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The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of theHomo sapiensandMus musculusgenomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and availableviathe ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL;https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environmentsviaCromwell. Access to the pipelines and dataviathe cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE c

The occurrence and formation of genomic structural variants (SV) is known to be influenced by the 3D chromatin architecture, but the extent and magnitude have been challenging to study. Here, we apply Hi-C to study chromatin organization before and after induction of chromothripsis in human cells. We use Hi-C to manually assemble the derivative chromosomes following the occurrence of massive complex rearrangements, which allowed us to study the sources of SV formation and their consequences on gene regulation. We observe an action-reaction interplay whereby the 3D chromatin architecture directly impacts the location and formation of SVs. In turn, the SVs reshape the chromatin organization to alter the local topologies, replication timing, and gene regulation in cis We show that SVs have a strong tendency to occur between similar chromatin compartments and replication timing regions. Moreover, we find that SVs frequently occur at 3D loop-anchors, that SVs can cause a switch in chromatin compartments and replication timing, and that this is a major source of SV-mediated effects on nearby gene expression changes. Finally, we provide evidence for a general mechanistic bias of the 3D chromatin on SV occurrence using data from more than 2,700 patient-derived cancer genomes.

The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci—almost always bound by CTCF and cohesin—lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid. Mapping the nucleome in 4D during cohesin loss and recovery reveals that cohesin degradation eliminates loop domains but has only modest transcriptional consequences. Keywords: cohesion; genome architecture; loop extrusion; chromatin loops; superenhancers; gene regulation; nuclear compartments; Hi-C; 4D Nucleome; CTCF

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic “tension globule.” In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair., National Science Foundation (U.S.) (Grant PHY-1427654), National Institutes of Health (U.S.) (New Innovator Award 1DP2OD008540-01), Cancer Prevention and Research Institute of Texas (Scholar Award R1304), Baylor College of Medicine (McNair Medical Institute Scholar Award), Presidential Early Career Award for Scientists and Engineers

We present a dynamical model of the high mass X-ray binary LMC X-1 based on high-resolution optical spectroscopy and extensive optical and near-infrared photometry. From our new optical data we find an orbital period of P = 3.90917 ± 0.00005 days. We present a refined analysis of the All Sky Monitor data from RXTE and find an X-ray period of P = 3.9094 ± 0.0008 days, which is consistent with the optical period. A simple model of Thomson scattering in the stellar wind can account for the modulation seen in the X-ray light curves. The V – K color of the star (1.17 ± 0.05) implies AV = 2.28 ± 0.06, which is much larger than previously assumed. For the secondary star, we measure a radius of R 2 = 17.0 ± 0.8 R ☉ and a projected rotational velocity of V rotsin i = 129.9 ± 2.2 km s–1. Using these measured properties to constrain the dynamical model, we find an inclination of i = 36fdg38 ± 1fdg92, a secondary star mass of M 2 = 31.79 ± 3.48 M ☉, and a black hole mass of 10.91 ± 1.41 M ☉. The present location of the secondary star in a temperature-luminosity diagram is consistent with that of a star with an initial mass of 35 M ☉ that is 5 Myr past the zero-age main sequence. The star nearly fills its Roche lobe (≈90% or more), and owing to the rapid change in radius with time in its present evolutionary state, it will encounter its Roche lobe and begin rapid and possibly unstable mass transfer on a timescale of a few hundred thousand years., United States. National Aeronautics and Space Administration (NASA guest observer program), Science and Technology Facilities Council (Great Britain) (STFC advanced fellowship), United States. National Aeronautics and Space Administration (NASA grant NNX08AJ55G), National Science Foundation (U.S.) (NSF grant AST 04-53609), National Science Foundation (U.S.) (NSF grant NSF-AST 0707627)