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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The Rhododendron genome and chromosomal organization provide insight into shared whole genome duplications across the heath family (Ericaceae).
Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B (Genome Biol Evol. 2019 Nov 08;:)
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of more than 1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were......
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.
Xiong K, Ma J (Nat Commun. 2019 Nov 07;10(1):5069)
Higher-order genome organization and its variation in different cellular conditions remain poorly understood. Recent high-coverage genome-wide chromatin interaction mapping using Hi-C has revealed spatial segregation of chromosomes in the human genome into distinct subcompartments. However, subcompartment annotation, which requires Hi-C data with high sequencing coverage, is currently only availab......
HiCBricks: building blocks for efficient handling of large Hi-C datasets.
Pal K, Tagliaferri I, Livi CM, Ferrari F (Bioinformatics. 2019 Nov 07;:)
SUMMARY: Genome-wide chromosome conformation capture based on high-throughput sequencing (Hi-C) has been widely adopted to study chromatin architecture by generating datasets of ever-increasing complexity and size. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more c......
Higher-order chromosomal structures mediate genome function.
Jerkovic I, Szabo Q, Bantignies F, Cavalli G (J Mol Biol. 2019 Nov 02;:)
How chromosomes are organized within the tridimensional space of the nucleus and how can this organization affect genome function have been long-standing questions on the path to understanding genome activity and its link to diseases. In the last decade, high-throughput chromosome conformation capture techniques, such as Hi-C, have facilitated the discovery of new principles of genome folding. Chr......
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.
Abramo K, Valton AL, Venev SV, Ozadam H, Fox AN, Dekker J (Nat Cell Biol. 2019 Nov 04;:)
Chromosome folding is modulated as cells progress through the cell cycle. During mitosis, condensins fold chromosomes into helical loop arrays. In interphase, the cohesin complex generates loops and topologically associating domains (TADs), while a separate process of compartmentalization drives segregation of active and inactive chromatin. We used synchronized cell cultures to determine how the m......