OpenLooper (OLP)

Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription,replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time.

OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays, such as Hi-C, ChIA-PET, ChIP-seq, and RNA-seq. Simultaneously, OLP provides a platform that supports opening and sharing high-throughput sequencing datasets.
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In Focus Articles (last modified: 2020-03-29 21:32:40)

[1] Chromosome-level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood).  (Mol Ecol Resour. 2020 Mar 27;:)

Chromosome-level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood).

Xie W, He C, Fei Z, Zhang Y (Mol Ecol Resour. 2020 Mar 27;:)
The greenhouse whitefly, Trialeurodes vaporariorum Westwood, is an agricultural pest of global importance. Here we report a 787-Mb high-quality draft genome sequence of T. vaporariorum assembled from PacBio long reads and Hi-C chromatin interaction maps, which has scaffold and contig N50 lengths of 70 Mb and 500 kb, respectively, and contains 18,275 protein-coding genes. About 98.8% of the assembl......
[2] Ultrastructural Details of Mammalian Chromosome Architecture.  (Mol Cell. 2020 Mar 14;:)

Ultrastructural Details of Mammalian Chromosome Architecture.

Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ (Mol Cell. 2020 Mar 14;:)
Over the past decade, 3C-related methods have provided remarkable insights into chromosome folding in vivo. To overcome the limited resolution of prior studies, we extend a recently developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human ESCs and fibroblasts. Micro-C robustly captures known features of chromosome folding including compartment organization......
[3] TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains.  (Front Genet. 2020;11:158)

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains.

Cresswell KG, Dozmorov MG (Front Genet. 2020;11:158)
Recent research using chromatin conformation capture technologies, such as Hi-C, has demonstrated the importance of topologically associated domains (TADs) and smaller chromatin loops, collectively referred hereafter as "interacting domains." Many such domains change during development or disease, and exhibit cell- and condition-specific differences. Quantification of the dynamic behavior of inter......
[4] Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.  (Nat Plants. 2019 08;5(8):833-845)

Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data.

Zhang X, Zhang S, Zhao Q, Ming R, Tang H (Nat Plants. 2019 08;5(8):833-845)
Construction of chromosome-level assembly is a vital step in achieving the goal of a 'Platinum' genome, but it remains a major challenge to assemble and anchor sequences to chromosomes in autopolyploid or highly heterozygous genomes. High-throughput chromosome conformation capture (Hi-C) technology serves as a robust tool to dramatically advance chromosome scaffolding; however, existing approaches......
[5] Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization.  (Biophys J. 2020 Mar 03;:)

Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization.

Shinkai S, Sugawara T, Miura H, Hiratani I, Onami S (Biophys J. 2020 Mar 03;:)
The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and topologically associating domains (TADs). Moreover, single-nucleosome live-cell i......