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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Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.
Lando D, Basu S, Stevens TJ, Riddell A, Wohlfahrt KJ, Cao Y, Boucher W, Leeb M, Atkinson LP, Lee SF, Hendrich B, Klenerman D, Laue ED (Nat Protoc. 2018 May;13(5):1034-1061)
Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allo......
Polymer physics predicts the effects of structural variants on chromatin architecture.
Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M (Nat Genet. 2018 Apr 16;:)
Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformatio......
NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes.
Zang C, Luyten A, Chen J, Liu XS, Shivdasani RA (Sci Rep. 2016 07 26;6:30255)
Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome-wide chromatin dynamics and ChIP-seq to determine these transcription factors' (TFs) activities in terminal megakaryocyte (MK) maturation. Enhancers with H3K4me2-marked nucleosome pairs were most enriched for NF-E2, FLI and RUNX sequence motifs, suggesting that this TF triad controls much of the late MK pro......
Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice.
Dong Q, Li N, Li X, Yuan Z, Xie D, Wang X, Li J, Yu Y, Wang J, Ding B, Zhang Z, Li C, Bian Y, Zhang A, Wu Y, Liu B, Gong L (Plant J. 2018 Apr 16;:)
The non-random spatial packing of chromosomes in the nucleus plays critical roles in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate ......
Chromatin Architectural Changes during Cellular Senescence and Aging.
Sun L, Yu R, Dang W (Genes (Basel). 2018 Apr 16;9(4):)
Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics of genome architecture, their associated proteins, and......