ArticleBMC genomics2017
NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish.Nature communications · 2026Article
- A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements.bioRxiv : the preprint server for biology · 2025Article
- HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs.Nature communications · 2025Article
- Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor.Genome medicine · 2025Article
- A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development.Nature genetics · 2024Article
- Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Article
- Nucleosome reorganisation in breast cancer tissues.Clinical epigenetics · 2024Article
- A genome-wide comprehensive analysis of nucleosome positioning in yeast.PLoS computational biology · 2024Article
- Nucleosome repositioning in chronic lymphocytic leukemia.Genome research · 2023Article
- Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis.Nature structural & molecular biology · 2023Article
- NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.PLoS computational biology · 2022Article
- NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.Chromosoma · 2022Article
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
- The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes.Nature communications · 2022Article
- Article
- Identification of key mutations in central nervous diffuse large B-cell lymphoma (DLBCL) by comprehensive analysis between sequencing and TCGA database.Translational cancer research · 2021Article
- Linker histone epitopes are hidden by in situ higher-order chromatin structure.Epigenetics & chromatin · 2020Article
- Analytical Approaches for ATAC-seq Data Analysis.Current protocols in human genetics · 2020Article
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3 authors.
Funding
Abstract
backgroundBiomedical applications of high-throughput sequencing methods generate a vast amount of data in which numerous chromatin features are mapped along the genome. The results are frequently analysed by creating binary data sets that link the presence/absence of a given feature to specific genomic loci. However, the nucleosome occupancy or chromatin accessibility landscape is essentially continuous. It is currently a challenge in the field to cope with continuous distributions of deep sequencing chromatin readouts and to integrate the different types of discrete chromatin features to reveal linkages between them.
resultsHere we introduce the NucTools suite of Perl scripts as well as MATLAB- and R-based visualization programs for a nucleosome-centred downstream analysis of deep sequencing data. NucTools accounts for the continuous distribution of nucleosome occupancy. It allows calculations of nucleosome occupancy profiles averaged over several replicates, comparisons of nucleosome occupancy landscapes between different experimental conditions, and the estimation of the changes of integral chromatin properties such as the nucleosome repeat length. Furthermore, NucTools facilitates the annotation of nucleosome occupancy with other chromatin features like binding of transcription factors or architectural proteins, and epigenetic marks like histone modifications or DNA methylation. The applications of NucTools are demonstrated for the comparison of several datasets for nucleosome occupancy in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs).
conclusionsThe typical workflows of data processing and integrative analysis with NucTools reveal information on the interplay of nucleosome positioning with other features such as for example binding of a transcription factor CTCF, regions with stable and unstable nucleosomes, and domains of large organized chromatin K9me2 modifications (LOCKs). As potential limitations and problems we discuss how inter-replicate variability of MNase-seq experiments can be addressed.
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