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: 2019-08-10 06:54:23)

[1] Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualizat...  (Nucleic Acids Res. 2018 07 02;46(W1):W11-W16)

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.


Wolff J, Bhardwaj V, Nothjunge S, Richard G, Renschler G, Gilsbach R, Manke T, Backofen R, Ramírez F, Grüning BA (Nucleic Acids Res. 2018 07 02;46(W1):W11-W16)
Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction o......
PubMed:29901812
[2] Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences.  (Genes Chromosomes Cancer. 2019 07;58(7):427-436)

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences.


Cremer M, Cremer T (Genes Chromosomes Cancer. 2019 07;58(7):427-436)
Transcription regulatory elements (TREs) have been extensively studied on the biochemical level with respect to their interactions with transcription factors (TFs), other DNA segments, and larger protein complexes. In this review, we describe concepts and preliminary experimental evidence for positional changes of TREs within a dynamic, functional nuclear architecture. We suggest a multilayered sh......
PubMed:30520215
[3] 3DIV: A 3D-genome Interaction Viewer and database.  (Nucleic Acids Res. 2018 01 04;46(D1):D52-D57)

3DIV: A 3D-genome Interaction Viewer and database.


Yang D, Jang I, Choi J, Kim MS, Lee AJ, Kim H, Eom J, Kim D, Jung I, Lee B (Nucleic Acids Res. 2018 01 04;46(D1):D52-D57)
Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C dat......
PubMed:29106613
[4] Characterization of Structural Variations in the Context of 3D Chromatin Structure.  (Mol Cells. 2019 Jul 31;42(7):512-522)

Characterization of Structural Variations in the Context of 3D Chromatin Structure.


Kim K, Eom J, Jung I (Mol Cells. 2019 Jul 31;42(7):512-522)
Chromosomes located in the nucleus form discrete units of genetic material composed of DNA and protein complexes. The genetic information is encoded in linear DNA sequences, but its interpretation requires an understanding of threedimensional (3D) structure of the chromosome, in which distant DNA sequences can be juxtaposed by highly condensed chromatin packing in the space of nucleus to precisely......
PubMed:31362468
[5] Cut-C: cleavage under tethered nuclease for conformational capture.  (BMC Genomics. 2019 Jul 29;20(1):614)

Cut-C: cleavage under tethered nuclease for conformational capture.


Shimbo T, Kawamura M, Wijaya E, Takaki E, Kaneda Y, Tamai K (BMC Genomics. 2019 Jul 29;20(1):614)
BACKGROUND: Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a c......
PubMed:31357933