Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
PLoS Biology (Impact Factor: 9.34). 06/2011; 9(6):e1001075. DOI: 10.1371/journal.pbio.1001075
Source: PubMed


Replicating chromatin involves disruption of histone-DNA contacts and subsequent reassembly of maternal histones on the new daughter genomes. In bulk, maternal histones are randomly segregated to the two daughters, but little is known about the fine details of this process: do maternal histones re-assemble at preferred locations or close to their original loci? Here, we use a recently developed method for swapping epitope tags to measure the disposition of ancestral histone H3 across the yeast genome over six generations. We find that ancestral H3 is preferentially retained at the 5' ends of most genes, with strongest retention at long, poorly transcribed genes. We recapitulate these observations with a quantitative model in which the majority of maternal histones are reincorporated within 400 bp of their pre-replication locus during replication, with replication-independent replacement and transcription-related retrograde nucleosome movement shaping the resulting distributions of ancestral histones. We find a key role for Topoisomerase I in retrograde histone movement during transcription, and we find that loss of Chromatin Assembly Factor-1 affects replication-independent turnover. Together, these results show that specific loci are enriched for histone proteins first synthesized several generations beforehand, and that maternal histones re-associate close to their original locations on daughter genomes after replication. Our findings further suggest that accumulation of ancestral histones could play a role in shaping histone modification patterns.

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Available from: Marta Radman-Livaja, Oct 01, 2015
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    • "The short epitope tags can be used for immunoblot and affinity purification protocols such as ChIP. Thereby, RITE can be combined with proteomics methods, genomics methods, or DNA-based highthroughput screens (Verzijlbergen et al. 2010; De Vos et al. 2011; Radman-Livaja et al. 2011; Verzijlbergen et al. 2011). The fluorescent tags in the RITE cassettes can be applied to measure protein dynamics in single cells by live imaging (Verzijlbergen et al. 2010; Hotz et al. 2012; Menendez-Benito et al. 2013) and further expanded toward high-throughput genetic screening. "
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    ABSTRACT: Proteins are not static entities. They are highly mobile and their steady state levels are achieved by a balance between ongoing synthesis and degradation. The dynamic properties of a protein can have important consequences for its function. For example, when a protein is degraded and replaced by a newly synthesized one, post-translational modifications are lost and need to be reincorporated in the new molecules. Protein stability and mobility are also relevant for duplication of macromolecular structures or organelles, which involves coordination of protein inheritance with the synthesis and assembly of newly synthesized proteins. To measure protein dynamics we recently developed a genetic pulse-chase assay called Recombination-Induced Tag Exchange (RITE). RITE has been successfully used in Saccharomyces cerevisiae to measure turnover and inheritance of histone proteins, to study changes in post-translational modifications on aging proteins, and to visualize the spatiotemporal inheritance of protein complexes and organelles in dividing cells. Here we describe a series of successful RITE cassettes that are designed for biochemical analyses, genomics studies, as well as single cell fluorescence applications. Importantly, the genetic nature and the stability of the tag-switch offer the unique possibility to combine RITE with high-throughput screening for protein dynamics mutants and mechanisms. The RITE cassettes are widely applicable, modular by design, and can therefore be easily adapted for use in other cell types or organisms.
    G3-Genes Genomes Genetics 05/2013; 3(8). DOI:10.1534/g3.113.006213 · 3.20 Impact Factor
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    • "ASF1 has a similar function in histone recycling during transcription (31), and has recently been shown to play a role in heterochromatin assembly in Schizosaccharomyces pombe (39). Thus, the inheritance of epigenetic states is thought to depend upon the reassembly of locally displaced nucleosomes (43), thereby re-establishing the prior nucleosomes and their modifications, initially in a hemi-modified form, which could then serve as a signal for the addition of further similar modifications. Histone H3K56 acetylation appears to be central to this process, and for checkpoint signalling (44). "
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    Nucleic Acids Research 08/2012; 40(20). DOI:10.1093/nar/gks813 · 9.11 Impact Factor
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    • "Recently, the Rando group has shown that maternal histones re-associate close to their original locations on daughter genomes after replication [25]. They suggest that the re-association of maternal histones can transmit the histone modification pattern that maternal histones possess onto the same locations on daughter genomes [25]. Our findings are consistent with this idea. "
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    ABSTRACT: Histone modifications are important epigenetic features of chromatin that must be replicated faithfully. However, the molecular mechanisms required to duplicate and maintain histone modification patterns in chromatin remain to be determined. Here, we show that the introduction of histone modifications into newly deposited nucleosomes depends upon their location in the chromosome. In Saccharomyces cerevisiae, newly deposited nucleosomes consisting of newly synthesized histone H3-H4 tetramers are distributed throughout the entire chromosome. Methylation of lysine 4 on histone H3 (H3-K4), a hallmark of euchromatin, is introduced into these newly deposited nucleosomes, regardless of whether the neighboring preexisting nucleosomes harbor the K4 mutation in histone H3. Furthermore, if the heterochromatin-binding protein Sir3 is unavailable during DNA replication, histone H3-K4 methylation is introduced onto newly deposited nucleosomes in telomeric heterochromatin. Thus, a conservative distribution model most accurately explains the inheritance of histone modifications because the location of histones within euchromatin or heterochromatin determines which histone modifications are introduced.
    PLoS ONE 12/2011; 6(12):e28980. DOI:10.1371/journal.pone.0028980 · 3.23 Impact Factor
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