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Methyl CpG binding protein 2 (MeCP2) is a key component of constitutive heterochromatin, which is crucial for chromosome maintenance and transcriptional silencing1–3. Mutations in the MECP2 gene cause the progressive neurodevelopmental disorder Rett syndrome3–5, which is associated with severe mental disability and autism-like symptoms that affect girls during early childhood. Although previously thought to be a dense and relatively static structure1,2, heterochromatin is now understood to exhibit properties consistent with a liquid-like condensate6,7. Here we show that MeCP2 is a dynamic component of heterochromatin condensates in cells, and is stimulated by DNA to form liquid-like condensates. MeCP2 contains several domains that contribute to the formation of condensates, and mutations in MECP2 that lead to Rett syndrome disrupt the ability of MeCP2 to form condensates. Condensates formed by MeCP2 selectively incorporate and concentrate heterochromatin cofactors rather than components of euchromatic transcriptionally active condensates. We propose that MeCP2 enhances the separation of heterochromatin and euchromatin through its condensate partitioning properties, and that disruption of condensates may be a common consequence of mutations in MeCP2 that cause Rett syndrome. The chromatin protein MeCP2 is a component of dynamic, liquid-like heterochromatin condensates, and the ability of MeCP2 to form condensates is disrupted by mutations in the MECP2 gene that occur in the neurodevelopmental disorder Rett syndrome.

The incidence of posttransplant hepatic arterial stenosis (HAS) has been reported in 5 to 10% of orthotopic liver transplants and, left untreated, can lead to hepatic arterial thrombosis. Most vascular complications develop less than 3 months after initial transplant, with thrombosis representing over half of all complications. There has been a trend toward minimally invasive, endovascular techniques for treating HAS with angioplasty and stenting. In one review of endovascular therapies for HAS, primary technical success was achieved in 95% of the interventions. Complication rates following endovascular repair of HAS have been reported to be between 0 and 23% in the literature. The main risk factors for complications include tortuosity of the hepatic artery and history of a second liver transplant. Other associated risk factors include female gender, age greater than 60 years, prior history of transarterial chemoembolization, and multiple arterial graft anastomoses. The case presented here is representative of a complication of balloon rupture and fragmentation in a patient undergoing hepatic arterial stent placement post–liver transplant.

Highlights • Video-conference platforms (VCPs) have rapidly become utilized in the current COVID-19 pandemic to promote social distancing. • Radiology trainee education, as regulated by the ACGME, necessitates active learning based on image review and VCPs can facilitate and support this. • Patient protected health information and HIPAA requirements must be adhered to even with VCPs and many platforms have the appropriate security measures to comply. • Tools within the VCP permit two-way interaction, screen control/sharing, and annotation features, which enable appropriate education even in a remote setting., Technologic advances have resulted in the expansion of web-based conferencing and education. While historically video-conferencing has been used for didactic educational sessions, we present its novel use in virtual radiology read-outs in the face of the COVID-19 pandemic. Knowledge of key aspects of set-up, implementation, and possible pitfalls of video-conferencing technology in the application of virtual read-outs can help to improve the educational experience of radiology trainees and promote potential future distance learning and collaboration.

Phase separation and gene control Many components of eukaryotic transcription machinery—such as transcription factors and cofactors including BRD4, subunits of the Mediator complex, and RNA polymerase II—contain intrinsically disordered low-complexity domains. Now a conceptual framework connecting the nature and behavior of their interactions to their functions in transcription regulation is emerging (see the Perspective by Plys and Kingston). Chong et al. found that low-complexity domains of transcription factors form concentrated hubs via functionally relevant dynamic, multivalent, and sequence-specific protein-protein interaction. These hubs have the potential to phase-separate at higher concentrations. Indeed, Sabari et al. showed that at super-enhancers, BRD4 and Mediator form liquid-like condensates that compartmentalize and concentrate the transcription apparatus to maintain expression of key cell-identity genes. Cho et al. further revealed the differential sensitivity of Mediator and RNA polymerase II condensates to selective transcription inhibitors and how their dynamic interactions might initiate transcription elongation. Science , this issue p. eaar2555 , p. eaar3958 , p. 412 ; see also p. 329

The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity., National Science Foundation (U.S.). (Grant PHY1743900), National Institutes of Health (U.S.) (Grants GM123511, GM117370 and T32CA009172), German Research Foundation Research Fellowship (DE 3069/1-1)

Percutaneous renal transplant biopsy (PRTB) is the gold standard for evaluating allograft rejection after renal transplant. Hemorrhage is the predominant complication. We describe the implementation of a standardized protocol for PRTB at a single institution, with the aim of reducing bleeding complications. Utilizing the plan-do-study-act model for quality improvement, we created and deployed a protocol centered on controlling patient's hypertension, platelet function, and anticoagulation status. The 4-year study encompassed a total of 880 PRTBs, before and after implementation of the protocol. Total complication rate, which was 5.8% in the 2 years leading up to implementation of the protocol, was reduced to 2.9% after the protocol was introduced ( P = .04). A standardized approach to PRTB can potentially lower complication rates; we present a framework for implementating a quality improvement protocol at other institutions.

The spread of bad neighborhoods Our genomes have complex three-dimensional (3D) arrangements that partition and regulate gene expression. Cancer cells frequently have their genomes grossly rearranged, disturbing this intricate 3D organization. Hnisz et al. show that the disruption of these 3D neighborhoods can bring oncogenes under the control of regulatory elements normally kept separate from them (see the Perspective by Wala and Beroukim). These novel juxtapositions can result in the inappropriate activation of oncogenes. Science , this issue p. 1454 ; see also p. 1398

Extracranial metastasis of glioblastoma multiforme (GBM) is rare, but has recently been reported with increasing frequency. GBM metastases typically present after a biopsy or resection of the primary tumor. An otherwise healthy 54year-old woman presented with recurring pleural effusions originally believed to be from a primary lung malignancy. The patient subsequently experienced a generalized tonic clonic seizure and a right temporal brain mass was discovered. The patient later developed weakness and radiculopathy, and an extramedullary extradural mass spreading from C7 to T6 was discovered. She underwent resection of both central nervous system lesions as well as a lung biopsy, and all pathologic specimens were consistent with GBM. The case presented is unique in that the patient's initial symptoms were related to her metastasis. Furthermore, a purely epidural spread of GBM that respects the leptomeninges and intramedullary parenchyma is highly unusual.

Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well characterized, but little is known about the mechanisms by which ADs effect gene activation. Here, we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation., National Institutes of Health (U.S.) (Grant GM123511), National Institutes of Health (U.S.) (Grant GM117370), Swedish Research Council (Postdoctoral Fellowship VR 2017-00372), Damon Runyon Cancer Research Foundation ( Fellowship 2309-17)

Background Lumbar spinal stenosis (LSS) is the most common indication for spine surgery among the geriatric population. Although decompressive surgery is effective, older patients do not benefit as much as younger patients, and they are frequently excluded from studies assessing postoperative physiotherapy. We sought to evaluate the long-term outcomes after surgery when a novel postoperative physiotherapy regimen was included. Methods We performed a retrospective review of patients with LSS greater than 70 years old who underwent lumbar decompressive surgery by the senior author over the past five years. We evaluated patients who participated in a novel postoperative physiotherapy regimen involving four phases of rehabilitation aimed at progressively independent ambulation. The visual analog scale (VAS), lower extremity motor strength, and functional independence measure (FIM) were collected preoperatively and after physiotherapy to measure outcomes. Results Ten consecutive patients with an average age of 83 years (range: 71 - 96) met the inclusion criteria. Nine patients underwent minimally invasive laminotomies at L4-L5 and one underwent a laminotomy at L3-L4. The average follow-up time was 41.9 months. The preoperative mean VAS was 7.35, and at the end of the study, it was 1.7 (p = 0.005). Three of the four patients with preoperative motor deficits improved. The median transfer and locomotion subscores of the FIM were six preoperatively and increased to seven postoperatively. Neither of these improvements was significant. Conclusions Patients older than 70 years undergoing decompressive surgery and a novel postoperative physiotherapy regimen experienced significant reductions in pain. Independence also increased; however, this did not reach statistical significance.

Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes with prominent roles in cell identity. Here we demonstrate that the SE-enriched transcriptional coactivators BRD4 and MED1 form nuclear puncta at SEs that exhibit properties of liquid-like condensates and are disrupted by chemicals that perturb condensates. The intrinsically disordered regions (IDRs) of BRD4 and MED1 can form phase-separated droplets, and MED1-IDR droplets can compartmentalize and concentrate the transcription apparatus from nuclear extracts. These results support the idea that coactivators form phase-separated condensates at SEs that compartmentalize and concentrate the transcription apparatus, suggest a role for coactivator IDRs in this process, and offer insights into mechanisms involved in the control of key cell-identity genes., National Institutes of Health (U.S.) (Grant GM123511), National Institutes of Health (U.S.) (Grant P01-CA042063), National Science Foundation (U.S.) (Grant PHY-1743900), National Cancer Institute (U.S.) (Grant P30-CA14051)

Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy. Keywords: chromosome structure; insulated neighborhood; oncogene regulation, National Institutes of Health (U.S.) (Grant HG002668)

Fragile X syndrome (FXS), the most common genetic form of intellectual disability in males, is caused by silencing of the FMR1 gene associated with hypermethylation of the CGG expansion mutation in the 5′ UTR of FMR1 in FXS patients. Here, we applied recently developed DNA methylation editing tools to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/single guide RNA (sgRNA) switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state, restoring a persistent expression of FMR1 in FXS iPSCs. Neurons derived from methylation-edited FXS iPSCs rescued the electrophysiological abnormalities and restored a wild-type phenotype upon the mutant neurons. FMR1 expression in edited neurons was maintained in vivo after engrafting into the mouse brain. Finally, demethylation of the CGG repeats in post-mitotic FXS neurons also reactivated FMR1. Our data establish that demethylation of the CGG expansion is sufficient for FMR1 reactivation, suggesting potential therapeutic strategies for FXS. Rescue of fragile X syndrome neurons by CRISPR-mediated DNA methylation editing of the FMR1 gene., National Institutes of Health (Grant HD045022), National Institutes of Health (Grant MH104610), National Institutes of Health (Grant R01NS088538), National Institutes of Health (Grant R01GM123511)

The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events.We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide. Using pharmacological and genetic approaches, we identified mitogen- and stress-activated protein kinases (MSKs) as primary mediators of H3S28ph in macrophages. Cell-free transcription assays demonstrated that H3S28ph directly promotes p300/CBP-dependent transcription. Further, MSKs can activate both signal-responsive transcription factors and the chromatin template with additive effects on transcription. Specific inhibition of MSKs in macrophages selectively reduced transcription of stimulation-induced genes. Our results suggest that MSKs incorporate upstream signaling inputs and control multiple downstream regulators of inducible transcription.

The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers., United States. National Institutes of Health (HG002668), United States. National Institutes of Health (CA109901)

There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not employ this structural protein. Here, we show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements and forms dimers that facilitate the interaction of these DNA elements. Deletion of YY1 binding sites or depletion of YY1 protein disrupts enhancer-promoter looping and gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control. YY1 is a structural regulator of enhancer-promoter interactions and facilitates gene expression., National Institutes of Health (U.S.) (Grant HG002668/GM123511), National Institutes of Health (U.S.) (Grant R37HD045022/R01-NS088538/R01-MH104610), Virginia and Daniel K. Ludwig Graduate Fellowship, National Science Foundation (U.S.). Graduate Research Fellowship Program

Nature Communications 8: Article number:14385 (2017); Published: 9 February 2017; Updated: 1 June 2017 In the original version of Supplementary Data 1 associated with this Article, the list of predicted enhancer-associated insertions was inadvertently truncated. The HTML has now been updated to include the correct version of the Supplementary Data 1.

Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (−) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (−) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex., Author Summary Mucormycosis is recognized as an emerging infectious disease. Compared to other fungal infections, mucormycosis results in high mortality: ∼50% of overall infections and >90% in disseminated infections. There is therefore an ongoing need to study these fungal pathogens. However, surprisingly little is known about the pathogenesis of mucormycosis. Our findings reveal a correlation between sporangiospore size and virulence: larger sporangiospores are more virulent than small spores. Larger spores start invasive hyphal growth immediately upon phagocytosis by host immune cells, whereas smaller spores have a long period of isotropic growth. Differential host immune response explains their difference in virulence, whereby larger spores escape host immune cells by germinating inside of macrophages. Our findings revealed an example of adaptation through fungal cell gigantism, which enable pathogenic fungi to survive within and establish infection in the host. Knowledge of the mechanisms of pathogenicity and the molecular basis of the sexual cycle in M. circinelloides will contribute to advance our understanding of pathogenic zygomycetes.