Beltran, B. | Search bioRxiv

bioRxiv2021

Homologous locus pairing is a transient, diffusion-mediated process in meiotic prophase

The pairing of homologous chromosomes (homologs) in meiosis is essential for distributing the correct numbers of chromosomes into haploid gametes. In budding yeast, pairing depends on the formation of 150-200 Spo11-mediated double-strand breaks (DSBs) that are distributed among 16 homolog pairs, but it is not known if all, or only a subset of these DSBs, contribute to the close juxtaposition of homologs. Having established a system to measure the position of fluorescently tagged chromosomal loci in 3D space over time, we analyzed locus trajectories to determine how frequently, and how long, loci spend colocalized or apart. Continuous imaging revealed highly heterogeneous cell-to-cell behavior of foci, with the majority of cells exhibiting a "mixed" phenotype where foci move into and out of proximity, even at late stages of prophase, suggesting that the axial structures of the synaptonemal complex may be more dynamic than anticipated. The observed plateaus of the mean-squared change in distance (MSCD) between foci informed the development of a biophysical model of two diffusing polymers that captures the loss of centromere linkages as cells enter meiosis, nuclear confinement, and the formation of Spo11-dependent linkages. The predicted number of linkages per chromosome in our theoretical model closely approximates the small number (~2-4) of estimated synapsis-initiation sites, suggesting that excess DSBs have negligible effects on the overall juxtaposition of homologs. These insights into the dynamic in-terchromosomal behavior displayed during homolog pairing demonstrate the power of combining time-resolved in vivo analysis with modeling at the granular level. Significance StatementEssential for sexual reproduction, meiosis is a specialized cell division required for the production of haploid gametes. Critical to this process is the pairing, recombination, and segregation of homologous chromosomes (homologs). While pairing and recombination are linked, it is not known how many linkages are sufficient to hold homologs in proximity. Here, we reveal that random diffusion and the placement of a small number of linkages are sufficient to establish the apparent "pairing" of homologs. We also show that colocalization between any two loci is more dynamic than anticipated. Our study is the first to provide observations of live interchromosomal dynamics during meiosis and illustrates the power of combining single-cell measurements with theoretical polymer modeling.

genetics↗

bioRxiv2019

Heterogeneity in Nucleosome Spacing Governs Chromatin Elasticity

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain (WLC) model to include statistically spaced, rigid kinks. On time scales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can differ by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer time scales, we show that continuous re-randomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that heterogeneity in nucleosome spacing acts as the dominant source of chromatin elasticity and governs both local and global chromatin organization.

biophysics↗

bioRxiv2018

RNA polymerases display collaborative and antagonistic group behaviors over long distances through DNA supercoiling

Transcription by RNA polymerases (RNAPs) is essential for cellular life. Genes are often transcribed by multiple RNAPs. While the properties of individual RNAPs are well appreciated, it remains less explored whether group behaviors can emerge from co-transcribing RNAPs under most physiological levels of gene expression. Here, we provide evidence in Escherichia coli that well-separated RNAPs can exhibit collaborative and antagonistic group dynamics. Co-transcribing RNAPs translocate faster than a single RNAP, but the density of RNAPs has no significant effect on their average speed. When a promoter is inactivated, RNAPs that are far downstream from the promoter slow down and experience premature dissociation, but only in the presence of other co-transcribing RNAPs. These group behaviors depend on transcription-induced DNA supercoiling, which can also mediate inhibitory dynamics between RNAPs from neighboring divergent genes. Our findings suggest that transcription on topologically-constrained DNA, a norm across organisms, can provide an intrinsic mechanism for modulating the speed and processivity of RNAPs over long distances according to the promoters on/off state.

microbiology↗