No abstract

UCSC Xena is a visual exploration resource for both public and private omics data, supported through the web-based Xena Browser and multiple turn-key Xena Hubs. This unique archecture allows researchers to view their own data securely, using private Xena Hubs, simultaneously visualizing large public cancer genomics datasets, including TCGA and the GDC. Data integration occurs only within the Xena Browser, keeping private data private. Xena supports virtually any functional genomics data, including SNVs, INDELs, large structural variants, CNV, expression, DNA methylation, ATAC-seq signals, and phenotypic annotations. Browser features include the Visual Spreadsheet, survival analyses, powerful filtering and subgrouping, statistical analyses, genomic signatures, and bookmarks. Xena differentiates itself from other genomics tools, including its predecessor, the UCSC Cancer Genomics Browser, by its ability to easily and securely view public and private data, its high performance, its broad data type support, and many unique features.

The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.

Chromatin looping is key to gene regulation, yet no broadly applicable methods to selectively modify chromatin loops have been described. We have engineered a method for chromatin loop reorganization using CRISPR-dCas9 (CLOuD9) to selectively and reversibly establish chromatin loops. We demonstrate the power of this technology to selectively modulate gene expression at targeted loci.

eThe minichromosome maintenance protein homologs MCM8 and MCM9 have previously been implicated in DNA replication elongation and prereplication complex (pre-RC) formation, respectively. We found that MCM8 and MCM9 physically associate with each other and that MCM8 is required for the stability of MCM9 protein in mammalian cells. Depletion of MCM8 or MCM9 in human cancer cells or the loss of function MCM9 mutation in mouse embryo fibroblasts sensitizes cells to the DNA interstrand cross-linking (ICL) agent cisplatin. Consistent with a role in the repair of ICLs by homologous recombination (HR), knockdown of MCM8 or MCM9 significantly reduces HR repair efficiency. Chromatin immunoprecipitation analysis using human DR-GFP cells or Xenopus egg extract demonstrated that MCM8 and MCM9 proteins are rapidly recruited to DNA damage sites and promote RAD51 recruitment. Thus, these two metazoan-specific MCM homologs are new components of HR and may represent novel targets for treating cancer in combination with DNA cross-linking agents. Homologous recombination (HR) is critical for the repair of DNA damage induced by endogenous or exogenous agents. For example, ionizing radiation or the DNA-damaging agent doxorubicin induces double-stranded DNA breaks (DSBs) that are repaired by HR and nonhomologous end joining (NHEJ) (1). On the other hand, the repair of DNA interstrand cross-links (ICLs), induced by cisplatin, or by natural cellular metabolites such as lipid peroxides (2) usually occurs during the S phase of the cell cycle of proliferating cells (3, 4) and is dependent on translesion DNA synthesis (TLS), followed by HR (4-6). Several proteins, including the Fanconi anemia-related proteins (3, 7) and structure-specific endonucleases such as FAN1 (8-10), MUS81-EME1 (11), XPF-ERCC1 (12), and SLX1-SLX4 (13), as well as translesion DNA polymerases (4, 6) and HR-related proteins (5), are essential for the repair of ICLs.HR consists of three steps: presynapsis, synapsis, and postsynapsis (1). During presynapsis, the MRN complex (MRE11, RAD50, and NBS1) interacts with CtIP (14, 15) and recognizes DNA breaks to make a short 3= overhang structure. In yeast, the SGS1-DNA2 helicase/nuclease complex, as well as exonuclease 1 (EXO1), further resect the DNA ends to produce extended 3= overhangs (16). Protein-protein interaction studies and in vitro assays suggest that the human BLM helicase may function as an ortholog of SGS1 (17), but it remains unclear whether BLM promotes the DNA resection step in vivo. After DNA resection, the RPA single-stranded DNA-binding protein is recruited to singlestranded DNA to stabilize the structure, and mediator proteins, including RAD51C, RAD52, and BRCA2, promote the formation of a RAD51 filament. RAD51, a key element in HR, binds singlestranded DNA at DNA breaks and facilitates the search for a homology donor (18). During the synapsis stage, strand invasion makes the D-loop, followed by RAD51 displacement, to promote DNA synthesis. Branch migration occurs during the postsynapsis stage, and the repair...