Highlights d Stress granule formation requires RNA-binding nodes with high network connectivity d Capping of nodes by ligands lacking connectivity prevents condensation d Protein disorder and RNA-binding specificity play nonessential, modulatory roles d Competition of RNP networks for connecting nodes controls multiphase organization

Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. We used single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of adenosine triphosphate hydrolysis–dependent translocation along double-stranded DNA. Condensin’s translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ~60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil subunits, indicative of a translocation mechanism that is distinct from any reported for a DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.

One Sentence Summary: Single-molecule imaging reveals that eukaryotic condensin is a highly processive DNA-translocating motor complex. Abstract:Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. Here, we use single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of ATP hydrolysis-dependent translocation along double-stranded DNA. Condensin's translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ~60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil subunits, suggestive of a translocation mechanism that is distinct from any reported DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.Main Text: Structural maintenance of chromosomes (SMC) complexes are the major organizers of chromosomes in all living organisms (1, 2). These protein complexes play essential roles in sister chromatid cohesion, chromosome condensation and segregation, DNA replication, DNA damage repair, and gene expression. A distinguishing feature of SMC complexes is their large ring-like architecture, the circumference of which is made up of two SMC protein coiled-coil proteins and a single kleisin subunit (Fig.1A) (1-4). The ~50-nm long antiparallel coiled-coils are connected at one end by a stable dimerization interface, referred to as the hinge domain, and at the other end by globular ATP-binding cassette (ABC) family ATPase domains (5). The ATPase domains are bound by a protein of the kleisin family, along with additional accessory subunits, which vary for different types of SMC complexes (Fig. 1A). The relationship between SMC peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/137711 doi: bioRxiv preprint first posted online May. 13, 2017; 2 structures and their functions in chromosome organization is not completely understood (6), but many models envision that the coiled-coil domains allow the complexes to topologically embrace DNA (1-4). Given the general resemblance to myosin and kinesin, some early models postulated that SMC proteins might be mechanochemical motors (7-10).SMC complexes are thought to regulate genome architecture by physically linking distal chromosomal loci, but how these bridging interactions might be formed remains unknown (1, 2, 11). An early model suggested that many three-dimensional (3D) features of eukaryotic chromosomes might be explained by DNA loop extrusion (Fig. 1B) (12), and recent polymer dynamics simulations have shown that loop extrusion can recapitulate the formation of topologically associating domains (TADs), chromatin compaction, and sister chromatid segr...

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.

Euchromatin histone methyltransferase 1 (EHMT1) is a highly conserved protein that catalyzes mono- and dimethylation of histone H3 lysine 9, thereby epigenetically regulating transcription. Kleefstra syndrome (KS), is caused by haploinsufficiency of the EHMT1 gene, and is an example of an emerging group of intellectual disability (ID) disorders caused by genes encoding epigenetic regulators of neuronal gene activity. Little is known about the mechanisms underlying this disorder, prompting us to study the Euchromatin histone methyltransferase 1 heterozygous knockout (Ehmt1(+/-)) mice as a model for KS. In agreement with the cognitive disturbances observed in patients with KS, we detected deficits in fear extinction learning and both novel and spatial object recognition in Ehmt1(+/-) mice. These learning and memory deficits were associated with a significant reduction in dendritic arborization and the number of mature spines in hippocampal CA1 pyramidal neurons of Ehmt1(+/-) mice. In-depth analysis of the electrophysiological properties of CA3-CA1 synapses revealed no differences in basal synaptic transmission or theta-burst induced long-term potentiation (LTP). However, paired-pulse facilitation (PPF) was significantly increased in Ehmt1(+/-) neurons, pointing to a potential deficiency in presynaptic neurotransmitter release. Accordingly, a reduction in the frequency of miniature excitatory post-synaptic currents (mEPSCs) was observed in Ehmt1(+/-) neurons. These data demonstrate that Ehmt1 haploinsufficiency in mice leads to learning deficits and synaptic dysfunction, providing a possible mechanism for the ID phenotype in patients with KS.