Relevant bibliographies by topics / Chromatin Assembly

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Chromatin Assembly'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2023

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Journal articles on the topic "Chromatin Assembly"

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Tyler, Jessica K. "Chromatin assembly." European Journal of Biochemistry 269, no. 9 (April 22, 2002): 2268–74. http://dx.doi.org/10.1046/j.1432-1033.2002.02890.x.

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Adkins, Melissa W., and Jessica K. Tyler. "The Histone Chaperone Asf1p Mediates Global Chromatin Disassemblyin Vivo." Journal of Biological Chemistry 279, no. 50 (September 26, 2004): 52069–74. http://dx.doi.org/10.1074/jbc.m406113200.

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The packaging of the eukaryotic genome into chromatin is likely to be mediated by chromatin assembly factors, including histone chaperones. We investigated the function of the histone H3/H4 chaperones anti-silencing function 1 (Asf1p) and chromatin assembly factor 1 (CAF-1)in vivo. Analysis of chromatin structure by accessibility to micrococcal nuclease and DNase I digestion demonstrated that the chromatin from CAF-1 mutant yeast has increased accessibility to these enzymes. In agreement, the supercoiling of the endogenous 2μ plasmid is reduced in yeast lacking CAF-1. These results indicate that CAF-1 mutant yeast globally under-assemble their genome into chromatin, consistent with a role for CAF-1 in chromatin assemblyin vivo. By contrast,asf1mutants globally over-assemble their genome into chromatin, as suggested by decreased accessibility of their chromatin to micrococcal nuclease and DNase I digestion and increased supercoiling of the endogenous 2μ plasmid. Deletion ofASF1causes a striking loss of acetylation on histone H3 lysine 9, but this is not responsible for the altered chromatin structure inasf1mutants. These data indicate that Asf1p may have a global role in chromatin disassembly and an unexpected role in histone acetylationin vivo.
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Yadav, Rajesh K., Atsushi Matsuda, Brandon R. Lowe, Yasushi Hiraoka, and Janet F. Partridge. "Subtelomeric Chromatin in the Fission Yeast S. pombe." Microorganisms 9, no. 9 (September 17, 2021): 1977. http://dx.doi.org/10.3390/microorganisms9091977.

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Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.
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Moree, Ben, Corey B. Meyer, Colin J. Fuller, and Aaron F. Straight. "CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly." Journal of Cell Biology 194, no. 6 (September 12, 2011): 855–71. http://dx.doi.org/10.1083/jcb.201106079.

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Eukaryotic chromosomes segregate by attaching to microtubules of the mitotic spindle through a chromosomal microtubule binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, which is characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant CENP-A (centromere protein A). Understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation mechanisms. CENP-A nucleosome assembly requires the Mis18 complex and the CENP-A chaperone HJURP. These factors localize to centromeres in telophase/G1, when new CENP-A chromatin is assembled. The mechanisms that control their targeting are unknown. In this paper, we identify a mechanism for recruiting the Mis18 complex protein M18BP1 to centromeres. We show that depletion of CENP-C prevents M18BP1 targeting to metaphase centromeres and inhibits CENP-A chromatin assembly. We find that M18BP1 directly binds CENP-C through conserved domains in the CENP-C protein. Thus, CENP-C provides a link between existing CENP-A chromatin and the proteins required for new CENP-A nucleosome assembly.
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Lu, Lei, Mark S. Ladinsky, and Tomas Kirchhausen. "Formation of the postmitotic nuclear envelope from extended ER cisternae precedes nuclear pore assembly." Journal of Cell Biology 194, no. 3 (August 8, 2011): 425–40. http://dx.doi.org/10.1083/jcb.201012063.

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During mitosis, the nuclear envelope merges with the endoplasmic reticulum (ER), and nuclear pore complexes are disassembled. In a current model for reassembly after mitosis, the nuclear envelope forms by a reshaping of ER tubules. For the assembly of pores, two major models have been proposed. In the insertion model, nuclear pore complexes are embedded in the nuclear envelope after their formation. In the prepore model, nucleoporins assemble on the chromatin as an intermediate nuclear pore complex before nuclear envelope formation. Using live-cell imaging and electron microscope tomography, we find that the mitotic assembly of the nuclear envelope primarily originates from ER cisternae. Moreover, the nuclear pore complexes assemble only on the already formed nuclear envelope. Indeed, all the chromatin-associated Nup107–160 complexes are in single units instead of assembled prepores. We therefore propose that the postmitotic nuclear envelope assembles directly from ER cisternae followed by membrane-dependent insertion of nuclear pore complexes.
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Isaji, Mamiko, Hisataka Iwata, Hiroshi Harayama, and Masashi Miyake. "The localization of LAP2β during pronuclear formation in bovine oocytes after fertilization or activation." Zygote 14, no. 2 (May 2006): 157–67. http://dx.doi.org/10.1017/s0967199406003613.

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SummaryWe have shown that the assembly of lamin-associated polypeptide (LAP) 2β was detected surrounding the chromatin mass around the time of extrusion of the second polar body (PB) in some fertilized oocytes, but not in most activated oocytes, by using A23187 and cycloheximide (CaA + CH). Here, we immunohistologically analysed the correlation between LAP2β assembly and chromatin condensation in fertilized and activated oocytes during the second meiosis. In bovine cumulus cells, the onset of LAP2β assembly was observed around anaphase chromosomes with strongly phosphorylated histone H3. No LAP2β assembled around the chromosomes in the first and second polar bodies and the alternative oocyte chromatin (oCh) if histone H3 was phosphorylated. Only histone H3 of oCh was completely dephosphorylated during the telophase II/G1 transition (Tel II/G1), and then LAP2β assembled around only the oCh without phosphorylated histone H3. In the oocytes activated by CaA + CH, LAP2β did not assemble around the condensed oCh during the Tel II/G1 transition, although their histone H3 dephosphorylation occurred rather rapidly compared with that of the fertilized oocytes. The patterns of histone H3 dephosphorylation and LAP2β assembly in oocytes activated by CaA alone showed greater similarity to those in fertilized oocytes than to those in oocytes activated by CaA + CH. These results show that LAP2β assembles around only oCh after complete dephosphorylation of histone H3 after fertilization and activation using CaA alone, and that the timing of histone H3 dephosphorylation and LAP2β assembly in these oocytes is different from that of somatic cells. The results also indicate that CH treatment inhibits LAP2β assembly around oCh but not histone H3 dephosphorylation.
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Yan, Jie, Thomas J. Maresca, Dunja Skoko, Christian D. Adams, Botao Xiao, Morten O. Christensen, Rebecca Heald, and John F. Marko. "Micromanipulation Studies of Chromatin Fibers in Xenopus Egg Extracts Reveal ATP-dependent Chromatin Assembly Dynamics." Molecular Biology of the Cell 18, no. 2 (February 2007): 464–74. http://dx.doi.org/10.1091/mbc.e06-09-0800.

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We have studied assembly of chromatin using Xenopus egg extracts and single DNA molecules held at constant tension by using magnetic tweezers. In the absence of ATP, interphase extracts were able to assemble chromatin against DNA tensions of up to 3.5 piconewtons (pN). We observed force-induced disassembly and opening–closing fluctuations, indicating our experiments were in mechanochemical equilibrium. Roughly 50-nm (150-base pair) lengthening events dominated force-driven disassembly, suggesting that the assembled fibers are chiefly composed of nucleosomes. The ATP-depleted reaction was able to do mechanical work of 27 kcal/mol per 50 nm step, which provides an estimate of the free energy difference between core histone octamers on and off DNA. Addition of ATP led to highly dynamic behavior with time courses exhibiting processive runs of assembly and disassembly not observed in the ATP-depleted case. With ATP present, application of forces of 2 pN led to nearly complete fiber disassembly. Our study suggests that ATP hydrolysis plays a major role in nucleosome rearrangement and removal and that chromatin in vivo may be subject to highly dynamic assembly and disassembly processes that are modulated by DNA tension.
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Becker, P. B., and C. Wu. "Cell-free system for assembly of transcriptionally repressed chromatin from Drosophila embryos." Molecular and Cellular Biology 12, no. 5 (May 1992): 2241–49. http://dx.doi.org/10.1128/mcb.12.5.2241-2249.1992.

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We describe a cell-free system, derived from preblastoderm Drosophila embryos, for the efficient assembly of cloned DNA into chromatin. The chromatin assembly system utilizes endogenous core histones and assembly factors and yields long arrays of regularly spaced nucleosomes with a repeat length of 180 bp. The assembly system is also capable of complementary-strand DNA synthesis accompanied by rapid nucleosome formation when the starting template is single-stranded circular DNA. Chromatin assembled with the preblastoderm embryo extract is naturally deficient in histone H1, but exogenous H1 can be incorporated during nucleosome assembly in vitro. Regular spacing of nucleosomes with or without histone H1 is sufficient to maximally repress transcription from hsp70 and fushi tarazu gene promoters. The Drosophila assembly system should be particularly useful for in vitro studies of chromatin assembly during DNA synthesis and for elucidating the action of transcription factors in the context of native chromatin.
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Becker, P. B., and C. Wu. "Cell-free system for assembly of transcriptionally repressed chromatin from Drosophila embryos." Molecular and Cellular Biology 12, no. 5 (May 1992): 2241–49. http://dx.doi.org/10.1128/mcb.12.5.2241.

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We describe a cell-free system, derived from preblastoderm Drosophila embryos, for the efficient assembly of cloned DNA into chromatin. The chromatin assembly system utilizes endogenous core histones and assembly factors and yields long arrays of regularly spaced nucleosomes with a repeat length of 180 bp. The assembly system is also capable of complementary-strand DNA synthesis accompanied by rapid nucleosome formation when the starting template is single-stranded circular DNA. Chromatin assembled with the preblastoderm embryo extract is naturally deficient in histone H1, but exogenous H1 can be incorporated during nucleosome assembly in vitro. Regular spacing of nucleosomes with or without histone H1 is sufficient to maximally repress transcription from hsp70 and fushi tarazu gene promoters. The Drosophila assembly system should be particularly useful for in vitro studies of chromatin assembly during DNA synthesis and for elucidating the action of transcription factors in the context of native chromatin.
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Kamakaka, R. T., M. Bulger, P. D. Kaufman, B. Stillman, and J. T. Kadonaga. "Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1." Molecular and Cellular Biology 16, no. 3 (March 1996): 810–17. http://dx.doi.org/10.1128/mcb.16.3.810.

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To study the relationship between DNA replication and chromatin assembly, we have purified a factor termed Drosophila chromatin assembly factor 1 (dCAF-1) to approximately 50% homogeneity from a nuclear extract derived from embryos. dCAF-1 appears to consist of four polypeptides with molecular masses of 180, 105, 75, and 55 kDa. dCAF-1 preferentially mediates chromatin assembly of newly replicated DNA relative to unreplicated DNA during T-antigen-dependent simian virus 40 DNA replication in vitro, as seen with human CAF-1. Analysis of the mechanism of DNA replication-coupled chromatin assembly revealed that both dCAF-1 and human CAF-1 mediate chromatin assembly preferentially with previously yet newly replicated DNA relative to unreplicated DNA. Moreover, the preferential assembly of the postreplicative DNA was observed at 30 min after inhibition of DNA replication by aphidicolin, but this effect slowly diminished until it was no longer apparent at 120 min after inhibition of replication. These findings suggest that the coupling between DNA replication and chromatin assembly may not necessarily involve a direct interaction between the replication and assembly factors at a replication fork.
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Dissertations / Theses on the topic "Chromatin Assembly"

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Jansen, Hailey Janice. "Characterization of chromatin assembly in murine embryos." Thesis, University of British Columbia, 2013. http://hdl.handle.net/2429/44768.

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During differentiation, changes in chromatin proteins lead to the establishment and maintenance of gene expression patterns. Histone H3 trimethylated at lysine 4 (H3K4me3) by the trithorax group (trxG) gene family Mixed lineage leukemia (MLL) is associated with active genes. H3K27me3 is trimethylated by the Polycomb group (PcG) Enhancer of Zeste (EZH2) at repressed genes. In Drosophila embryos, trxG and PcG proteins but not H3K4me3 or H3K27me3 are stable to DNA replication. In contrast, methylated histones are detected on nascent DNA in Drosophila and murine cell lines. Therefore some aspect of chromatin assembly or histone trimethylation must differ in different cells. My first aim was to determine if there is a change in the abundance of methylated histones at the replication fork in undifferentiated versus differentiated murine ES cells using two novel in vivo assays. Most undifferentiated ES cells lack early H3K4me3 and H3K27me3, but after 4 days of differentiation, most cells have early trimethylation of H3K4 and H3K27. I propose that the change in kinetics of histone methylation correlates with differentiation. To test this hypothesis, I carried out similar experiments on cells dissociated from day 9.5 (E9.5) and 14.5 (E14.5) murine embryos. In E9.5 cells there are two populations of cells, one that lacks methylated histones and the other contains methylated histones on nascent DNA. By E14.5 most cells exhibit H3K4me3 and H3K27me3 on nascent DNA. To determine if the presence of histone methyltransferases could account for the changes in histone methylation, I tested MLL1 and a subunit of the EZH2 complex, Su(z)12. Both are present continuously on nascent DNA, suggesting that their activity is regulated. Methylation and acetylation antagonize each other at the same residue. However I showed that the presence of acetylated H3K27 is not anticorrelated with H3K27me3 in most murine embryos cells. My results using inhibitors of the appropriate histone acetyltransferase were not conclusive owing to toxicity of the inhibitors. Overall, my results support the hypothesis that trimethylation of H3K4 and H3K27 on nascent DNA is developmentally regulated.
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Dunleavy, Elaine. "Assembly of centromeric chromatin in fission yeast." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/13739.

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Fission yeast centromeres are composed of a central domain surrounded on both sides by outer repeat heterochromatin. Marker genes inserted within the central domain or the outer repeats are transcriptionally silenced. A screen performed to identify mutants that specifically alleviate silencing at the central domain, identified the sim (silencing in the middle of the centromere) mutants. The sim6 mutant was unusual in that it was found to alleviate both central domain and outer repeat silencing and suggests that there may be cross talk between kinetochore assembly and the integrity of neighbouring heterochromatin. To identify other factors with a similar phenotype a screen was performed in which the cos (central core and outer repeat silencing) mutants were isolated. Several mutants allelic to sim6+ (renamed cos1+) were isolated. Cos1+ is allelic to fission yeast mcl1+  (mini-chromosome loss 1) and may function to ensure that features of silent chromatin and sister chromatin cohesion are properly maintained after replication. sim3 mutants were found to specifically alleviate silencing at the central domain. Sim3 is homologous to the histone binding proteins mammalian NASP (nuclear autoantigenic sperm protein) and Xenopus laevis N1/N2. Cells with defective Sim3 have reduced levels CENP-ACnp1 at centromeres and subsequently display defects in mititotic chromosome segregation. Sim3 may be acting as a CENP-ACnp1 ‘escort’, assisting in the replication independent assembly of CENP-ACnp1 chromatin at centromeres, however Sim3 may also contribute to the loading of Sim3 at other stages of the cell cycle. It remains to be determined whether NASP/N1/N2 plays a similar role in metazoa.
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Kats, Ellen Simona. "De-caf-einated life without chromatin assembly factors /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3221182.

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Thesis (Ph. D.)--University of California, San Diego, 2006.
Title from first page of PDF file (viewed September 8, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Royle, Nikki. "Expression, purification and characterisation of recombinant chromatin assembly factor 1." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/244243.

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Chromatin Assembly Factor 1 (CAF-1) is the only known replication dependant histone chaperone, responsible for the deposition of the histone H3/H4 tetramer onto DNA. Found in all eukaryotes, CAF-1 consists of three subunits, p150, p60 and p48. Since its identification work on CAF-1 has mainly focused on in vivo studies due to the lack of a reliable method to produce large quantities of recombinant protein for biochemical studies. Herein the cloning, production and purification of the three subunits of recombinant CAF-1 is described. The proteins were expressed as complexes and individually in insect cells and Escherichia coli, optimised protocols are described for maximum protein recovery and purity. Constructs of p150 and p60 were also produced and used to analyse the binding regions and modes of both the p48 and p60 proteins to p150. It is shown that the two smaller subunits of CAF-1 do not interact in the absence of p150 and that the p150 subunit of CAF-1 acts as a scaffold for assembly of the complex, binding directly to both p48 and p60. The stoichiometry of the CAF-1 complex was also investigated and a basis for further work, including structural studies, discussed.
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Rasala, Beth A. "Defining the early steps in nuclear pore assembly chromatin-associated ELYS initiates pore assembly /." Diss., View abstract only; access to full text of dissertation for UC IP will be available after 1/1/2011, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3296834.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed June 3, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Pietrobon, Violena. "Chromatin assembly by CAF-1 during homologous recombination : a novel step of regulation." Phd thesis, Université Paris Sud - Paris XI, 2012. http://tel.archives-ouvertes.fr/tel-00977568.

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The replication of chromosomes can be challenged by endogenous and environmental factors, interfering with the progression of replication forks. Therefore, cells have to coordinate DNA synthesis with mechanisms ensuring the stability and the recovery of halted forks. Homologous recombination (HR) is a universal mechanism that supports DNA repair and the robustness of DNA replication. Nonetheless, mechanisms regulating HR pathways, such as ectopic versus allelic recombination, remain poorly understood. Another essential pathway for genome stability is the wrapping of newly replicated DNA around nucleosomes, leading to the constitution of a chromatin fibre, which allows the structural organization of the genetic material. In Saccharomyces cerevisiae, deficiencies in chromatin assembly pathways lead to replication forks instability and consequent increase in the rate of HR. Histone chaperones play a crucial role during chromatin assembly, thus I decided to focus on the H3-H4 histone chaperone Chromatin Assembly Factor 1 (CAF-1), to study its role in HR processes in Schizosaccharomyces pombe. Indeed, HR includes a DNA synthesis step and little is known about the associated chromatin assembly. My data excluded a role for CAF-1 in allelic recombination and in the maintenance of forks stability. However, CAF-1 was found to play an important role during ectopic recombination, in promoting chromosomal rearrangements induced by halted replication forks. My data support a model according to which CAF-1 allows the stabilization of early recombination intermediates (D-loop), via nucleosome deposition during the elongation of these intermediates. Doing so, CAF-1 counteracts the dissociation of early recombination intermediates by the helicase Rqh1. Therefore, CAF-1 appears to be part of an equilibrium that regulates stability/dissociation of early steps of recombination events. Importantly, I found that the role of CAF-1 in this equilibrium is of particular importance during non-allelic recombination, revealing a novel regulation level of HR mechanisms and outcomes by chromatin assembly.
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Nabatiyan, Arman. "The role of chromatin assembly factor-1 in human cells." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615283.

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Wong, Hiu-ting. "A role of TSPYL2, a novel nucleosome assembly protein, in transcriptional regulation." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43085726.

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Huanyu, Wang. "Characterization of N1/N2 Family Histone Chaperones: Hif1p and NASP." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1279815431.

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Hunt, Spencer Philip. "Whole-Genome Assembly of Atriplex hortensis L. Using OxfordNanopore Technology with Chromatin-Contact Mapping." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8580.

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Atriplex hortensis (2n = 2x = 18, 1C genome size ~1.1 gigabases), also known as garden orach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae family that has spread from its native Eurasia to other temperate and subtropical environments worldwide. Atriplex is a highly complex and polyphyletic genus of generally halophytic and/or xerophytic plants, some of which have been used as food sources for humans and animals alike. Although there is some literature describing the taxonomy and ecology of orach, there is a lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic position, and future potential of this species. Here, we report the assembly of the first highquality, chromosome-scale reference genome for orach cv. ‘Golden’. Sequence data was produced using Oxford Nanopore’s MinION sequencing technology in conjunction with Illumina short-reads and chromatin-contact mapping. Genome assembly was accomplished using the high-noise, single-molecule sequencing assembler, Canu. The genome is enriched for highly repetitive DNA (68%). The Canu assembly combined with the Hi-C chromatin-proximity data yielded a final assembly containing 1,325 scaffolds with a contig N50 of 98.9 Mb and with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-eight percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy and Copia-like LTRs. The annotation was completed using MAKER which identified 31,010 gene models and 2,555 tRNA genes. Completeness of the genome was assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) platform, which quantifies functional gene content using a large core set of highly conserved orthologous genes (COGs). Of the 1,375 plant-specific COGs in the Embryophyta database, 1,330 (96.7%) were identified in the Atriplex assembly. We also report the results of a resequencing panel consisting of 21 accessions which illustrates a high degree of genetic similarity among cultivars and wild material from various locations in North America and Europe. These genome resources provide vital information to better understand orach and facilitate future study and comparison.
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Books on the topic "Chromatin Assembly"

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McQuibban, Angus. Yeast nucleosome and chromatin assembly. Ottawa: National Library of Canada, 1995.

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Chromatin remodeling: Methods and protocols. New York: Humana Press, 2012.

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Kallgren, Scott. The Roles of Splicing and H2A.Z in Chromatin Assembly. [New York, N.Y.?]: [publisher not identified], 2014.

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Ashok, Agarwal, and SpringerLink (Online service), eds. Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction. New York, NY: Springer Science+Business Media, LLC, 2011.

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O, Tollefsbol Trygve, ed. Epigenetics protocols. Totowa, N.J: Humana Press, 2004.

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Sang-Woon, Choi, and Friso Simonetta, eds. Nutrients and epigenetics. Boca Raton: Taylor & Francis, 2009.

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Workman, Jerry L., and Susan M. Abmayr. Fundamentals of Chromatin. Springer, 2016.

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Workman, Jerry L., and Susan M. Abmayr. Fundamentals of Chromatin. Springer, 2013.

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Workman, Jerry L., and Susan M. Abmayr. Fundamentals of Chromatin. Springer London, Limited, 2013.

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Morse, Randall H. Chromatin Remodeling: Methods and Protocols. Humana Press, 2016.

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Book chapters on the topic "Chromatin Assembly"

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Dennehey, Briana K., and Jessica Tyler. "Histone Chaperones in the Assembly and Disassembly of Chromatin." In Fundamentals of Chromatin, 29–67. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-8624-4_2.

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Blasquez, Veronica, Christine Ambrose, Henry Lowman, and Minou Bina. "SV40 Chromatin Structure and Virus Assembly." In Molecular Aspects of Papovaviruses, 219–37. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-2087-6_11.

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Fukagawa, Tatsuo. "Centromeric Chromatin and Kinetochore Assembly in Vertebrate Cells." In DNA Replication, Recombination, and Repair, 365–87. Tokyo: Springer Japan, 2016. http://dx.doi.org/10.1007/978-4-431-55873-6_14.

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Gehrke, Andrew R., and Mansi Srivastava. "Assessing Chromatin Accessibility During WBR in Acoels." In Methods in Molecular Biology, 549–61. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_29.

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AbstractDynamic gene expression seen during whole-body regeneration is likely controlled by genomic regulatory elements that dictate the spatiotemporal activity of the regeneration transcriptome. Identifying and characterizing these non-coding regulatory sequences are key to understanding how genes are connected into networks to deploy the process of whole-body regeneration. Here, we describe the application of the Assay for Transposase Accessible Chromatin (ATAC-seq) in the acoel Hofstenia miamia to identify regions of open chromatin that represent putative regulatory elements. Notably, when paired with gene knockdown techniques such as RNAi, ATAC-seq can be implemented in a functional genomics approach to validate putative regulatory elements. ATAC-seq requires no species-specific reagents, is amenable to small input cell numbers, and can be completed in a single day, making it an ideal assay to identify dynamic chromatin at high resolution during whole-body regeneration in virtually any species with a quality genome assembly.
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Laskey, R. A., A. D. Mills, A. Phillpott, G. H. Leno, S. M. Dillworth, and C. Dingwall. "The role of nucleoplasmin in chromatin assembly and disassembly." In Molecular Chaperones, 7–13. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-2108-8_2.

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Bonte, Edgar, and Peter B. Becker. "Preparation of Chromatin Assembly Extracts from Preblastoderm Drosophila Embryos." In Methods in Molecular Biology, 1–10. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-190-1_1.

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Roche, Danièle, Geneviève Almouzni, and Jean-Pierre Quivy. "Chromatin Assembly of DNA Templates Microinjected Into Xenopus Oocytes." In Xenopus Protocols, 139–47. Totowa, NJ: Humana Press, 2006. http://dx.doi.org/10.1007/978-1-59745-000-3_10.

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Bao, Xiucong. "Glutarylation at Histone H4 Lysine 91 Modulates Chromatin Assembly." In Study on the Cellular Regulation and Function of Lysine Malonylation, Glutarylation and Crotonylation, 81–95. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-2509-4_4.

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Ciccone, David, and Marjorie Oettinger. "Chromatin Modifications as Clues to the Regulation of Antigen Receptor Assembly." In Reversible Protein Acetylation, 146–62. Chichester, UK: John Wiley & Sons, Ltd, 2008. http://dx.doi.org/10.1002/0470862637.ch10.

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Haynes, Karmella A., and J. Harrison Priode. "Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering." In Methods in Molecular Biology, 191–214. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2847-8_14.

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Conference papers on the topic "Chromatin Assembly"

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Mittereder, Tobias, Bernhard Ferstl, Terry Heidmann, and Christian Hollerith. "Temperature-Dependent Die Warpage Measurements Up to 400°C." In ISTFA 2017. ASM International, 2017. http://dx.doi.org/10.31399/asm.cp.istfa2017p0046.

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Abstract Temperature-dependent die warpage measurements show the possibility to analyze the thermomechanical behavior during assembly, e.g. within soldering processes. The warpage data acquisition is realized by confocal chromatic white light profilometry in combination with a precision heating/cooling chuck encapsulated in a chamber with optical access. The combination of these two tools allows precise die warpage evaluation under varied device temperature up to +400°C. This method helps to solve emerging challenges due to warpage during assembly of state of the art packages including thin dies and stacked dies as in e.g. 3D-SIPs.
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Barbu, Daniela. "A LOW-COST DEVICE FOR INVESTIGATING CHROMATIC VISION." In eLSE 2017. Carol I National Defence University Publishing House, 2017. http://dx.doi.org/10.12753/2066-026x-17-251.

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The retina is the light sensitive portion of the eye that contains cone cells responsible for color vision and cone cells responsible for order in darkness. When the rods and cones are stimulated, light signals are transmitted successively by neurons retina, optic nerve fibers then finally reaching the cerebral cortex. Normal eye retina shows three types of color light-sensitive cells; cone cells are sensitive to red light, green or blue. View color deficiency is the inability or decreased ability to see colors or the perception of differences between colors. Depending on the number of cells absent or impaired color vision impairment operation is called: monocromatism, when all the cones are missing or not working, dicromatism when one of three types of cells and tricromatism missing or when one of three cell types has a poor spectral sensitivity. In 1802, Thomas Young consider that all human sight is produced by combining sensitivity to red, green and blue. This theory, amended by Hermann von Helmholtz in 1852, it is known as Young-Helmholtz theory or trichromatic color vision. The fundamental idea was that the eye responds to the three primary colors and combining the three primary colors through additive synthesis of colors forms all other colors. These theories underlie the eye color deficiencies investigation. The paper aims to provide an inexpensive device necessary to investigate color vision in humans. This is achieved in the components recovered from the other old systems, reconditioned and assembled using a simple technology. Research presented the paper will refer both to the device and for tests with it. Studies will be made on different age groups in order to detect any abnormal chromatic vision.
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Mennerat, Sophie, and Sylvain Paineau. "A novel design of diffractive optical interconnects for multichip clock distribution." In The European Conference on Lasers and Electro-Optics. Washington, D.C.: Optica Publishing Group, 1998. http://dx.doi.org/10.1364/cleo_europe.1998.cpd2.3.

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We report a novel system of diffractive optical interconnects for very high speed clock distribution among multichip modules. Our system distributes two clock signals, each from one separate Vertical Cavity Surface Emitting Laser (VCSEL) over four PIN diodes positioned within a radius of 9 mm along a light-guiding glass plate. The incoming optical gaussian beams from VCSEL are splitted by diffractive optical elements into four output beams and the glass plate propagates the light through multiple reflections onto the golden metallized faces towards the detectors. The overall alignment and chromatic acceptance is highly improved by the use of SELFOC micro-lenses that collimate the laser beam onto the diffractive optical element and that focus the output beam onto the active area of the detectors. The proposed architecture allows tolerance on the light source wavelength as high as Δλ = 10 nm and global tolerances of assembly of the glass plate of 1.5 degrees in rotation and 10 µm in translation making it compatible with the processes of hybridization in microelectronics.
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Vasquez, Daniel J., Amy J. Smith, and Keshab K. Dwivedy. "Structural Evaluation of Degraded Containment Penetration Sleeves." In ASME 2008 Pressure Vessels and Piping Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/pvp2008-61514.

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The design of a nuclear plant includes “hot” containment penetration assemblies designed to protect the containment building concrete walls from the effects of localized high temperature and degradation due to thermal cycling resulting from the process piping. Typically, a penetration assembly is jacketed by coolers inside and outside a sleeve originating at a flued head on the process pipe and penetrating the containment wall. The coolers are supplied by either chromated component cooling (CC) or raw service water. Recently, a minor leak of chromated water from the penetration coolers rendered the Class 3 safety-related CC system inoperable and was isolated. Subsequently, Non-Destructive Examination (NDE) inspections of the sleeve were conducted and significant degradation was noted. The root cause of the degradation under the jacketed cooler was due to raw service water, which was used in the cooler prior to switching to CC water. Weld repairs were subsequently performed to restore degraded areas. The coolers were also removed since the air gap could provide adequate insulation to keep the sleeve below a threshold temperature for degradation of concrete. An evaluation of past functionality was still required, however, to demonstrate that the degradation did not affect the structural integrity of the sleeve and breach containment boundary. The NDE data was processed to characterize the degradation for analysis. A novel application of ASME Section XI Non-mandatory Appendix C with a simple extension of the methodology was used in the evaluation to assist the operability determination. The paper concludes that a simple extension of the code methodology was useful in establishing plant operability.
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Fujime, Satoru, Shigeaki Miyamoto, Takashi Funatsu, and S. Ishiwata. "Dynamic light-scattering study on changes in mobility of chromaffin granules in actin network with its assembly and Ca2+-dependent disassembly by gelsolin." In Laser Spectroscopy of Biomolecules: 4th International Conference on Laser Applications in Life Sciences, edited by Jouko E. Korppi-Tommola. SPIE, 1993. http://dx.doi.org/10.1117/12.146216.

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Reports on the topic "Chromatin Assembly"

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Adams, Peter D. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2005. http://dx.doi.org/10.21236/ada443724.

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Adams, Peter. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2004. http://dx.doi.org/10.21236/ada434608.

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Adams, Peter D. Testing Whether Defective Chromatin Assembly in S-Phase Contributes to Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2003. http://dx.doi.org/10.21236/ada423415.

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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