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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A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data.
Oluwadare O, Zhang Y, Cheng J (BMC Genomics. 2018 Feb 23;19(1):161)
BACKGROUND: The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal inte......
Macrophage production and activation are dependent on TRIM33.
Gallouet AS, Ferri F, Petit V, Parcelier A, Lewandowski D, Gault N, Barroca V, Le Gras S, Soler E, Grosveld F, Davidson I, Romeo PH (Oncotarget. 2017 Jan 17;8(3):5111-5122)
The tripartite motif (TRIM) family of proteins plays important roles in innate immunity and antimicrobial infection. None of these proteins has been shown to directly regulate transcription of genes in monocyte/macrophage except TRIM33 that we have recently shown to be a macrophage specific transcriptional inhibitor of Ifnb1. Using ChIP-seq analyses, we now report that TRIM33 is bound to two fold ......
Proximal and distal regulation of the HYAL1 gene cluster by the estrogen receptor α in breast cancer cells.
Edjekouane L, Benhadjeba S, Jangal M, Fleury H, Gévry N, Carmona E, Tremblay A (Oncotarget. 2016 11 22;7(47):77276-77290)
Chromosomal and genome abnormalities at the 3p21.3 locus are frequent events linked to epithelial cancers, including ovarian and breast cancers. Genes encoded in the 3p21.3 cluster include HYAL1, HYAL2 and HYAL3 members of hyaluronidases involved in the breakdown of hyaluronan, an abundant component of the vertebrate extracellular matrix. However, the transcriptional regulation of HYAL genes is po......
Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells.
Wang Q, Sun Q, Czajkowsky DM, Shao Z (Nat Commun. 2018 01 15;9(1):188)
Topologically associating domains (TADs) are fundamental elements of the eukaryotic genomic structure. However, recent studies suggest that the insulating complexes, CTCF/cohesin, present at TAD borders in mammals are absent from those in Drosophila melanogaster, raising the possibility that border elements are not conserved among metazoans. Using in situ Hi-C with sub-kb resolution, here we show ......
Epigenomic analysis in a cell-based model reveals the roles of H3K9me3 in breast cancer transformation.
Li QL, Lei PJ, Zhao QY, Li L, Wei G, Wu M (Epigenomics. 2017 Aug;9(8):1077-1092)
AIM: Epigenetic marks are critical regulators of chromatin and gene activity. Their roles in normal physiology and disease states, including cancer development, still remain elusive. Herein, the epigenomic change of H3K9me3, as well as its potential impacts on gene activity and genome stability, was investigated in an in vitro breast cancer transformation model....