For the computational sequence-directed mapping of the nucleosomes, the knowledge of the nucleosome positioning motifs - 10-11 base long sequences - and respective matrices of bendability, is not sufficient, since there is no justified way to fuse these motifs in one continuous nucleosome DNA sequence. Discovery of the strong nucleosome (SN) DNA sequences, with visible sequence periodicity allows derivation of the full-length nucleosome DNA bendability pattern as matrix or consensus sequence. The SN sequences of three species (A. thaliana, C. elegans, and H. sapiens) are aligned (512 sequences for each species), and long (115 dinucleotides) matrices of bendability derived for the species. The matrices have strong common property - alternation of runs of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotides, with average period 10.4 bases. On this basis the universal [R,Y] consensus of the nucleosome DNA sequence is derived, with exactly defined positions of respective penta- and hexamers RRRRR, RRRRRR, YYYYY, and YYYYYY.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1080/07391102.2014.891262 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Histone N-tails modulate sequence-specific positioning of nucleosomes.
J Biol Chem
December 2024
National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:
Spatial organization of chromatin is essential for cellular functioning. However, the precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA still remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo.
View Article and Find Full Text PDFIdentification of modulators of the ALT pathway through a native FISH-based optical screen.
Cell Rep
December 2024
Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:
A significant portion of human cancers utilize a recombination-based pathway, alternative lengthening of telomeres (ALT), to extend telomeres. To gain further insights into this pathway, we developed a high-throughput imaging-based screen named TAILS (telomeric ALT in situ localization screen) to identify genes that either promote or inhibit ALT activity. Screening over 1,000 genes implicated in DNA transactions, TAILS reveals both well-established and putative ALT modulators.
View Article and Find Full Text PDFGeometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.
J Chem Phys
December 2024
Department of Chemistry and Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA.
The dynamic organization of chromatin plays an essential role in the regulation of genetic activity, interconverting between open and compact forms at the global level. The mechanisms underlying these large-scale changes remain a topic of widespread interest. The simulations of nucleosome-decorated DNA reported herein reveal profound effects of the nucleosome itself on overall chromatin properties.
View Article and Find Full Text PDFCHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer.
Mol Ther Nucleic Acids
December 2024
Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China.
CHD6, a member of the chromodomain helicase DNA-binding protein family, has been implicated in various diseases and tumors. However, its precise binding model of CHD6 on regulatory functional genes remains poorly understood. In this study, we discovered sharp peaks of CHD6, as the first member of CHD family for housekeeping process, binding only to the promoter region of genes in the C4-2 cell line.
View Article and Find Full Text PDFContributing factors to the oxidation-induced mutational landscape in human cells.
Nat Commun
December 2024
Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
8-oxoguanine (8-oxoG) is a common oxidative DNA lesion that causes G > T substitutions. Determinants of local and regional differences in 8-oxoG-induced mutability across genomes are currently unknown. Here, we show DNA oxidation induces G > T substitutions and insertion/deletion (INDEL) mutations in human cells and cancers.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!