The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is an intrinsically disordered low-complexity region that is critical for pre-mRNA transcription and processing. The CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast. Here we report that human and yeast CTDs undergo cooperative liquid phase separation, with the shorter yeast CTD forming less-stable droplets. In human cells, truncation of the CTD to the length of the yeast CTD decreases Pol II clustering and chromatin association, whereas CTD extension has the opposite effect. CTD droplets can incorporate intact Pol II and are dissolved by CTD phosphorylation with the transcription initiation factor IIH kinase CDK7. Together with published data, our results suggest that Pol II forms clusters or hubs at active genes through interactions between CTDs and with activators and that CTD phosphorylation liberates Pol II enzymes from hubs for promoter escape and transcription elongation.

After purification of EC* by size exclusion chromatography and mild crosslinking with 85 glutaraldehyde, we determined its cryo-EM structure at a nominal resolution of 3.1 Å (Fig. 2, 86 Supplementary Video 1, Extended Data Fig. 2j). 2D classification revealed densities on the 87 Pol II surface (Extended Data Fig. 3, 4; Extended Data Table 2) and resulted in a 3D 88 reconstruction from 374,964 particles. The core of Pol II extended to ~2.6 Å resolution. 89 Vos et al.,: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6Elongation factors were resolved at lower resolutions (~12 Å for the most flexible domains), 90 and their corresponding densities were improved by focused classification and refinement 91 (Extended Data Figs. 3-5, Methods). This led to a total of eight cryo-EM density maps that 92 enabled us to fit available structures and homology models (Extended Data Fig. 3; 93 Supplementary Table 1). Modeling was aided by lysine crosslinking data (Extended Data 94 Fig. 6, Supplementary Tables 2-4). 225 unique crosslinks were detected in structured regions, 95 of which 210 fell into the permitted 30 Å range. The remaining 15 crosslinks formed between 96 mobile elements of the structure (Extended Data Fig. 6; Supplementary Table 2). 97 To complete the EC* structure, we determined the crystal structure of the isolated 98 human SPT6 tandem SH2 (tSH2) domain at 1.8 Å resolution, and unambiguously docked this 99 new structure into the corresponding density of EC* (Fig. 3, Methods, Extended Data Fig. 5f, 100 6f, 7, Extended Data Table 3). The resulting structure of EC* shows good stereochemistry 101 and lacks only mobile regions, including the terminal regions of PAF1 and LEO1, most of 102 CDC73, the acidic N-terminal region of SPT6, and the C-terminal extensions of SPT5, SPT6, 103 and CTR9 ( Supplementary Table 1). 104 105 PAF and SPT6 structure and contacts 106 DSIF, PAF, and SPT6 are modular proteins that coat the outer surface of Pol II (Fig. 2). DSIF 107 domains are arrayed around the Pol II cleft and RNA exit tunnel 4 . PAF extends along the RPB2 108 side and docks on the Pol II funnel. PAF is anchored to the external domains of RPB2 via its 109 PAF1-LEO1 dimerization module (Fig. 2b, c). The central PAF subunit CTR9 contains 19 110 tetratricopeptide repeats (TPRs; residues 41-750) that each form two antiparallel ɑ-helices ( Fig. 111 3a, Supplementary Table 6, Extended Data Fig. 5b). The CTR9 TPRs form a right-handed 112 superhelix that extends from the Pol II subunit RPB11 along RPB8 via the polymerase funnel 113 to the foot (Fig. 3a). The TPRs are followed by a pair of helices that create a 'vertex' and 114 connect to a prominent 'trestle' helix in CTR9 (CTR9 residues 807-892) (Extended Data Fig. 115 5c). The trestle extends ~100 Å from the Pol II foot to subunit RPB5 where downstream DNA 116 enters the Pol II cleft. The vertex and TPRs 13, 14, and 18 buttress the PAF subunit WDR61, 117 which forms a seven-bladed β-propeller 28 and faces away from Pol II (Fig. 3a, Extended Data 118 Fi...

Liquid-liquid phase separation is a key organizational principle in eukaryotic cells, on par with intracellular membranes. It allows cells to concentrate specific proteins into condensates, increasing reaction rates and achieving switch-like regulation. However, it is unclear how cells trigger condensate formation or dissolution and regulate their sizes. We predict from first principles two mechanisms of active regulation by post-translational modifications such as phosphorylation: In enrichment-inhibition, the regulating modifying enzyme enriches in condensates and the modifications of proteins inhibit their interactions. Stress granules, Cajal bodies, P granules, splicing speckles, and synapsin condensates obey this model. In localization-induction, condensates form around an immobilized modifying enzyme, whose modifications strengthen protein interactions. Spatially targeted condensates formed during transmembrane signaling, microtubule assembly, and actin polymerization conform to this model. The two models make testable predictions that can guide studies into the many emerging roles of biomolecular condensates.Eukaryotic cells contain numerous types of membraneless organelles, which contain between a few and thousands of protein and RNA species that are highly enriched in comparison to the surrounding nucleoplasm or cytoplasm. These biomolecular condensates are held together by weak, multivalent and highly collaborative interactions, often between intrinsically disordered regions of their constituent proteins (Banani et al., 2017;Shin and Brangwynne, 2017).In contrast to membrane-bound organelles, cells can regulate the formation and size of condensates by posttranslational modifications of one or a few key proteins, most prominently by phosphorylation. The modifications usually lie within intrinsically disordered regions and modulate the strength of attractive interactions with other condensate components (Bah and Forman-Kay, 2016; Fung et al., 2018). Due to the highly cooperative nature of phase transitions, small changes in interaction strengths can result in the formation or dissolution of condensates, and this switch-like, dynamic nature makes them ideal for regulation.For instance the nucleolus, Cajal bodies, splicing speckles, paraspeckles, and PML bodies in the nucleus and P-bodies in the cytoplasm have to be dissolved during mitosis and reformed afterwards to ensure a balanced distribution of their content to daughter cells (Rai et al., 2018;Dundr and Misteli, 2010). Stress granules form upon cellular stress and are dissolved when the stress ceases (Wippich et al., 2013).Whereas these long-known, floating droplet or-ganelles are large enough to be visible using simpler 31 light microscopic techniques, in the past years liquid-32 liquid phase separation has been implicated in mul-33 tifarious processes in which -often sub-micrometer-34 sized -condensates are formed at particular sites in the 35 cell: at sites of DNA repair foci (Altmeyer et al., 2015), 36 Polycomb-mediated chromatin silencing (Tatavo...

Summary In response to stress, human cells coordinately downregulate transcription and translation of housekeeping genes. To downregulate transcription, the negative elongation factor (NELF) is recruited to gene promoters impairing RNA polymerase II elongation. Here we report that NELF rapidly forms nuclear condensates upon stress in human cells. Condensate formation requires NELF dephosphorylation and SUMOylation induced by stress. The intrinsically disordered region (IDR) in NELFA is necessary for nuclear NELF condensation and can be functionally replaced by the IDR of FUS or EWSR1 protein. We find that biomolecular condensation facilitates enhanced recruitment of NELF to promoters upon stress to drive transcriptional downregulation. Importantly, NELF condensation is required for cellular viability under stressful conditions. We propose that stress-induced NELF condensates reported here are nuclear counterparts of cytosolic stress granules. These two stress-inducible condensates may drive the coordinated downregulation of transcription and translation, likely forming a critical node of the stress survival strategy.

Liquid-liquid phase separation is a key organizational principle in eukaryotic cells, on par with intracellular membranes. It allows cells to concentrate specific proteins into condensates, increasing reaction rates and achieving switch-like regulation. However, it is unclear how cells trigger condensate formation or dissolution and regulate their sizes. We predict from first principles two mechanisms of active regulation by post-translational modifications such as phosphorylation: In enrichment-inhibition, the regulating modifying enzyme enriches in condensates and the modifications of proteins inhibit their interactions. Stress granules, Cajal bodies, P granules, splicing speckles, and synapsin condensates obey this model. In localization-induction, condensates form around an immobilized modifying enzyme, whose modifications strengthen protein interactions. Spatially targeted condensates formed during transmembrane signaling, microtubule assembly, and actin polymerization conform to this model. The two models make testable predictions that can guide studies into the many emerging roles of biomolecular condensates. Eukaryotic cells contain numerous types of mem-1 braneless organelles, which contain between a few 2 and thousands of protein and RNA species that are 3 highly enriched in comparison to the surrounding nu-4 cleoplasm or cytoplasm. These biomolecular conden-5 sates are held together by weak, multivalent and highly 6 collaborative interactions, often between intrinsically 7 54 active promoters. Here, we propose two active mecha-55 nisms used by cells for these purposes.56 Phase separation and condensate size behaviour 57 To keep the model simple, we consider only one type of 58 condensate protein. In the dilute regime below the sat-59 1 Cellular control of liquid droplet formation, size, and localization • July 5, 2019 Figure 1: Phase separation and condensate droplet size behaviour. A When protein-protein and solvent-solventinteractions are more favorable than protein-solvent interactions, demixing into two phases can occur, a dilute phase with low protein concentration c out and a dense phase with high concentration c in . This happens when the sum of free energies of the two phases is lower (tip of blue arrow) than the energy of the single phase (base of blue arrow) . B c out is the limiting concentration for infinite condensate droplet radius R. The concentration on the outside of a condensate of radius R is larger the smaller the condensate is (green double-headed arrows), as it cannot hold on to its proteins as well as large ones. This leads to a concentration gradient (∇concentration), which fuels a diffusive flux from small to large condensates (wiggly arrows). (l c is a measure of interaction strength between proteins in comparison to the solvent.) C As a result, condensates below a radius R crit will shrink and larger ones will grow. uration protein concentration c out , condensate droplets 60 cannot form ( Figure 1A). Above c out , in the phase sepa-61 ration regime, condensates can be stable...

The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is an intrinsically disordered low-complexity region that is critical for pre-mRNA transcription and processing.The CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast. Here we report that human and yeast CTDs undergo cooperative liquid phase separation at increasing protein concentration, with the shorter yeast CTD forming less stable droplets. In human cells, truncation of the CTD to the length of the yeast CTD decreases Pol II clustering and chromatin association. CTD droplets can incorporate intact Pol II and are dissolved by CTD phosphorylation with the transcription initiation factor IIH kinase CDK7. Together with published data, our results suggest that Pol II forms clusters at active genes through interactions between CTDs and with activators, and that CTD phosphorylation removes Pol II enzymes from clusters for transcription elongation.Cellular processes often require clustering of molecules to facilitate their interactions and reactions 1,2 . During transcription of protein-coding genes, RNA polymerase (Pol) II clusters in localized nuclear hubs 3 . Whereas Pol II concentration in the nucleus is estimated to be ~1 µM, it 2 increases locally by several orders of magnitude 4 . Such high Pol II concentrations are reminiscent of the clustering of proteins in membrane-less compartments such as P granules, Cajal bodies and nuclear speckles 1,2,5,6 . These cellular compartments are stabilized by interactions between intrinsically disordered low-complexity domains (LCD) and depend on liquid-liquid phase separation (LLPS) 1,2,6-11 . However, the molecular basis of Pol II clustering remains unknown.The largest subunit of Pol II, RPB1, contains a C-terminal low-complexity domain (CTD) that is critical for pre-mRNA synthesis and co-transcriptional processing 12 . The CTD is conserved from humans to fungi, but differs in the number of its hepta-peptide repeats with the consensus sequence Y 1 S 2 P 3 T 4 S 5 P 6 S 7 13,14 . The human CTD (hCTD) contains a N-terminal half, which comprises 26 repeats and resembles the CTD from the yeast Saccharomyces cerevisiae (yCTD), and a C-terminal half containing 26 repeats of more divergent sequence ( Supplementary Fig. 1a).CTD sequences from different species all contain a high number of tyrosine, proline and serine residues ( Supplementary Fig. 1b) 13,15 . The most conserved CTD residues are Y 1 and P 6 that are present in all 52 repeats of hCTD. Truncation of the CTD of RPB1 in Saccharomyces cerevisiae to less than 13 repeats leads to growth defects and a minimum of eight repeats is required for yeast viability 16 . The CTD forms a mobile, tail-like extension from the core of Pol II 14 that is thought to facilitate the binding of factors for co-transcriptional RNA processing and histone modification 13,14 .Despite its extremely high conservation, its essential functions, and a large number of related published studies, the unique CTD structure and properties have remained enigm...

Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth’s phosphatase pools.

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