Heterogeneous chromatin mobility derived from chromatin states is a determinant of genome organisation inS. cerevisiae

Abstract

Spatial organisation of the genome is essential for regulating gene activity, yet the mechanisms that shape this three-dimensional organisation in eukaryotes are far from understood. Here, we combine bioinformatic determination of chromatin states during normal growth and heat shock, and computational polymer modelling of genome structure, with quantitative microscopy and Hi-C to demonstrate that differential mobility of yeast chromosome segments leads to spatial self-organisation of the genome. We observe that more than forty percent of chromatin-associated proteins display a poised and heterogeneous distribution along the chromosome, creating a heteropolymer. This distribution changes upon heat shock in a concerted, state-specific manner. Simulating yeast chromosomes as heteropolymers, in which the mobility of each segment depends on its cumulative protein occupancy, results in functionally relevant structures, which match our experimental data. This thermodynamically driven self-organisation achieves spatial clustering of poised genes and mechanistically contributes to the directed relocalisation of active genes to the nuclear periphery upon heat shock. One Sentence Summary:Unequal protein occupancy and chromosome segment mobility drive 3D organisation of the genome.Main Text: Eukaryotic genomes are highly organised in three dimensions ( 1 , 2 ) and this spatial organisation has to be maintained in order to achieve the correct gene expression profiles ( 3 -6 ) . The 3D organisation of the genome is thus central to many aspects of cell biology and has been intensely investigated during normal growth ( 7 -9 ) , differentiation ( 10 -12 ) , cell division ( 13 ) , senescence ( 14 ) , and disease ( 5 , 6 , 15 ) , and has been shown to arise independently of transcription ( 16 ) . In the budding yeast Saccharomyces cerevisiae , target genes of most transcription factors are enriched in specific regions along the chromosome in one dimension ( 17 ) , or in the genome in three dimensions ( 18 ) . A central question in the field is by which mechanisms this 3D organisation is achieved.Any mechanism that organises genome structure has to do so in a highly dynamic and crowded nucleoplasm ( 19 , 20 ) . The prevalent view is that 3D genome organisation comes about despite the known intrinsic fluctuations of the chromatin fibre. Most studies focus on stable interactions between DNA-bound proteins that connect two chromatin loci ( 9 , 21 -27 ) . Here, we propose and validate a fundamentally different mechanism: The mobility of the chromatin fibre is not uniform, but heterogeneous, along its length, as a result of the unequal distribution of protein binding along the genome. This leads to thermodynamically driven self-organisation, which we observe experimentally, and which we show to have important functional implications.Determination and characterisation of chromatin states. In order to analyse the global effects of protein binding on spatial organisation of yeast chromosomes, and incorporate these data into pe...

Interfacial Properties of Active-Passive Polymer Mixtures

“…While the critical ratio is unfeasibly high for colloidal particles, if the particles are polymers, the ordered phase may be experimentally realized, as the critical ratio decreases with their length [ 10 ]. This supports the hypothesis that the effect might play a role in separation of active and passive DNA strands in living cells [ 9 , 10 , 11 , 12 ]. There, the activity can originate from transcription, repair or looping extrusion processes that consume energy to fuel the molecular motors that drag the DNA strands.…”

Polymer folding through active processes recreates features of genome organization

“…Consistent with prior work (50,52,54,55), we also find that pairs of active segments get farther apart while inactive segments come closer together [above the diagonal in Fig. 2B].…”

Hi-D: nanoscale mapping of nuclear dynamics in single living cells

“…Heterogeneous chromatin motion arises due to irregular protein binding along the chromosomes and can lead to thermodynamic or electrostatic self-organization of nuclear compartments [46,47]. Local patches of large anomalous exponents indicate super-diffusive behavior of chromatin which may result, among others, from active noise acting on the chromatin fiber [48,49], even in quiescent cells.…”