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: 2019-10-12 21:33:40)

[1] Inference of chromosome 3D structures from GAM data by a physics computational approach.  (Methods. 2019 Oct 08;:)

Inference of chromosome 3D structures from GAM data by a physics computational approach.


Fiorillo L, Bianco S, Chiariello AM, Barbieri M, Esposito A, Annunziatella C, Conte M, Corrado A, Prisco A, Pombo A, Nicodemi M (Methods. 2019 Oct 08;:)
The combination of modelling and experimental advances can provide deep insights for understanding chromatin 3D organization and ultimately its underlying mechanisms. In particular, models of polymer physics can help comprehend the complexity of genomic contact maps, as those emerging from technologies such as Hi-C, GAM or SPRITE. Here we discuss a method to reconstruct 3D structures from Genome A......
PubMed:31604121
[2] FACT mediates cohesin function on chromatin.  (Nat Struct Mol Biol. 2019 Oct;26(10):970-979)

FACT mediates cohesin function on chromatin.


Garcia-Luis J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, Cournac A, García A, González S, Sánchez M, Jarmuz A, Montoya A, Dore M, Kramer H, Karimi MM, Antequera F, Koszul R, Aragon L (Nat Struct Mol Biol. 2019 Oct;26(10):970-979)
Cohesin is a regulator of genome architecture with roles in sister chromatid cohesion and chromosome compaction. The recruitment and mobility of cohesin complexes on DNA is restricted by nucleosomes. Here, we show that the role of cohesin in chromosome organization requires the histone chaperone FACT ('facilitates chromatin transcription') in Saccharomyces cerevisiae. We find that FACT interacts d......
PubMed:31582854
[3] Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand g...  (Sci Adv. 2018 12;4(12):eaav8550)

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.


Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ (Sci Adv. 2018 12;4(12):eaav8550)
As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsi......
PubMed:30555922
[4] Recent evidence that TADs and chromatin loops are dynamic structures.  (Nucleus. 2018 01 01;9(1):20-32)

Recent evidence that TADs and chromatin loops are dynamic structures.


Hansen AS, Cattoglio C, Darzacq X, Tjian R (Nucleus. 2018 01 01;9(1):20-32)
Mammalian genomes are folded into spatial domains, which regulate gene expression by modulating enhancer-promoter contacts. Here, we review recent studies on the structure and function of Topologically Associating Domains (TADs) and chromatin loops. We discuss how loop extrusion models can explain TAD formation and evidence that TADs are formed by the ring-shaped protein complex, cohesin, and that......
PubMed:29077530
[5] Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cel...  (Methods. 2019 Sep 16;:)

Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells.


Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z (Methods. 2019 Sep 16;:)
The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among i......
PubMed:31536770