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: 2018-10-13 03:37:17)

[1] Systems analysis of dilated cardiomyopathy in the next generation sequencing era.  (Wiley Interdiscip Rev Syst Biol Med. 2018 07;10(4):e1419)

Systems analysis of dilated cardiomyopathy in the next generation sequencing era.


Harakalova M, Asselbergs FW (Wiley Interdiscip Rev Syst Biol Med. 2018 07;10(4):e1419)
Dilated cardiomyopathy (DCM) is a form of severe failure of cardiac muscle caused by a long list of etiologies ranging from myocardial infarction, DNA mutations in cardiac genes, to toxics. Systems analysis integrating next-generation sequencing (NGS)-based omics approaches, such as the sequencing of DNA, RNA, and chromatin, provide valuable insights into DCM mechanisms. The outcome and interpreta......
PubMed:29485202
[2] CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive ...  (Genome Biol. 2018 Oct 08;19(1):160)

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops.


Guo Y, Perez AA, Hazelett DJ, Coetzee GA, Rhie SK, Farnham PJ (Genome Biol. 2018 Oct 08;19(1):160)
BACKGROUND: Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer....
PubMed:30296942
[3] Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo.  (Proc Natl Acad Sci U S A. 2018 Oct 08;:)

Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo.


Cai S, Chen C, Tan ZY, Huang Y, Shi J, Gan L (Proc Natl Acad Sci U S A. 2018 Oct 08;:)
Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription. Here, we use cryo-electron tomography (cryo-ET) to determine the 3D arrangement of nuclear macromolecular complexes, including nucleosomes, in frozen-hydrated Schizosaccharomyces pombe cells. Using 3D classification analysis, we did not......
PubMed:30297429
[4] Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.  (Genome Res. 2018 04;28(4):497-508)

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.


Rossi MJ, Lai WKM, Pugh BF (Genome Res. 2018 04;28(4):497-508)
General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence. It is assumed that sequence recognition via direct base readout suffices for specificity and that spurious nonfunctional sites are rendered inaccessible by chromatin. We tested these assumptions through genome-wide mapping of GR......
PubMed:29563167
[5] Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially ...  (Epigenetics Chromatin. 2018 08 01;11(1):43)

Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements.


Mishra LN, Shalini V, Gupta N, Ghosh K, Suthar N, Bhaduri U, Rao MRS (Epigenetics Chromatin. 2018 08 01;11(1):43)
BACKGROUND: Linker histones establish and maintain higher-order chromatin structure. Eleven linker histone subtypes have been reported in mammals. HILS1 is a spermatid-specific linker histone, and its expression overlaps with the histone-protamine exchange process during mammalian spermiogenesis. However, the role of HILS1 in spermatid chromatin remodeling is largely unknown....
PubMed:30068355