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: 2018-09-22 20:34:27)

[1] Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus.  (Gigascience. 2018 Sep 18;:)

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus.


Shao C, Li C, Wang N, Qin Y, Xu W, Liu Q, Zhou Q, Zhao Y, Li X, Liu S, Chen X, Mahboob S, Liu X, Chen S (Gigascience. 2018 Sep 18;:)
Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking....
PubMed:30239684
[2] Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation.  (Genome Res. 2018 Sep 19;:)

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation.


Werner MS, Sieriebriennikov B, Prabh N, Loschko T, Lanz C, Sommer RJ (Genome Res. 2018 Sep 19;:)
Species-specific, new, or 'orphan' genes account for 10-30% of eukaryotic genomes. Although initially considered to be of limited function, an increasing number of orphan genes have been shown to provide important phenotypic innovation. How new genes acquire regulatory sequences for proper temporal and spatial expression is unknown. Orphan gene regulation may rely in part on origination in open ch......
PubMed:30232198
[3] Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer.  (Nat Genet. 2018 Sep 17;:)

Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer.


Orlando G, Law PJ, Cornish AJ, Dobbins SE, Chubb D, Broderick P, Litchfield K, Hariri F, Pastinen T, Osborne CS, Taipale J, Houlston RS (Nat Genet. 2018 Sep 17;:)
Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1-6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the genome in which to search for such mutations. Here we use high-throughput chromosome conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog the regulator......
PubMed:30224643
[4] But where did the centromeres go in the chicken genome models?  (Chromosome Res. 2018 Sep 17;:)

But where did the centromeres go in the chicken genome models?


PiƩgu B, Arensburger P, Guillou F, Bigot Y (Chromosome Res. 2018 Sep 17;:)
The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide ......
PubMed:30225548
[5] Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles.  (Methods Mol Biol. 2018;1861:221-245)

Practical Analysis of Hi-C Data: Generating A/B Compartment Profiles.


Miura H, Poonperm R, Takahashi S, Hiratani I (Methods Mol Biol. 2018;1861:221-245)
Recent advances in next-generation sequencing (NGS) and chromosome conformation capture (3C) analysis have led to the development of Hi-C, a genome-wide version of the 3C method. Hi-C has identified new levels of chromosome organization such as A/B compartments, topologically associating domains (TADs) as well as large megadomains on the inactive X chromosome, while allowing the identification of ......
PubMed:30218370