ArticleGenome research2006
Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
111 citing papers in PubMed, 206 citations in OpenAlex.
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- High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq.Nucleic acids research · 2024Article
- KSHV genome harbors both constitutive and lytically induced enhancers.Journal of virology · 2024Article
- Canalizing cell fate by transcriptional repression.Molecular systems biology · 2024Review
- Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection.Genome medicine · 2024Article
- DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network.BMC bioinformatics · 2023Article
- Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research.The Plant journal : for cell and molecular biology · 2023Review
- Review
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- HiCognition: a visual exploration and hypothesis testing tool for 3D genomics.Genome biology · 2023Article
- Manipulating chromatin architecture in C. elegans.Epigenetics & chromatin · 2022Article
- NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.PLoS computational biology · 2022Article
- Genomic architecture of 5S rDNA cluster and its variations within and between species.BMC genomics · 2022Article
51 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in a model genetic organism, Caenorhabditis elegans, we have carried out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores were liberated using an enzyme (micrococcal nuclease) with a strong preference for cleavage in non-nucleosomal regions. Sequence analysis of 284,091 putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As has previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.