Faculty Opinions recommendation of Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al. 1997) and the relations of this compartmentalization to chromosome structure and the spatial organization of transcription. Our aim was to provide a comprehensive and integrated view on the relations between chromosome structure and functional nuclear architecture. Using different mammalian cell types, we show that distinct higher order compartments whose DNA displays a specific replication timing are stably maintained during all interphase stages. The organizational principle is clonally inherited. We directly demonstrate the presence of polar chromosome territories that align to build up higher order compartments, as previously suggested (Ferreira et al. 1997). Polar chromosome territories display a specific orientation of early and late replicating subregions that correspond to R- or G/C-bands of mitotic chromosomes. Higher order compartments containing G/C-bands replicating during the second half of the S phase display no transcriptional activity detectable by BrUTP pulse labeling and show no evidence of transcriptional competence. Transcriptionally competent and active chromatin is confined to a coherent compartment within the nuclear interior that comprises early replicating R-band sequences. As a whole, the data provide an integrated view on chromosome structure, nuclear higher order compartmentalization, and their relation to the spatial organization of functional nuclear processes.

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Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction

Nature Communications ◽

10.1038/s41467-021-22899-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Stefano Gnan ◽

Ilya M. Flyamer ◽

Kyle N. Klein ◽

Eleonora Castelli ◽

Alexander Rapp ◽

...

Keyword(s):

Three Dimensional ◽

Nuclear Architecture ◽

Replication Timing ◽

Function Approach ◽

Dual Function ◽

Genome Organisation ◽

Full Complement ◽

Nuclear Organisation ◽

Molecular Bases

AbstractThree-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture.

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Sites of chromosomal instability in the context of nuclear architecture and function

Cellular and Molecular Life Sciences ◽

10.1007/s00018-020-03698-2 ◽

2020 ◽

Author(s):

Constanze Pentzold ◽

Miriam Kokal ◽

Stefan Pentzold ◽

Anja Weise

Keyword(s):

Nuclear Architecture ◽

Nuclear Lamina ◽

Replication Timing ◽

Fragile Sites ◽

Chromosomal Breakage ◽

Metaphase Chromosomes ◽

Chromosomal Fragile Sites ◽

And Function ◽

Genomic Regions ◽

Mitotic Chromatin

AbstractChromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.

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Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction

10.1101/812156 ◽

2019 ◽

Cited By ~ 3

Author(s):

Stefano Gnan ◽

Ilya M. Flyamer ◽

Kyle N. Klein ◽

Eleonora Castelli ◽

Alexander Rapp ◽

...

Keyword(s):

Three Dimensional ◽

Nuclear Architecture ◽

Replication Timing ◽

Function Approach ◽

Dual Function ◽

Genome Organisation ◽

Full Complement ◽

Nuclear Organisation ◽

Molecular Bases

AbstractThree-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.

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A stochastic hybrid model for DNA replication incorporating protein mobility dynamics

10.1101/583187 ◽

2019 ◽

Author(s):

Jonas Windhager ◽

Amelia Paine ◽

Patroula Nathanailidou ◽

Eve Tasiudi ◽

María Rodríguez Martínez ◽

...

Keyword(s):

Dna Replication ◽

Spindle Pole Body ◽

Nuclear Architecture ◽

Replication Timing ◽

Spindle Pole ◽

Full Genome ◽

Origin Firing ◽

Protein Mobility ◽

Pole Body

SummaryDNA replication, the basis of genetic information maintenance, is a remarkably robust yet highly stochastic process. We present a computational model that incorporates experimental genome structures and protein mobility dynamics to mechanistically describe the stochastic foundations of DNA replication. Analysis of about 300,000 in silico profiles for fission yeast indicates that the number of firing factors is rate-limiting and dominates completion time. Incorporating probabilistic activation and binding, a full-genome duplication was achieved with at least 300 firing factors, with the only assumption that factors get recycled upon replication fork collision. Spatial patterns of replication timing were reproduced only when firing factors were explicitly activated proximally to the spindle pole body. Independent in vivo experiments validate that the spindle pole body acts as a replication activator, driving origin firing. Our model provides a framework to realistically simulate full-genome DNA replication and investigate the effects of nuclear architecture.

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