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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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......
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......
Large-scale mammalian genome rearrangements coincide with chromatin interactions.
Swenson KM, Blanchette M (Bioinformatics. 2019 Jul 15;35(14):i117-i126)
MOTIVATION: Genome rearrangements drastically change gene order along great stretches of a chromosome. There has been initial evidence that these apparently non-local events in the 1D sense may have breakpoints that are close in the 3D sense. We harness the power of the Double Cut and Join model of genome rearrangement, along with Hi-C chromosome conformation capture data to test this hypothesis b......
Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis.
He M, Li Y, Tang Q, Li D, Jin L, Tian S, Che T, He S, Deng L, Gao G, Gu Y, Jiang Z, Li X, Li M (Int J Biol Sci. 2018;14(11):1571-1585)
The recently developed high-throughput chromatin conformation capture (Hi-C) technology enables us to explore the spatial architecture of genomes, which is increasingly considered an important regulator of gene expression. To investigate the changes in three-dimensional (3D) chromatin structure and its mediated gene expression during adipogenesis and myogenesis, we comprehensively mapped 3D chroma......
Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation.
Li Y, He Y, Liang Z, Wang Y, Chen F, Djekidel MN, Li G, Zhang X, Xiang S, Wang Z, Gao J, Zhang MQ, Chen Y (Cell Death Dis. 2018 02 08;9(2):200)
Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-i......