatin is unclear. Here we uncover a role for histone H3K36 modification in regulating DSB repair pathway choice in fission yeast. We find Set2-dependent H3K36 methylation reduces chromatin accessibility, reduces resection and promotes NHEJ, while antagonistic Gcn5-dependent H3K36 acetylation increases chromatin accessibility, increases resection and promotes HR. Accordingly, loss of Set2 increases H3K36Ac, chromatin accessibility and resection, while Gcn5 loss results in the opposite phenotypes following DSB induction. Further, H3K36 modification is cell cycle regulated with Set2-dependent H3K36 methylation peaking in G1 when NHEJ occurs, while Gcn5-dependent H3K36 acetylation peaks in S/G2 when HR prevails. These findings support an H3K36 chromatin switch in regulating DSB repair pathway choice.
    Subject(s): Acetylation ; Acetyltransferases - metabolism ; Chromatin - metabolism ; DNA End-Joining Repair ; DNA Repair ; DNA, Fungal - metabolism ; Histone-Lysine N-Methyltransferase - metabolism ; Histones - metabolism ; Methylation ; Recombinational DNA Repair ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - metabolism
    ISSN: 2041-1723
    E-ISSN: 2041-1723
    Source: Nature Open Access
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 2
    Language: English
    In: Cell reports (Cambridge), 2021-10-19, Vol.37 (3), p.109835-109835
    Description: The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell-cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline-specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell-cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function. [Display omitted] •THAP domain proteins LIN-36 and LIN-15B cooperate with the Rb-DREAM complex•LIN-36 and LIN-15B repress distinct sets of DREAM targets via different mechanisms•With LIN-36, DREAM represses cell-cycle genes through gene body enrichment of H2A.Z•With LIN-15B, DREAM represses germline genes through H3K9me2 promoter marking Gal et al. show that two THAP domain proteins are key mediators of retinoblastoma-DREAM function in C. elegans, repressing distinct targets by different mechanisms. With LIN-36, DREAM represses cell-cycle genes through gene body enrichment of H2A.Z; with LIN-15B, DREAM represses germline-specific genes in the soma through H3K9me2 promoter marking.
    Subject(s): Animals ; Animals, Genetically Modified ; Caenorhabditis elegans - genetics ; Caenorhabditis elegans - metabolism ; Caenorhabditis elegans Proteins - genetics ; Caenorhabditis elegans Proteins - metabolism ; Cell Cycle Proteins - genetics ; Cell Cycle Proteins - metabolism ; DNA Methylation ; DREAM ; E2F Transcription Factors - genetics ; E2F Transcription Factors - metabolism ; Gene Expression Regulation ; H2A.Z ; H3K9me2 ; Histones - genetics ; Histones - metabolism ; lin-15B ; lin-35 ; lin-36 ; Promoter Regions, Genetic ; Protein Binding ; Protein Interaction Domains and Motifs ; quiescence ; retinoblastoma ; Retinoblastoma Protein - genetics ; Retinoblastoma Protein - metabolism ; THAP ; Transcription Factors - genetics ; Transcription Factors - metabolism ; transcriptional repression
    ISSN: 2211-1247
    E-ISSN: 2211-1247
    Source: Alma/SFX Local Collection
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 3
    Language: English
    In: EMBO reports, 2016-01, Vol.17 (1), p.79-93
    Description: Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA‐ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis‐positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re‐establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis‐segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome‐wide. Synopsis Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function. Loss of Abo1 results in a global reduction of histone levels. Nucleosome organisation at gene sequences is perturbed in the absence of Abo1. Abo1 co‐purifies with FACT and suppresses cryptic intragenic transcription. Abo1 function is required for silent centromeric heterochromatin and accurate chromosome segregation. Loss of Abo1 function—a bromodomain AAA‐ATPase—results in global perturbations to nucleosome occupancy and organisation with effects on transcription and heterochromatin function.
    Subject(s): Abo1 ; Adenosine Triphosphatases - chemistry ; Adenosine Triphosphatases - genetics ; Adenosine Triphosphatases - metabolism ; bromodomain AAA-ATPases ; Chromatin ; Chromatin - genetics ; Chromatin - metabolism ; Chromatin Assembly and Disassembly ; Chromatin, Epigenetics, Genomics & Functional Genomics ; Chromosomal Proteins, Non-Histone - metabolism ; Chromosome Segregation ; DNA, Intergenic ; Gene Silencing ; Genes ; Genomes ; Histone Chaperones - genetics ; Histone Chaperones - metabolism ; Histones - genetics ; Histones - metabolism ; nucleosome mapping ; Nucleosomes - genetics ; Nucleosomes - metabolism ; Promoter Regions, Genetic ; RNA Polymerase II - genetics ; Schizosaccharomyces - genetics ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe ; Schizosaccharomyces pombe Proteins - chemistry ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Transcription Factors - metabolism ; Transcription, Genetic
    ISSN: 1469-221X
    E-ISSN: 1469-3178
    Source: HighWire Press (Free Journals)
    Source: Wiley Online Library All Journals
    Source: PubMed Central
    Source: Get It Now
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  • 4
    Language: English
    In: Cell cycle (Georgetown, Tex.), 2015-01-02, Vol.14 (1), p.123-134
    Description: HIRA is an evolutionarily conserved histone chaperone that mediates replication-independent nucleosome assembly and is important for a variety of processes such as cell cycle progression, development, and senescence. Here we have used a chromatin sequencing approach to determine the genome-wide contribution of HIRA to nucleosome organization in Schizosaccharomyces pombe. Cells lacking HIRA experience a global reduction in nucleosome occupancy at gene sequences, consistent with the proposed role for HIRA in chromatin reassembly behind elongating RNA polymerase II. In addition, we find that at its target promoters, HIRA commonly maintains the full occupancy of the −1 nucleosome. HIRA does not affect global chromatin structure at replication origins or in rDNA repeats but is required for nucleosome occupancy in silent regions of the genome. Nucleosome organization associated with the heterochromatic (dg-dh) repeats located at the centromere is perturbed by loss of HIRA function and furthermore HIRA is required for normal nucleosome occupancy at Tf2 LTR retrotransposons. Overall, our data indicate that HIRA plays an important role in maintaining nucleosome architecture at both euchromatic and heterochromatic loci.
    Subject(s): Chromatin ; Chromatin - metabolism ; Chromatin Assembly and Disassembly ; heterochromatin ; HIRA ; histone chaperone ; Histones - metabolism ; nucleosome assembly ; Nucleosomes - metabolism ; Promoter Regions, Genetic ; Reports ; RNA Polymerase II - genetics ; RNA Polymerase II - metabolism ; S. pombe ; Schizosaccharomyces - metabolism ; Schizosaccharomyces pombe Proteins - genetics ; Schizosaccharomyces pombe Proteins - metabolism ; Transcription Factors - genetics ; Transcription Factors - metabolism
    ISSN: 1538-4101
    E-ISSN: 1551-4005
    Source: Taylor & Francis Open Access
    Source: PubMed Central
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  • 5
    Language: English
    In: EMBO reports, 2016-01, Vol.17 (1), p.79-93
    ISSN: 1469-221X
    E-ISSN: 1469-3178
    Source: HighWire Press (Free Journals)
    Source: Wiley Online Library All Journals
    Source: PubMed Central
    Source: Get It Now
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  • 6
    Language: English
    Description: HIRA is an evolutionarily conserved histone H3-H4 chaperone that mediates replication-independent nucleosome deposition and is important in a variety of contexts such as transcription, the response to DNA damage and cellular quiescence. Here the genome-wide contribution of HIRA to nucleosome organization in Schizosaccharomyces pombe was determined using a chromatin sequencing approach. Cells lacking HIRA (hip1Δ) experience a global reduction in nucleosome occupancy over the 3’ end of genes, consistent with the proposed role for HIRA in nucleosome re-assembly in the wake of RNA polymerase II. In addition, at HIRA-regulated promoters, it commonly maintains the proper occupancy of the -1 and +1 nucleosomes. Thus HIRA likely exerts its transcriptional regulatory roles through assembly/disassembly of specific target nucleosomes. In addition to transcription-coupled functions, HIRA has been implicated in the DNA damage response pathway. Indeed HIRA deficient cells present with increased sensitivity to DNA damaging agents and experience delays to the repair of DNA double strand breaks. Furthermore, hip1+ exhibits interactions with components of both the homologous recombination (HR) and non-homologous end joining (NHEJ) repair pathways. HIRA has also been identified as a regulator of nitrogen-starvation induced quiescence in S. pombe. Cells lacking HIRA are defective in both their ability to maintain and exit quiescence. Consistent with this, quiescent hip1Δ cells fail to properly induce MBF-dependent gene transcription in response to the restoration of a nitrogen source. During the course of this study Abo1, a bromodomain containing AAA-ATPase, was identified as a factor whose function potentially overlaps with histone chaperones such as HIRA. Therefore the contribution of Abo1 to global chromatin architecture was also assessed. Consistent with a nucleosome assembly function, abo1Δ cells have widespread changes to nucleosome occupancy and positioning in both euchromatic and heterochromatic regions of the genome. Furthermore, Abo1 physically interacts with the FACT histone chaperone and the distribution of Abo1 on chromatin is perturbed by loss of FACT subunits.
    Source: ProQuest Dissertations & Theses Global
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  • 7
    Language: English
    Description: The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell-cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline-specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell-cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
    Source: Cambridge University Library IR - DSpace@Cambridge
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  • 8
    Language: English
    Description: ABSTRACT The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
    Source: Cambridge University Library IR - DSpace@Cambridge
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  • 9
    Language: English
    In: The Journal of immunology (1950), 2018-04-01, Vol.200 (7), p.2247-2252
    Description: The complement system is a sophisticated network of proteases. In this article, we describe an unexpected link between two linear activation routes of the complement system: the lectin pathway (LP) and the alternative pathway (AP). Mannose-lectin binding-associated serine protease (MASP)-1 is known to be the initiator protease of the LP. Using a specific and potent inhibitor of MASP-1, SGMI-1, as well as other MASP-1 inhibitors with different mechanisms of action, we demonstrated that, in addition to its functions in the LP, MASP-1 is essential for bacterial LPS-induced AP activation, whereas it has little effect on zymosan-induced AP activation. We have shown that MASP-1 inhibition prevents AP activation, as well as attenuates the already initiated AP activity on the LPS surface. This newly recognized function of MASP-1 can be important for the defense against certain bacterial infections. Our results also emphasize that the mechanism of AP activation depends on the activator surface.
    Subject(s): Abridged Index Medicus ; Alternative pathway ; Complement ; Complement activation ; Lipopolysaccharides ; Mannose ; MASP-1 protein ; Protease ; Serine ; Serine proteinase
    ISSN: 0022-1767
    E-ISSN: 1550-6606
    Source: HighWire Press (Free Journals)
    Source: Alma/SFX Local Collection
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