Changes in nucleosome occupancy occur in a chromosome specific manner

Sexton, Brittany S.; Druliner, Brooke R.; Avey, Denis; Zhu, Fanxiu; Dennis, Jane A

doi:10.1016/j.gdata.2014.06.006

Cited by 3 publications

(3 citation statements)

References 4 publications

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“…We call these datasets “replicates” for generality, while in practice some of these data can be from unrelated laboratories, which use different experimental protocols for the same cell state/type as demonstrated below. For each replicate, the strength of the MNase-seq or ChIP-seq signal critically depends on the quality of antibody, chromatin digestion conditions, sequencing depth and variations of the experimental protocol [ 59 – 63 ]. Therefore, cross-platform comparison of datasets obtained in different laboratories is challenging [ 64 – 66 ].…”

Section: Methodsmentioning

confidence: 99%

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

2017

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3580-2) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

2017

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“…To isolate mononucleosomal DNA, the DNA samples were resolved on 2% agarose gel. The area of the gel containing mononucleosomal DNA (200 bps and below) was excised and purified by the freeze-squeeze method [1] , [2] , [3] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“… In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1] , [2] . We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium , and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500.…”

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confidence: 99%

Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy

Ren¹,

Vera²,

Hughes³

et al. 2015

Genomics Data

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In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1], [2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation. Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE64507.

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Recent advances in the study of Kaposi’s sarcoma-associated herpesvirus replication and pathogenesis

Avey

Brewers²,

Zhu³

2015

Virol. Sin.

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It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus (KSHV; also known as human herpesvirus 8 (HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis.

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Changes in nucleosome occupancy occur in a chromosome specific manner

Cited by 3 publications

References 4 publications

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

NucTools: analysis of chromatin feature occupancy profiles from high-throughput sequencing data

Stimulation of the Drosophila immune system alters genome-wide nucleosome occupancy

Recent advances in the study of Kaposi’s sarcoma-associated herpesvirus replication and pathogenesis

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