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: 2018-06-25 17:09:46)

[1] Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx.  (Epigenetics Chromatin. 2018 Jun 22;11(1):34)

Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx.


Hensel KO, Cantner F, Bangert F, Wirth S, Postberg J (Epigenetics Chromatin. 2018 Jun 22;11(1):34)
BACKGROUND: In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication. The functional nuclear localization of cccDNA and HBx remains unexplored....
PubMed:29933745
[2] ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.  (BMC Bioinformatics. 2018 Jun 20;19(1):234)

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.


Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL (BMC Bioinformatics. 2018 Jun 20;19(1):234)
BACKGROUND: The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our appro......
PubMed:29925315
[3] BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblas...  (Int J Cancer. 2018 Jun 19;:)

BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia.


de Smith AJ, Walsh KM, Francis SS, Zhang C, Hansen HM, Smirnov I, Morimoto L, Whitehead TP, Kang A, Shao X, Barcellos LF, McKean-Cowdin R, Zhang L, Fu C, Wang R, Yu H, Hoh J, Dewan AT, Metayer C... (Int J Cancer. 2018 Jun 19;:)
Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latin......
PubMed:29923177
[4] Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome.  (EMBO J. 2018 Jun 19;:)

Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome.


Maass PG, Weise A, Rittscher K, Lichtenwald J, Barutcu AR, Liehr T, Aydin A, Wefeld-Neuenfeld Y, Pölsler L, Tinschert S, Rinn JL, Luft FC, Bähring S (EMBO J. 2018 Jun 19;:)
Chromosomes occupy distinct interphase territories in the three-dimensional nucleus. However, how these chromosome territories are arranged relative to one another is poorly understood. Here, we investigated the inter-chromosomal interactions between chromosomes 2q, 12, and 17 in human mesenchymal stem cells (MSCs) and MSC-derived cell types by DNA-FISH We compared our findings in normal karyotype......
PubMed:29921581
[5] Chromatin Immunoprecipitation (ChIP) with Erythroid Samples.  (Methods Mol Biol. 2018;1698:229-236)

Chromatin Immunoprecipitation (ChIP) with Erythroid Samples.


Krivega I, Dean A (Methods Mol Biol. 2018;1698:229-236)
Chromatin immunoprecipitation (ChIP) allows determination of the locations to which a select protein is bound in chromatin. Chemical crosslinking of DNA and protein with bi-functional reagents such as formaldehyde and precipitation of the protein with a specific antibody permit PCR amplification (ChIP) or sequencing (ChIP-seq) to identify the bound sites. Here, we present methodology for these app......
PubMed:29076093