Testicular and renal tissue, obtained from adult cattle, pigs, rats, and human was processed by image digital segmentation and pixel texture analytical techniques for comparative evaluation of nuclear chromatin pattern of testicular primary spermatocytes and renal glomerular endothelial cells. The post mortem performed for the animals and the human subject were for reasons not related with either testicular or renal conditions. The objective was to establish a benchmark for identification of rapidly multiplying cells in images of sections of normal, as well as abnormal mammalian tissue. Based on the observed morphological and texture pattern of the nuclear chromatin of the testicular primary spermatocytes, it was determined that the renal glomerular endothelial cells exhibit similar nuclear chromatin morphology consistent with an ongoing rapid multiplication process. The nuclear chromatin of both cell types manifest identical mitotic figures which are strongly indicative of cellular proliferation.
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http://dx.doi.org/10.1016/j.compmedimag.2006.10.005 | DOI Listing |
Histone H3K9 methylation (H3K9me) by Setdb1 silences retrotransposons (rTE) by sequestering them in constitutive heterochromatin. Atf7IP is a constitutive binding partner of Setdb1 and is responsible for Setdb1 nuclear localization, activation and chromatin recruitment. However, structural details of the Setdb1/Atf7IP interaction have not been evaluated.
View Article and Find Full Text PDFA large fraction of the genome interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in genome organization and gene regulation across development. Despite much work, LAD structure and regulation are not fully understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here we profile Lamin B1, HP1β, H3K9me3, H3K9me2, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony and cluster LADs based on the abundance and distribution of these features across LADs.
View Article and Find Full Text PDFNuclear DNA is organized into a compact three-dimensional (3D) structure that impacts critical cellular processes. High-throughput chromosome conformation capture (Hi-C) is the most widely used method for measuring 3D genome architecture, while linear epigenomic assays, such as ATAC-seq, DNase-seq, and ChIP-seq, are extensively employed to characterize epigenomic regulation. However, the integrative analysis of chromatin interactions and associated epigenomic regulation remains challenging due to the pairwise nature of Hi-C data, mismatched resolution between Hi-C and epigenomic assays, and inconsistencies among analysis tools.
View Article and Find Full Text PDFCellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles of chromatin fibers as a mechanism regulating chromatin organization . Here we combine biochemistry and molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls chromatin phase separation.
View Article and Find Full Text PDFHuntington's Disease (HD), a progressive neurodegenerative disorder with no disease-modifying therapies, is caused by a CAG repeat expansion in the HD gene encoding polyglutamine-expanded huntingtin (HTT) protein. Mechanisms of HD cellular pathogenesis and cellular functions of the normal and mutant HTT proteins are still not completely understood. HTT protein has numerous interaction partners, and it likely provides a scaffold for assembly of multiprotein complexes many of which may be altered in HD.
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