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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Tripartite Chromatin Localization of Budding Yeast Shugoshin Involves Higher-Ordered Architecture of Mitotic Chromosomes.
Deng X, Kuo MH (G3 (Bethesda). 2018 Jul 12;:)
The spindle assembly checkpoint (SAC) is key to faithful segregation of chromosomes. One requirement that satisfies SAC is appropriate tension between sister chromatids at the metaphase-anaphase juncture. Proper tension generated by poleward pulling of mitotic spindles signals biorientation of the underlying chromosome. In the budding yeast, the tension status is monitored by the conserved Shugosh......
Systematic Mapping of RNA-Chromatin Interactions In Vivo.
Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S (Curr Biol. 2017 Feb 20;27(4):602-609)
RNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where the genomic target loci of these RNAs are. Here, we present MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their tar......
Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.
McCole RB, Erceg J, Saylor W, Wu CT (Cell Rep. 2018 Jul 10;24(2):479-488)
This study explores the relationship between three-dimensional genome organization and ultraconserved elements (UCEs), an enigmatic set of DNA elements that are perfectly conserved between the reference genomes of distantly related species. Examining both human and mouse genomes, we interrogate the relationship of UCEs to three features of chromosome organization derived from Hi-C studies. We find......
Rich Chromatin Structure Prediction from Hi-C Data.
Malik L, Patro R (IEEE/ACM Trans Comput Biol Bioinform. 2018 Jun 28;:)
Recent studies involving the 3-dimensional conformation of chromatin have revealed the important role it has to play in different processes within the cell. These studies have also led to the discovery of densely interacting segments of the chromosome, called topologically associating domains. The accurate identification of these domains from Hi-C interaction data is an interesting and important c......
ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data.
Caudai C, Salerno E, Zoppe M, Merelli I, Tonazzini A (IEEE/ACM Trans Comput Biol Bioinform. 2018 May 21;:)
A method and a stand-alone Python(TM) code to estimate the 3D chromatin structure from chromosome conformation capture data are presented. The method is based on a multiresolution, modified-bead-chain chromatin model, evolved through quaternion operators in a Monte Carlo sampling. The solution space to be sampled is generated by a score function with a data-fit part and a constraint part where the......