The alteration of chromatin structure plays an integral role in gene regulation. One means by which eukaryotes manipulate chromatin structure involves the use of ATP-dependent chromatin-remodelling enzymes. It appears likely that these enzymes play a widespread role in the regulation of many nuclear processes. Recently, significant progress has been made in defining the alterations to chromatin structure that these enzymes generate. The ability to alter nucleosome positioning may be a common feature of all ATP-dependent remodelling enzymes, but the spectrum of positions to which nucleosomes are relocated varies. Mounting evidence supports the ability of remodelling enzymes to translocate along DNA. This provides a means by which they could alter both the twist and writhe of DNA on the surface of nucleosomes, and so accelerate nucleosome repositioning.
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http://dx.doi.org/10.1042/bst0310893 | DOI Listing |
J Eukaryot Microbiol
January 2025
Laboratory of Cytology of Unicellular Organisms, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia.
The genus Pelomyxa includes 15 species of anaerobic Archamoebae with remarkable diverse nucleoplasm morphology. Nuclear structures, like chromatin and nucleoli, of several members of the genus was previously identified only based on their ultrastructural similarity to typical structures of somatic cells of higher eukaryotes. Here, we explored an easy-to-use, one-step intravital staining method with DAPI and pyronin to distinguish between DNA and RNA structures in nuclei of unfixed cells of Pelomyxa belevskii and P.
View Article and Find Full Text PDFNucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer.
View Article and Find Full Text PDFGene syntax-the order and arrangement of genes and their regulatory elements-shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that supercoiling-mediated feedback regulates expression of adjacent genes in a syntax-specific manner.
View Article and Find Full Text PDFThe formation of condensed heterochromatin is critical for establishing cell-specific transcriptional programs. To reveal structural transitions underlying heterochromatin formation in maturing mouse rod photoreceptors, we apply cryo-EM tomography, AI-assisted deep denoising, and molecular modeling. We find that chromatin isolated from immature retina cells contains many closely apposed nucleosomes with extremely short or absent nucleosome linkers, which are inconsistent with the typical two-start zigzag chromatin folding.
View Article and Find Full Text PDFEstablishing the anterior-posterior body axis is a fundamental process during embryogenesis, and the fruit fly, , provides one of the best-known case studies of this process. In Drosophila, localized mRNA of serves as anterior determinant (AD). Bicoid engages in a concentration-dependent competition with nucleosomes and initiates symmetry-breaking along the AP axis by promoting chromatin accessibility at the loci of transcription factor (TF) genes that are expressed in the anterior of the embryo.
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