The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring‐shaped protein complexes that are thought to function by entrapping DNA. It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three‐dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single‐molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA‐bound proteins and nucleosomes but is constrained in its movement by transcription and DNA‐bound CCCTC‐binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion.

We have generated a strain of mice lacking two DNA N-glycosylases of base excision repair (BER), NTH1 and NEIL1, homologs of bacterial Nth (endonuclease three) and Nei (endonuclease eight). Although these enzymes remove several oxidized bases from DNA, they do not remove the well-known carcinogenic oxidation product of guanine: 7,8-dihydro-8-oxoguanine (8-OH-Gua), which is removed by another DNA N-glycosylase, OGG1. The Nth1−/−Neil1−/− mice developed pulmonary and hepatocellular tumors in much higher incidence than either of the single knockouts, Nth1−/− and Neil1−/−. The pulmonary tumors contained, exclusively, activating GGT→GAT transitions in codon 12 of K-ras of their DNA. Such transitions contrast sharply with the activating GGT→GTT transversions in codon 12 of K-ras of the pathologically similar pulmonary tumors, which arose in mice lacking OGG1 and a second DNA N-glycosylase, MUTY. To characterize the biochemical phenotype of the knockout mice, the content of oxidative DNA base damage was analyzed from three tissues isolated from control, single and double knockout mice. The content of 8-OH-Gua was indistinguishable among all genotypes. In contrast, the content of 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) derived from adenine and guanine, respectively, were increased in some but not all tissues of Neil1−/− and Neil1−/−Nth1−/− mice. The high incidence of tumors in our Nth1−/−Neil1−/− mice together with the nature of the activating mutation in the K-ras gene of their pulmonary tumors, reveal for the first time, the existence of mutagenic and carcinogenic oxidative damage to DNA which is not 8-OH-Gua.

The ring-shaped cohesin complex is thought to topologically hold sister chromatids together from their synthesis in S phase until chromosome segregation in mitosis. How cohesin stably binds to chromosomes for extended periods, without impeding other chromosomal processes that also require access to the DNA, is poorly understood. Budding yeast cohesin is loaded onto DNA by the Scc2–Scc4 cohesin loader at centromeres and promoters of active genes, from where cohesin translocates to more permanent places of residence at transcription termination sites. Here we show that, at the GAL2 and MET17 loci, pre-existing cohesin is pushed downstream along the DNA in response to transcriptional gene activation, apparently without need for intermittent dissociation or reloading. We observe translocation intermediates and find that the distribution of most chromosomal cohesin is shaped by transcription. Our observations support a model in which cohesin is able to slide laterally along chromosomes while maintaining topological contact with DNA. In this way, stable cohesin binding to DNA and enduring sister chromatid cohesion become compatible with simultaneous underlying chromosomal activities, including but maybe not limited to transcription.

SummaryCohesin is best known as a crucial component of chromosomal stability. Composed of several essential subunits in budding yeast, cohesin forms a ring-like complex that is thought to embrace sister chromatids, thereby physically linking them until their timely segregation during cell division. The ability of cohesin to bind chromosomes depends on the Scc2-Scc4 complex, which is viewed as a loading factor for cohesin onto DNA. Notably, in addition to its canonical function in sister chromatid cohesion, cohesin has also been implicated in gene regulation and development in organisms ranging from yeast to human. Despite its importance, both as a mediator of sister chromatid cohesion and as a modulator of gene expression, the nature of the association of cohesin with chromosomes that enables it to fulfil both of these roles remains incompletely understood. The mechanism by which cohesin is loaded onto chromosomes, and how cohesin and the related condensin and Smc5-Smc6 complexes promote DNA interactions require further elucidation. In this Commentary, we critically review the evidence for cohesin loading and its subsequent apparent sliding along chromosomes, and discuss the implications gained from cohesin localisation studies for its important functions in chromosome biology. Journal of Cell Scienceand lethality. In this case, cohesin is thought to promote transcriptional activity of an ecdysone receptor gene (Pauli et al., 2008;Schuldiner et al., 2008). The requirement for cohesin in differentiated, post-mitotic cells provides clear evidence for a function of cohesin on chromosomes that is distinct from its role in cell division. A recent comprehensive analysis of the consequences of cohesin disruption on gene expression from polytene chromosomes in Drosophila salivary gland cells has revealed a role for cohesin in both the upregulation and downregulation of several genes in the vicinity of its binding sites (Pauli et al., 2010). How cohesin and changes to its expression levels result in distinct transcriptional outcomes at individual gene loci and in different cell types is incompletely understood (Schaaf et al., 2009).In zebrafish, cohesin has been shown to positively regulate the Runx transcription factors, which determine cell fate during early embryonic development. Downregulation of the Scc1 or Smc3 cohesin subunits leads to aberrant expression of Runx proteins in a dose-dependent manner, despite cell division being able to proceed (Horsfield et al., 2007). Finally, in mouse and human cells, cohesin-binding sites on chromosomes significantly overlap with those of the transcriptional insulator CCCTC-binding factor (CTCF) (Parelho et al., 2008;Wendt et al., 2008). This colocalisation is functionally relevant because depletion of cohesin subunits Scc1 or Smc3 recapitulates the loss of insulator function seen after CTCF depletion. Notably, the effect of cohesin on the well-characterised insulator at the H19-Igf2 locus is observed even in the G1 phase of the cell cycle, when sister chromatids are absent. Th...