Assessing cell lines with inducible depletion of cohesin and condensins components through analysis of metaphase chromosome morphology

One of the most productive strategies for finding the functions of proteins is to study the consequences of loss of protein function. For this purpose, cells or organisms with a knockout of the gene encoding the protein of interest are obtained. However, many proteins perform important functions and cells or organisms could suddenly lose fitness when the function of a protein is lost. For such proteins, the most productive strategy is to use inducible protein degradation systems. A system of auxin-dependent protein degradation is often implemented. To use this system, it is sufficient to introduce a transgene encoding a plant-derived auxin-dependent ubiquitin ligase into mammalian cells and insert a sequence encoding a degron domain into the gene of interest. A crucial aspect of development of cell lines engineered for inducible protein depletion is the selection of cell clones with efficient auxin-dependent degradation of the protein of interest. To select clones induced by depletion of the architectural chromatin proteins RAD21 (a component of the cohesin complex) and SMC2 (a component of the condensin complex), we propose to use the morphology of metaphase chromosomes as a convenient functional test. In this work, we obtained a series of clones of human HAP1 cells carrying the necessary genetic constructs for inducible depletion of RAD21 and SMC2. The degradation efficiency of the protein of interest was assessed by flow cytometry, Western blotting and metaphase chromosome morphology test. Based on our tests, we showed that the clones we established with the SMC2 degron effectively and completely lose protein function when induced by auxin. However, none of the HAP1 clones we created with the RAD21 degron showed complete loss of RAD21 function upon induction of degradation by auxin. In addition, some clones showed evidence of loss of RAD21 function even in the absence of induction. The chromosome morphology test turned out to be a convenient and informative method for clone selection. The results of this test are in good agreement with flow cytometry analysis and Western blotting data.

Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging

SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.

SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization

Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an epigenetic regulator that mediates gene expression silencing at targeted sites across the genome. Our current understanding of SMCHD1's molecular mechanism, and how substitutions within SMCHD1 lead to the diseases, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS), are only emerging. Recent structural studies of its two component domains - the N-terminal ATPase and C-terminal SMC hinge - suggest that dimerization of each domain plays a central role in SMCHD1 function. Here, using biophysical techniques, we demonstrate that the SMCHD1 ATPase undergoes dimerization in a process that is dependent on both the N-terminal UBL (Ubiquitin-like) domain and ATP binding. We show that neither the dimerization event, nor the presence of a C-terminal extension past the transducer domain, affect SMCHD1's in vitro catalytic activity as the rate of ATP turnover remains comparable to the monomeric protein. We further examined the functional importance of the N-terminal UBL domain in cells, revealing that its targeted deletion disrupts the localization of full-length SMCHD1 to chromatin. These findings implicate UBL-mediated SMCHD1 dimerization as a crucial step for chromatin interaction, and thereby for promoting SMCHD1-mediated gene silencing.

The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.

Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo

The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.

Alternating Dynamics of oriC, SMC, and MksBEF in Segregation of Pseudomonas aeruginosa Chromosome

Mechanisms that define the chromosome as a structural entity remain unknown. Key elements in this process are condensins, which globally organize chromosomes and contribute to their segregation. This study characterized condensin and chromosome dynamics in Pseudomonas aeruginosa, which harbors condensins from two major protein superfamilies, SMC and MksBEF. The study revealed that both proteins play a dual role in chromosome maintenance by spatially organizing the chromosomes and guiding their segregation but can substitute for each other in some activities. The timing of chromosome, SMC, and MksBEF relocation was highly ordered and interdependent, revealing causative relationships in the process. Moreover, MksBEF produced clusters at the site of chromosome replication that survived cell division and remained in place until replication was complete. Overall, these data delineate the functions of condensins from the SMC and MksBEF superfamilies, reveal the existence of a chromosome organizing center, and suggest a mechanism that might explain the biogenesis of chromosomes.

Condensins are essential for global chromosome organization in diverse bacteria. Atypically, the Pseudomonas aeruginosa chromosome encodes condensins from two superfamilies, SMC-ScpAB and MksBEF. Here, we report that the two proteins play specialized roles in chromosome packing and segregation and are synthetically lethal with ParB. Inactivation of SMC or MksB affected, in a protein-dependent manner, global chromosome layout and its timing of segregation and sometimes triggered a chromosomal inversion. The localization pattern was also unique to each protein. SMC clusters colocalized with oriC throughout the cell cycle except shortly after origin duplication, whereas MksB clusters emerged at cell quarters shortly prior to oriC duplication and stayed there even after cell division. The relocation of the proteins was abrupt and coordinated with oriC dynamic. These data reveal that the two condensins play distinct dual roles in chromosome maintenance by organizing it and mediating its segregation. Furthermore, the choreography of condensins and oriC relocations suggest an elegant mechanism for the birth and maturation of chromosomes.

IMPORTANCE Mechanisms that define the chromosome as a structural entity remain unknown. Key elements in this process are condensins, which globally organize chromosomes and contribute to their segregation. This study characterized condensin and chromosome dynamics in Pseudomonas aeruginosa, which harbors condensins from two major protein superfamilies, SMC and MksBEF. The study revealed that both proteins play a dual role in chromosome maintenance by spatially organizing the chromosomes and guiding their segregation but can substitute for each other in some activities. The timing of chromosome, SMC, and MksBEF relocation was highly ordered and interdependent, revealing causative relationships in the process. Moreover, MksBEF produced clusters at the site of chromosome replication that survived cell division and remained in place until replication was complete. Overall, these data delineate the functions of condensins from the SMC and MksBEF superfamilies, reveal the existence of a chromosome organizing center, and suggest a mechanism that might explain the biogenesis of chromosomes.

Genome organization via loop extrusion, insights from polymer physics models

Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.

Live-Cell Fluorescence Imaging of RecN in Caulobacter crescentus Under DNA Damage

Structural maintenance of chromosomes (SMC) proteins play a central role in the organization, segregation and maintenance of chromosomes across domains of life. In bacteria, an SMC-family protein, RecN, has been implicated to have important functions in DNA damage repair. Recent studies have suggested that RecN is required to increase chromosome cohesion in response to DNA damage and may also stimulate specific events during recombination-based repair. While biochemical and genetic assays provide insights into mechanism of action of RecN and other repair factors, in vivo understanding of activity and regulation of proteins can be predominantly gained via microscopy-based approaches. Here, we describe a protocol to study the localization of fluorescently tagged RecN to a site-specific double-strand break (DSB) in Caulobacter crescentus. We further outline a method to probe RecN dynamics in cells with a single, nonreplicating chromosome. This technique can be used to study the early steps of recombination-based repair and understand the regulation of protein recruitment to and further association with sites of damage.

MksB, an alternate condensin from Mycobacterium smegmatis is involved in DNA binding and condensation

The structural maintenance of chromosomes (SMC) proteins play a vital role in genome stability and chromosome organization in all domains of life. Previous reports show that smc deletion causes decondensation of chromosome and an increased frequency of anucleated cells in bacteria. However, smc deletion in both Mycobacterium smegmatis and Mycobacterium tuberculosis did not affect chromosome condensation or the frequency of anucleated cells. In an attempt to understand this difference in M. smegmatis, we investigated the function of MksB (MsMksB), an alternate SMC-like protein. Like other bacterial SMCs, MsMksB is also an elongated homodimer, in which a central hinge domain connects two globular ATPase head domains via two coiled-coil arms. We show that full-length MsMksB binds to different topological forms of DNA without any preferences. However, the hinge and headless domains prefer binding to single-stranded DNA (ssDNA) and linear double-stranded DNA (dsDNA), respectively. The binding of MsMksB to DNA was independent of ATP as its ATP hydrolysis deficient mutant was also proficient in DNA binding. Further, the cytological profiling studies revealed that only the full-length MsMksB and none of its structural domains could condense the bacterial chromosome. This observation indicates the plausibility of the concerted action of different structural domains of SMC to bind and condense the chromosome. Moreover, MsMksB exhibited DNA stimulated ATPase activity, in addition to its intrinsic ATPase activity. Taken together, we have elucidated the function of an alternate bacterial condensin protein MksB and its structural domains in DNA binding and condensation.

Factors, mechanisms and implications of chromatin condensation and chromosomal structural maintenance through the cell cycle

A series of well-orchestrated events help in the chromatin condensation and the formation of chromosomes. Apart from the formation of chromosomes, maintenance of their structure is important, especially for the cell division. The structural maintenance of chromosome (SMC) proteins, the non-SMC proteins and the SMC complexes are critical for the maintenance of chromosome structure. While condensins have roles for the DNA compaction, organization, and segregation, the cohesin functions in a cyclic manner through the cell cycle, as a "cohesin cycle." Specific mechanisms maintain the architecture of the centromere, the kinetochore and the telomeres which are in tandem with the cell cycle checkpoints. The presence of chromosomal territories and compactness differences through the length of the chromosomes might have implications on selective susceptibility of specific chromosomes for induced genotoxicity.

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins-such as cohesins and condensins-can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.

tRNA Genes Affect Chromosome Structure and Function via Local Effects

The genome is packaged and organized in an ordered, nonrandom manner, and specific chromatin segments contact nuclear substructures to mediate this organization. tRNA genes (tDNAs) are binding sites for transcription factors and architectural proteins and are thought to play an important role in the organization of the genome. In this study, we investigate the roles of tDNAs in genomic organization and chromosome function by editing a chromosome so that it lacked any tDNAs. Surprisingly our analyses of this tDNA-less chromosome show that loss of tDNAs does not grossly affect chromatin architecture or chromosome tethering and mobility. However, loss of tDNAs affects local nucleosome positioning and the binding of SMC proteins at these loci. The absence of tDNAs also leads to changes in centromere clustering and a reduction in the frequency of long-range HML-HMR heterochromatin clustering with concomitant effects on gene silencing. We propose that the tDNAs primarily affect local chromatin structure, which results in effects on long-range chromosome architecture.

Tracking Bacterial Chromosome Dynamics with Microfluidics-Based Live Cell Imaging

In bacteria, chromosomes are highly organized within the limited volume of the cell to form a nucleoid. Recent application of microscopy and chromosome conformation capture techniques have together provided a comprehensive understanding of the nature of this organization and the role of factors such as the structural maintenance of chromosomes (SMC) proteins in the establishment and maintenance of the same. In this chapter, we outline a microfluidics-based approach for live cell imaging of Escherichia coli chromosome dynamics in wild-type cells. This assay can be used to track the activity of the SMC complex, MukBEF, on DNA and assess the impact of perturbations such as DNA damage on chromosome organization and segregation.

Topological in vitro loading of the budding yeast cohesin ring onto DNA

The biochemical reconstitution of topological DNA binding by budding yeast cohesin yields surprises and opens opportunities to exploit experimental approaches developed in this model organism.

The ring-shaped chromosomal cohesin complex holds sister chromatids together by topological embrace, a prerequisite for accurate chromosome segregation. Cohesin plays additional roles in genome organization, transcriptional regulation, and DNA repair. The cohesin ring includes an ABC family ATPase, but the molecular mechanism by which the ATPase contributes to cohesin function is not yet understood. In this study, we have purified budding yeast cohesin, as well as its Scc2–Scc4 cohesin loader complex, and biochemically reconstituted ATP-dependent topological cohesin loading onto DNA. Our results reproduce previous observations obtained using fission yeast cohesin, thereby establishing conserved aspects of cohesin behavior. Unexpectedly, we find that nonhydrolyzable ATP ground state mimetics ADP·BeF₂, ADP·BeF₃⁻, and ADP·AlF_x, but not a hydrolysis transition state analog ADP·VO₄³⁻, support cohesin loading. The energy from nucleotide binding is sufficient to drive the DNA entry reaction into the cohesin ring. ATP hydrolysis, believed to be essential for in vivo cohesin loading, must serve a subsequent reaction step. These results provide molecular insights into cohesin function and open new experimental opportunities that the budding yeast model affords.

DNA replication stress and its impact on chromosome segregation and tumorigenesis

Genome instability and cell cycle dysregulation are commonly associated with cancer. DNA replication stress driven by oncogene activation during tumorigenesis is now well established as a source of genome instability. Replication stress generates DNA damage not only during S phase, but also in the subsequent mitosis, where it impacts adversely on chromosome segregation. Some regions of the genome seem particularly sensitive to replication stress-induced instability; most notably, chromosome fragile sites. In this article, we review some of the important issues that have emerged in recent years concerning DNA replication stress and fragile site expression, as well as how chromosome instability is minimized by a family of ring-shaped protein complexes known as SMC proteins. Understanding how replication stress impacts on S phase and mitosis in cancer should provide opportunities for the development of novel and tumour-specific treatments.

MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin

The Escherichia coli SMC complex, MukBEF, acts in chromosome segregation. MukBEF shares the distinctive architecture of other SMC complexes, with one prominent difference; unlike other kleisins, MukF forms dimers through its N-terminal domain. We show that a 4-helix bundle adjacent to the MukF dimerisation domain interacts functionally with the MukB coiled-coiled ‘neck’ adjacent to the ATPase head. We propose that this interaction leads to an asymmetric tripartite complex, as in other SMC complexes. Since MukF dimerisation is preserved during this interaction, MukF directs the formation of dimer of dimer MukBEF complexes, observed previously in vivo. The MukF N- and C-terminal domains stimulate MukB ATPase independently and additively. We demonstrate that impairment of the MukF interaction with MukB in vivo leads to ATP hydrolysis-dependent release of MukBEF complexes from chromosomes.

Most DNA in a cell is arranged in structures called chromosomes. From bacteria to humans, chromosomes have to be compacted and highly organized to allow the cells to maintain and use their genetic information. In all organisms, large ring-shaped protein complexes play a crucial role in managing chromosomes. They transport and organize DNA thanks to reactions whose precise mechanism remains unknown. In bacteria, MukB and a type of kleisin called MukF are two examples of molecules involved in chromosome management.

Two MukBs join at one end to form a hinge; at the other end, each MukB protein has a neck and a head. The two heads are linked by the kleisin to form a large protein ring, which can open to capture DNA. The MukB heads can trigger a biochemical reaction that creates the energy essential to trap and release DNA during DNA transport.

Here, Zawadzka et al. study how the different components of the MukB-kleisin complex interact with each other to undergo the biochemical reactions that lead to DNA transport. The experiments show that the kleisin joins two MukB heads by attaching the base of one to the neck of the other, asymmetrically closing the ring. The separate interactions of different regions of the kleisin to the head and neck of MukB independently activate the two MukB heads, thereby controlling essential steps in the reactions with DNA. Two MukB-kleisin ring complexes are joined to each other because of a tight interaction between the two kleisin molecules. This leads Zawadzka et al. to suggest that DNA is sequentially grabbed and released from these two rings during DNA transport, similar to how a climbing rope is attached and released through carabiners.

Cells cannot survive or be healthy without their chromosomes being accurately managed. It is still unclear how molecules such as MukBs and kleinsins drive this process. A better picture of their structure and interactions is an essential first step to understand these mechanisms.

Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism

Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual DNA molecules by the budding yeast condensin complex. We show that compaction can proceed in large steps, driving DNA molecules into a fully condensed state against forces of up to 2 pN. Compaction can be reversed by applying high forces or adding buffer of high ionic strength. While condensin can stably bind DNA in the absence of ATP, ATP hydrolysis by the SMC subunits is required for rendering the association salt insensitive and for the subsequent compaction process. Our results indicate that the condensin reaction cycle involves two distinct steps, where condensin first binds DNA through electrostatic interactions before using ATP hydrolysis to encircle the DNA topologically within its ring structure, which initiates DNA compaction. The finding that both binding modes are essential for its DNA compaction activity has important implications for understanding the mechanism of chromosome compaction.

Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes

In this study, Wang et al. perform genome-wide analyses that implicate condensin in the suppression of hundreds of loci, acting in both DNA methylation-dependent and methylation-independent pathways. They show that silencing of transposons in the pericentromeric heterochromatin of Arabidopsis thaliana requires SMC4, a core subunit of condensins I and II, acting in conjunction with CG methylation by MET1, CHG methylation by CMT3, the chromatin remodeler DDM1, and histone modifications, including H3K27me1, imparted by ATXR5 and ATXR6.

In eukaryotes, transcriptionally inactive loci are enriched within highly condensed heterochromatin. In plants, as in mammals, the DNA of heterochromatin is densely methylated and wrapped by histones displaying a characteristic subset of post-translational modifications. Growing evidence indicates that these chromatin modifications are not sufficient for silencing. Instead, they are prerequisites for further assembly of higher-order chromatin structures that are refractory to transcription but not fully understood. We show that silencing of transposons in the pericentromeric heterochromatin of Arabidopsis thaliana requires SMC4, a core subunit of condensins I and II, acting in conjunction with CG methylation by MET1 (DNA METHYLTRANSFERASE 1), CHG methylation by CMT3 (CHROMOMETHYLASE 3), the chromatin remodeler DDM1 (DECREASE IN DNA METHYLATION 1), and histone modifications, including histone H3 Lys 27 monomethylation (H3K27me1), imparted by ATXR5 and ATXR6. SMC4/condensin also acts within the mostly euchromatic chromosome arms to suppress conditionally expressed genes involved in flowering or DNA repair, including the DNA glycosylase ROS1, which facilitates DNA demethylation. Collectively, our genome-wide analyses implicate condensin in the suppression of hundreds of loci, acting in both DNA methylation-dependent and methylation-independent pathways.

The loading of condensin in the context of chromatin

The packaging of DNA into chromosomes is a ubiquitous process that enables living organisms to structure and transmit their genome accurately through cell divisions. In the three kingdoms of life, the architecture and dynamics of chromosomes rely upon ring-shaped SMC (Structural Maintenance of Chromosomes) condensin complexes. To understand how condensin rings organize chromosomes, it is essential to decipher how they associate with chromatin filaments. Here, we use recent evidence to discuss the role played by nucleosomes and transcription factors in the loading of condensin at transcribed genes. We propose a model whereby cis-acting features nestled in the promoters of active genes synergistically attract condensin rings and promote their association with DNA.

Condensins and 3D Organization of the Interphase Nucleus

Condensins are conserved multi-subunit protein complexes that participate in eukaryotic genome organization. Well known for their role in mitotic chromosome condensation, condensins have recently emerged as integral components of diverse interphase processes. Recent evidence shows that condensins are involved in chromatin organization, gene expression, and DNA repair and indicates similarities between the interphase and mitotic functions of condensin. Recent work has enhanced our knowledge of how chromatin architecture is dynamically regulated by condensin to impact essential cellular processes.