Eukaryotes have linear chromosomes with domains called telomeres at both ends. The telomere DNA consists of a simple tandem repeat sequence, and multiple telomere-binding proteins including the shelterin complex maintain chromosome-end structures and regulate various biological reactions, such as protection of chromosome ends and control of telomere DNA length. On the other hand, subtelomeres, which are located adjacent to telomeres, contain a complex mosaic of multiple common segmental sequences and a variety of gene sequences. This review focused on roles of the subtelomeric chromatin and DNA structures in the fission yeast . The fission yeast subtelomeres form three distinct chromatin structures; one is the shelterin complex, which is localized not only at the telomeres but also at the telomere-proximal regions of subtelomeres to form transcriptionally repressive chromatin structures. The others are heterochromatin and knob, which have repressive effects in gene expression, but the subtelomeres are equipped with a mechanism that prevents these condensed chromatin structures from invading adjacent euchromatin regions. On the other hand, recombination reactions within or near subtelomeric sequences allow chromosomes to be circularized, enabling cells to survive in telomere shortening. Furthermore, DNA structures of the subtelomeres are more variable than other chromosomal regions, which may have contributed to biological diversity and evolution while changing gene expression and chromatin structures.
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http://dx.doi.org/10.3390/biom13050810 | DOI Listing |
PLoS Comput Biol
January 2025
Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China.
In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin.
View Article and Find Full Text PDFGenes Dev
January 2025
Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, the Netherlands;
Enhancers are tissue-specific regulatory DNA elements that can activate transcription of genes over distance. Their target genes most often are located in the same contact domain-chromosomal entities formed by cohesin DNA loop extrusion and typically flanked by CTCF-bound boundaries. Enhancers shared by multiple unrelated genes are underexplored but may be more common than anticipated.
View Article and Find Full Text PDFJ 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.
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