Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic datasets across different species and enable users to compare them between syntenic regions. Here, we present the WashU Comparative Epigenome Browser. It allows users to load functional genomic datasets/annotations mapped to different genomes and display them over syntenic regions simultaneously. The browser also displays genetic differences between the genomes from single nucleotide variants (SNVs) to structural variants (SVs) to visualize the association between epigenomic differences and genetic differences. Instead of anchoring all datasets to the reference genome coordinates, it creates independent coordinates of different genome assemblies to faithfully present features and data mapped to different genomes. It uses a simple, intuitive genome-align track to illustrate the syntenic relationship between different species. It extends the widely used WashU Epigenome Browser infrastructure and can be expanded to support multiple species. This new browser function will greatly facilitate comparative genomic/epigenomic research, as well as support the recent growing needs to directly compare and benchmark the T2T CHM13 assembly and other human genome assemblies.

WashU Epigenome Browser update 2022

WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data exploration tool that provides visualization, integration, and analysis of epigenomic datasets. The newly renovated user interface and functions have enabled researchers to engage with the browser and genomic data more efficiently and effectively since 2018. Here, we introduce a new integrated panel design in the browser that allows users to interact with 1D (genomic features), 2D (such as Hi-C), 3D (genome structure), and 4D (time series) data in a single web page. The browser can display three-dimensional chromatin structures with the 3D viewer module. The 4D tracks, called ‘Dynamic’ tracks, animatedly display time-series data, allowing for a more striking visual impact to identify the gene or genomic region candidates as a function of time. Genomic data, such as annotation features, numerical values, and chromatin interaction data can all be viewed in the dynamic track mode. Imaging data from microscopy experiments can also be displayed in the browser. In addition to software development, we continue to service and expand the data hubs we host for large consortia including 4DN, Roadmap Epigenomics, TaRGET and ENCODE, among others. Our growing user/developer community developed additional track types as plugins, such as qBed and dynseq tracks, which extend the utility of the browser. The browser serves as a foundation for additional genomics platforms including the WashU Virus Genome Browser (for COVID-19 research) and the Comparative Genome Browser. The WashU Epigenome Browser can also be accessed freely through Amazon Web Services at https://epigenomegateway.org/.

The qBED track: a novel genome browser visualization for point processes

SUMMARY

Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here, we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as Combined Annotation-Dependent Depletion scores and GWAS/eQTL hits, and thus may have broad utility to the genomics community.

AVAILABILITY AND IMPLEMENTATION

The qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-react and http://github.com/lidaof/eg-react). A complete definition of the qBED format is available as part of the WashU Epigenome Browser documentation (https://eg.readthedocs.io/en/latest/tracks.html#qbed-track). We have also released a tutorial on how to upload qBED data to the browser (http://dx.doi.org/10.17504/protocols.io.bca8ishw).

Data for the evaluation of groundwater quality using water quality index and regression analysis in parts of Nalgonda district, Telangana, Southern India

The main focus of this study is to evaluate the groundwater quality through drinking water quality index and regression analysis in semi-arid region and the results are examined with reference to the drinking water quality standards laid down by WHO. Water quality index (WQI) was determined from fourteen physicochemical parameters like pH, EC, TDS, total hardness, total alkalinity, sodium, potassium, calcium, magnesium, chloride, bromide, nitrate, sulphate and fluoride. The drinking water quality index values range from 32.8 - 442.4, indicating three categories i.e. poor, very poor and unfit, which are inappropriate for drinking. Regarding correlation analysis results, EC, TDS, TH, Na⁺, Mg²⁺, Ca²⁺ and Cl⁻ shows high correlation. Most of the parameters are more or less correlated with each other, regression relations have the same correlation coefficients and pH, Na⁺, EC, TDS, Mg²⁺, Ca²⁺, Cl⁻, SO₄²⁻, CO₃²⁻, TH were significantly positively correlated (R>0.9), indicate the increase in the pollution load.

WashU Epigenome Browser update 2019

The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Recently, we refactored the codebase, redesigned the user interface, and developed various novel features. New features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the redesign at https://epigenomegateway.org/.

Identification of a murine methyl cytosine phosphate guanine binding domain-containing factor 3 (MBD3) promoter segment sufficient for driving reporter gene expression in neurons in vitro and in vivo

In this study, we characterize the functional properties of a segment of the murine methyl cytosine phosphate guanine binding domain-containing factor 3 (MBD3) promoter region. Transient transfection of a chimera consisting of a 1072 base pair region extending upstream from the MBD3 initiation codon fused to a luciferase complementary DNA (cDNA) confirmed the presence of a functional promoter unit. Primer extension analysis failed to identify a single predominant transcription initiation site, but rather detected multiple transcription initiation sites in both brain tissue and cultured neuroblastomaxglioma cell line (NG108-15) and rat pheochromocytoma cell line (PC12) cells. Reporter gene assays revealed that this 1072 base pair fragment efficiently drives expression in transfected NG108-15 cells, PC12 cells, cultured primary neurons, and in neurons of a transgenic mouse brain. Deletion analysis mapped the critical region for promoter activity to a segment of approximately 518 base pairs, located from positions -585 to -68 relative to the translational start codon. Taken together, these data indicate that a 1072 base pair fragment of the MBD3 promoter is sufficient to drive expression in cell lines and primary cultured neurons, and is able to direct transgene expression in the mouse brain in a pattern with spatial similarity to that of native MBD3.