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: 2020-02-19 11:44:02)

[1] The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.  (Nat Commun. 2019 10 03;10(1):4486)

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.


Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT (Nat Commun. 2019 10 03;10(1):4486)
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a ......
PubMed:31582744
[2] Highly structured homolog pairing reflects functional organization of the Drosophila genome.  (Nat Commun. 2019 10 03;10(1):4485)

Highly structured homolog pairing reflects functional organization of the Drosophila genome.


AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT (Nat Commun. 2019 10 03;10(1):4485)
Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with var......
PubMed:31582763
[3] De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alter...  (Gigascience. 2020 Feb 01;9(2):)

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas.


Chen MS, Niu L, Zhao ML, Xu C, Pan BZ, Fu Q, Tao YB, He H, Hou C, Xu ZF (Gigascience. 2020 Feb 01;9(2):)
BACKGROUND: Chromatin architecture is an essential factor regulating gene transcription in different cell types and developmental phases. However, studies on chromatin architecture in perennial woody plants and on the function of chromatin organization in sex determination have not been reported....
PubMed:32048715
[4] Chromatin interactome mapping at 139 independent breast cancer risk signals.  (Genome Biol. 2020 01 07;21(1):8)

Chromatin interactome mapping at 139 independent breast cancer risk signals.


Beesley J, Sivakumaran H, Moradi Marjaneh M, Lima LG, Hillman KM, Kaufmann S, Tuano N, Hussein N, Ham S, Mukhopadhyay P, Kazakoff S, Lee JS, Michailidou K, Barnes DR, Antoniou AC, Fachal L, Dunn... (Genome Biol. 2020 01 07;21(1):8)
BACKGROUND: Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression....
PubMed:31910858
[5] Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.  (Nat Methods. 2019 10;16(10):999-1006)

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.


Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR (Nat Methods. 2019 10;16(10):999-1006)
Dynamic three-dimensional chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of three-dimensional genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays......
PubMed:31501549