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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 DB Status: OK




In Focus Articles (last modified: 2018-08-15 19:15:04)

[1] A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.  (Gigascience. 2018 Aug 09;:)

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.


VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV (Gigascience. 2018 Aug 09;:)
Background: The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies....
PubMed:30107523
[2] Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.  (EMBO Rep. 2018 Aug 13;:)

Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.


Hiraga SI, Monerawela C, Katou Y, Shaw S, Clark KR, Shirahige K, Donaldson AD (EMBO Rep. 2018 Aug 13;:)
Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome-wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres thro......
PubMed:30104203
[3] The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkin...  (Gigascience. 2018 Aug 07;:)

The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana).


Zhao H, Wang S, Wang J, Chen C, Hao S, Chen L, Fei B, Han K, Li R, Shi C, Sun H, Wang S, Xu H, Yang K, Xu X, Shan X, Shi J, Feng A, Fan G, Liu X, Zhao S, Zhang C, Gao Q, Gao Z, Jiang Z (Gigascience. 2018 Aug 07;:)
Background: Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan....
PubMed:30101322
[4] In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Comp...  (Mol Cell. 2018 Aug 02;:)

In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex.


Wang X, Hughes AC, Brandão HB, Walker B, Lierz C, Cochran JC, Oakley MG, Kruse AC, Rudner DZ (Mol Cell. 2018 Aug 02;:)
Structural maintenance of chromosomes (SMC) complexes shape the genomes of virtually all organisms, but how they function remains incompletely understood. Recent studies in bacteria and eukaryotes have led to a unifying model in which these ring-shaped ATPases act along contiguous DNA segments, processively enlarging DNA loops. In support of this model, single-molecule imaging experiments indicate......
PubMed:30100265
[5] Functional characterization of open chromatin in bidirectional promoters of rice.  (Sci Rep. 2016 08 25;6:32088)

Functional characterization of open chromatin in bidirectional promoters of rice.


Fang Y, Wang X, Wang L, Pan X, Xiao J, Wang XE, Wu Y, Zhang W (Sci Rep. 2016 08 25;6:32088)
Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in......
PubMed:27558448