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: 2019-12-11 00:15:54)

[1] Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).  (Gigascience. 2019 Dec 01;8(12):)

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale D... (Gigascience. 2019 Dec 01;8(12):)
BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference......
[2] Spring Model - chromatin modeling tool based on OpenMM.  (Methods. 2019 Nov 29;:)

Spring Model - chromatin modeling tool based on OpenMM.

Kadlof M, Rozycka J, Plewczynski D (Methods. 2019 Nov 29;:)
Chromatin structures modeling is a rapidly developing field. Parallel to the enormous growth of available experimental data, there is a growing need of building and visualizing 3D structures of nuclei, chromosomes, chromatin domains, and single loops associated with particular genes locus. Here we present a tool for chromatin domain modeling. It is available as a webservice and standalone python s......
[3] Chromatin structure dynamics during the mitosis-to-G1 phase transition.  (Nature. 2019 Nov 27;:)

Chromatin structure dynamics during the mitosis-to-G1 phase transition.

Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA (Nature. 2019 Nov 27;:)
Features of higher-order chromatin organization-such as A/B compartments, topologically associating domains and chromatin loops-are temporarily disrupted during mitosis1,2. Because these structures are thought to influence gene regulation, it is important to understand how they are re-established after mitosis. Here we examine the dynamics of chromosome reorganization by Hi-C after mitosis in high......
[4] Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.  (Nat Commun. 2019 Nov 25;10(1):5355)

Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.

Pal K, Forcato M, Jost D, Sexton T, Vaillant C, Salviato E, Mazza EMC, Lugli E, Cavalli G, Ferrari F (Nat Commun. 2019 Nov 25;10(1):5355)
In Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational difference......
[5] DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.  (Nucleic Acids Res. 2019 06 04;47(10):e60)

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.

Li W, Wong WH, Jiang R (Nucleic Acids Res. 2019 06 04;47(10):e60)
Interactions between regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has been developed for genome-wide detection of chromatin contacts. However, unless extremely deep sequencing is performed on a very large number of input cells, which is technically limited and expensive, current Hi-C e......