1. Chromosomes and Gene Expression
  2. Computational and Systems Biology

Genome Organization: The loopy world of cohesin

DNA loops can be formed by a mechanism in which the cohesin complex pulls DNA strands through its ring structure using biased Brownian motion.
https://doi.org/10.7554/eLife.71585
  • Download
  • Cite
  • CommentOpen annotations (there are currently 0 annotations on this page).
Share this article
Cite this article
  1. Kazuhiro Maeshima
  2. Shiori Iida
(2021)
Genome Organization: The loopy world of cohesin
eLife 10:e71585.
https://doi.org/10.7554/eLife.71585
  2. Download BibTeX
  3. Download .RIS
  1. Kazuhiro Maeshima  Is a corresponding author
  2. Shiori Iida
  1. Genome Dynamics Laboratory, National Institute of Genetics, Japan
  2. Department of Genetics, School of Life Sciences, Sokendai (Graduate University for Advanced Studies), Japan

How are very long strands of genomic DNA stored in a tiny cell? In eukaryotes, genomic DNA is wrapped around core histones to form nucleosomes (Olins and Olins, 2003), which are associated with various proteins that package the DNA into chromatin so it can fit inside the nucleus (Maeshima et al., 2021). While some protein complexes are known to play a critical role in the organization of chromatin like loops that allow RNA transcription or DNA replication to be carried out, it remains unclear how chromatin is arranged into such loops.

A protein complex thought to be involved in these arrangements is a ring-like structure called cohesin (Figure 1A). It performs two main roles: firstly, it provides ‘cohesion’ between replicated chromatin by holding sister chromatids together during cell division until the cell is ready to segregate them into two daughter cells (Nasmyth and Haering, 2005; Davidson and Peters, 2021). Secondly, it makes chromatin loops that build functional domains, limitingcurbing chromatin motion (Nozaki et al., 2017; Davidson and Peters, 2021). But how does cohesin carry out these two distinct jobs?

Figure 1
Download asset Open asset
Structure and activity of cohesin.

(A) Structural overview of the cohesin complex subunits. The two main subunits Smc1/Smc3 (gray and yellow) associate at a hinge on one end and at their ATPase heads on the other. These subunits form …

A recent model, called loop extrusion, suggests that genomic DNA is constantly pushed out through the cohesin ring to form loops (Davidson and Peters, 2021). This mechanism is thought to keep local regions of DNA together while disentangling them from other parts of the genome. Previous in vitro experiments have shown that cohesin is able to capture protein-free DNA in its ring through a mechanism called topological DNA entrapping or loading (Figure 1B; Murayama and Uhlmann, 2014). More recent research has reported that cohesin can also form loops by extruding sections of DNA not bound to protein (Davidson et al., 2019). However, how cohesin pushes out DNA through its ring structure remained unclear. Now, in eLife, Frank Uhlmann and colleagues from the Francis Crick Institute and University College London – including Torahiko Higashi as first author – report a potential mechanism for how cohesin forms DNA loops in vitro based on cryo-electron microscopy and biochemical observations (Higashi et al., 2021).

Cohesin contains two subunits called Smc1 and Smc3 that each contain a hinge domain that joins the two molecules together (Figure 1A; Davidson and Peters, 2021). At the other end of each subunit is an ATPase head which can bind and hydrolyze ATP: this causes the ATPase head to join together or disassociate from one another depending on the situation. A third protein called kleisin connects to the Smc1 ATPase head via its C-terminal domain, while its N-terminal domain can associate and separate from the Smc3 ATPase head. Kleisin also interacts with two other subunits, the cohesin loader and the Scc3 protein. The cohesin ring structure has two ‘gates’ that DNA can go through: the ‘N-gate’, where the N-terminal of kleisin binds to Smc3, and the ‘head gate’, where the two ATPase head domains of Smc1 and Smc3 meet (Figure 1A).

Previously, a group of researchers – including some of the researchers involved in the Higashi et al. study – described how ATP-dependent structural changes in cohesin drive DNA entry into the ring for topological DNA entrapping (Figure 1B; Higashi et al., 2020). First, the N-gate opens upon ATP binding, and DNA crosses it, occupying the space between kleisin and the two ATPase heads. Then, the N-gate closes as the cohesin loader locks the DNA against the ATPase head gate, and cohesin enters the ‘DNA gripping state’, in which DNA is trapped between the two gates. Finally, the ATP is hydrolyzed, which opens the head gate, straightening up the complex, and the DNA goes through that gate, entering the ring and leading to topological DNA entrapping (Figure 1B).

Higashi et al. then realized that if DNA does not cross the kleisin N-gate, the DNA gripping state could extrude DNA into a loop (Figure 1C; Higashi et al., 2021). Cohesin’s DNA loop extrusion activity can therefore be explained as a ‘branching path’ of the topological DNA entrapping reaction. In this case, when DNA is in the gripping state, it is bound to cohesin in two places: at the Smc hinge (through Scc3) and at the ATPase heads (Figure 1C). Following ATP hydrolysis, these two binding sites (or modules) separate, but because the N-gate is closed, DNA cannot go through the gates to fully enter the ring, like in topological DNA entrapping. Instead it loops into a U shape. The hinge module, attached to DNA via Scc3, swings away from the head module by diffusion (biased Brownian motion)(Figure 1C), extruding DNA (Figure 1D, steps 1 and 2). When the hinge module returns to its original position to form of a new gripping state, the next loop extrusion cycle can proceed, driving loop growth (Figure 1D, steps 3 and 4).

Higashi et al.’s work provides mechanistic insight into the looping activity of cohesin, as well as posing important questions regarding its biological relevance. Firstly, how is the N-gate kept closed in the ‘branching path’ of loop extrusion the topological DNA entrapping? The electrostatic interactions that contribute to keeping the N-gate closed are facilitated by low salt conditions that are not physiological, implying that loop extrusion may be much easier in vitro.

Secondly, is loop extrusion activity conserved in other SMC-related complexes between different organisms? The family of SMC complexes is widely spread from bacteria to human, and loop extrusion activity has been reported using cohesin from both human and fission yeast, and condensin – a SMC complex involved in chromosome assembly during cell division – from budding yeast (Davidson et al., 2019; Higashi et al., 2021; Ganji et al., 2018; Hirano, 2016). Since loop extrusion seems to depend on the distance between the hinge and head modules, certain SMC-related complexes, like SMC5/6 complexes and bacterial Smc complexes, may not allow this activity (Higashi et al., 2021). This suggests that loop extrusion may be unique to specific SMC complexes, and potentially only possible in certain organisms.

Finally, the loop extrusion activity by cohesin and condensin has been only observed in vitro, with protein-free DNA (Davidson et al., 2019; Higashi et al., 2021; Ganji et al., 2018). But in vivo, how do these proteins cope with eukaryotic chromatin, which is bound to histones forming clusters seems to consist of nucleosome clusters with various binding proteins (e.g. Nozaki et al., 2017)? Higashi et al. expect cohesin (or condensin) to be able to bypass single nucleosomes, but not clusters of nucleosomes (Higashi et al., 2021). Therefore, another mechanism may be needed to explain how chromatin loops are formed in living cells. One possibility is diffusion capture in which cohesin (or condensin) stabilizes interactions between binding sites in chromatin (Gerguri et al., 2021).

References

Article and author information

Author details

  1. Kazuhiro Maeshima

    Kazuhiro Maeshima is in the Genome Dynamics Laboratory, National Institute of Genetics and the Department of Genetics, School of Life Sciences, Sokendai (Graduate University for Advanced Studies) in Mishima, Japan
    For correspondence
    kmaeshim@nig.ac.jp
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3909-0341

  2. Shiori Iida

    Shiori Iida is in the Genome Dynamics Laboratory, National Institute of Genetics and the Department of Genetics, School of Life Sciences, Sokendai (Graduate University for Advanced Studies) in Mishima, Japan
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1115-4705

Publication history

  1. Version of Record published:

Copyright

© 2021, Maeshima and Iida

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,999
    views
  • 206
    downloads
  • 3
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

Categories and tags

Research organisms

    1. Related to

    A Brownian ratchet model for DNA loop extrusion by the cohesin complex

    Torahiko L Higashi, Georgii Pobegalov ... Frank Uhlmann
  2. Further reading

Further reading

    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    A Brownian ratchet model for DNA loop extrusion by the cohesin complex

    Torahiko L Higashi, Georgii Pobegalov ... Frank Uhlmann
    Research Article

    The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin’s heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.

    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition

    Gülnihal Kavaklioglu, Alexandra Podhornik ... Christian Seiser
    Research Article

    Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.

    1. Chromosomes and Gene Expression

    Nuclear Argonaute protein NRDE-3 switches small RNA partners during embryogenesis to mediate temporal-specific gene regulatory activity

    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.