Unknown,Transcriptomics,Genomics,Proteomics

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Patterns and mechanisms of ancestral histone protein inheritance in budding yeast

ABSTRACT: It is widely believed that chromatin, the nucleoprotein packaging state of eukaryotic genomes, can carry epigenetic information to propagate gene expression patterns in replicating cells. However, inheritance of genomic packaging status is subject to mechanistic challenges that do not confront the inheritance of genomic DNA sequence. Most notably, histone proteins must at least transiently dissociate from the maternal genome during replication, and it is unknown whether maternal proteins re-associate with daughter genomes near the sequence they originally occupied on the maternal genome. Here, we use a novel method for tracking old proteins to measure where histone proteins accumulate after 1, 3, or 6 generations of growth in yeast. To our surprise, ancestral histones accumulate near the 5M-bM-^@M-^Y end of long, relatively inactive genes. Using a mathematical model, we show that our results can be explained by the combined effects of histone replacement, histone movement along genes from 3M-bM-^@M-^Y to 5M-bM-^@M-^Y, and histone spreading during replication. Our results show that old histones do move, but stay relatively close (~400 bp) to their original location, which places important constraints on how chromatin could potentially carry epigenetic information. Our findings also suggest that accumulation of ancestral histones can influence histone modification patterns. Solexa/Illumina sequencing of H3-HA and H3-T7 MNase-ChIP. Samples of HA and T7 libraries were taken after the tag swap (a) before release from arrest (0 generations), (b) at 1, 3 and 6 cell divisions or (c) after 5 hours of G2/M arrest. Gene deletion mutants for (d) cac1 (e) top1 and (f) H4-tail deletion were taken after 3 cell divisions.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Assaf Weiner

PROVIDER: E-GEOD-28269 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Patterns and mechanisms of ancestral histone protein inheritance in budding yeast.

Radman-Livaja Marta M Verzijlbergen Kitty F KF Weiner Assaf A van Welsem Tibor T Friedman Nir N Rando Oliver J OJ van Leeuwen Fred F

PLoS biology 20110607 6

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 g ...[more]

PMID: 21666805

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Project description:This model is described in the article: Kinetics of histone gene expression during early development of Xenopus laevis. Koster JG, Destrée OH and Westerhoff HV. J Theor Biol. 1988 Nov 21;135(2):139-67. PMID: 3267765 Abstract: Using literature data for transcriptional and translational rate constants, gene copy numbers, DNA concentrations, and stability constants, we have calculated the expected concentrations of histones and histone mRNA during embryogenesis of Xenopus laevis. The results led us to conclude that: (i) for X. laevis the gene copy number of the histone genes is too low to ensure the synthesis of sufficient histones during very early development, inheritance from the oocyte of either histone protein or histone mRNA (but not necessarily both) is necessary; (ii) from the known storage of histones in the oocyte and the rates of histone synthesis determined by Adamson and Woodland (1977), there would be sufficient histones to structure the newly synthesized DNA up to gastrulation but not thereafter (these empirical rates of histone synthesis may be underestimates); (iii) on the other hand, the amount of H3 mRNA recently observed during early embryogenesis (Koster, 1987, Koster et al., 1988) could direct a higher and sufficient synthesis of H3 protein, also after gastrulation. We present a quantitative model that accounts both for the observed H3 mRNA concentration as a function of time during embryogenesis and for the synthesis of sufficient histones to structure the DNA throughout early embryogenesis. The model suggests that X. laevis exhibits a major (i.e. some 14-fold) reduction in transcription of histone genes approximately 11 hours after fertilization. This reduction could be due to a decrease in the number of transcribed histone genes, a decreased rate constant of transcription with continued transcription of all the histone genes, and/or a reduction in the time during the cell cycle in which histone mRNA synthesis takes place. Alternatively, the histone mRNA stability might decrease approximately 16-fold 11 hours after fertilization. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Dataset Information

Patterns and mechanisms of ancestral histone protein inheritance in budding yeast

Publications

Patterns and mechanisms of ancestral histone protein inheritance in budding yeast.

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