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: 2018-11-20 22:50:24)

[1] Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots i...  (Genome Biol. 2018 07 30;19(1):101)

Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline.


Kaiser VB, Semple CA (Genome Biol. 2018 07 30;19(1):101)
BACKGROUND: Chromatin loops form a basic unit of interphase nuclear organization, with chromatin loop anchor points providing contacts between regulatory regions and promoters. However, the mutational landscape at these anchor points remains under-studied. Here, we describe the unusual patterns of somatic mutations and germline variation associated with loop anchor points and explore the underlyin......
PubMed:30060743
[2] Unique, Intersecting, and Overlapping Roles of C/EBP β and CREB in Cells of the Innate Immune Syste...  (Sci Rep. 2018 Nov 16;8(1):16931)

Unique, Intersecting, and Overlapping Roles of C/EBP β and CREB in Cells of the Innate Immune System.


Larabee JL, Hauck G, Ballard JD (Sci Rep. 2018 Nov 16;8(1):16931)
CREB and C/EBP β signaling pathways are modulated during inflammation and also targeted by Bacillus anthracis edema toxin (ET), but how these factors individually and jointly contribute to changes in immune cell function is poorly understood. Using CRISPR/Cas9 gene editing, macrophage cell lines lacking CREB and isoforms of C/EBP β were generated and analyzed for changes in responses to LPS, ET,......
PubMed:30446701
[3] Low level DUX4 expression disrupts myogenesis through deregulation of myogenic gene expression.  (Sci Rep. 2018 Nov 16;8(1):16957)

Low level DUX4 expression disrupts myogenesis through deregulation of myogenic gene expression.


Bosnakovski D, Gearhart MD, Toso EA, Ener ET, Choi SH, Kyba M (Sci Rep. 2018 Nov 16;8(1):16957)
Loss of silencing of the DUX4 gene on chromosome 4 causes facioscapulohumeral muscular dystrophy. While high level DUX4 expression induces apoptosis, the effects of low level DUX4 expression on human myogenic cells are not well understood. Low levels and sporadic expression of DUX4 have been reported in FSHD biopsy samples and myoblast cultures. Here, we show that a large set of human myogenic gen......
PubMed:30446688
[4] The medicinal plant Andrographis paniculata genome provides insight into biosynthesis of the bioacti...  (Plant J. 2018 Nov 16;:)

The medicinal plant Andrographis paniculata genome provides insight into biosynthesis of the bioactive diterpenoid neoandrographolide.


Sun W, Leng L, Yin Q, Xu M, Huang M, Xu Z, Zhang Y, Yao H, Wang C, Xiong C, Chen S, Jiang C, Xie N, Zheng X, Wang Y, Song C, Peters RJ, Chen S (Plant J. 2018 Nov 16;:)
Andrographis paniculata is a herbaceous dicot plant widely used for its anti-inflammatory and anti-viral properties across its distribution in China, India and other Southeast Asia countries. A. paniculata was used as a crucial therapeutic treatment during the influenza epidemic of 1919 in India and is still used for the treatment of infectious disease in China. A. paniculata produces large quanti......
PubMed:30444296
[5] Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial re...  (Proc Natl Acad Sci U S A. 2018 Nov 14;:)

Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics.


Krause MD, Huang RT, Wu D, Shentu TP, Harrison DL, Whalen MB, Stolze LK, Di Rienzo A, Moskowitz IP, Civelek M, Romanoski CE, Fang Y (Proc Natl Acad Sci U S A. 2018 Nov 14;:)
Biomechanical cues dynamically control major cellular processes, but whether genetic variants actively participate in mechanosensing mechanisms remains unexplored. Vascular homeostasis is tightly regulated by hemodynamics. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constitutive activation of vascular endothelium contributing to atherosclerosis, the major......
PubMed:30429326