Chromatin Remodeling and Nucleosome Positioning

Längst, Gernot; Teif, Vladimir B.; Rippe, Karsten

doi:10.1002/9783527639991.ch5

Cited by 6 publications

(5 citation statements)

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“…NRLs can be compared either between different regions of the same cell, or between different cell states for the same genomic regions. For example, the NRL in the regions around CTCF is about 10 bp smaller than genome average [ 83 , 84 ], while NRL changes during cell differentiation can be as large as dozens of base pairs [ 82 , 85 – 87 ].…”

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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“…Furthermore, nucleo some positions change dynamically with time. To clar ify this, let us look at such an integral parameter as the average DNA length between neighboring nucleo somes [51]. The linker length differs not only in differ ent organisms (~7 bp in Schizosaccharomyces pombe, 18 bp in S. cerevisiae, ~28 bp in Drosophila melano gaster and Caenorhabditis elegans, and ~38 bp in Homo sapiens [22,123]), but also in different cell types of the same organism although they share the same DNA sequence (e.g., ~26 bp in human cortical neurons and 60 bp in glial cells) [2]).…”

Section: Nucleosome Repositioningmentioning

confidence: 99%

“…Several sequences with small and large affinity to the histone octamer have been identified in vitro [20,30,49]. The energy difference of nucleosome formation for genomic sequences is between 0 and 2.4 kcal/mol, while it can reach 4.1 kcal/mol for artificial sequences [50,51].…”

Section: Affinity Of Histone Octamers To Dnamentioning

confidence: 99%

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Nucleosomes in gene regulation: Theoretical approaches

et al. 2012

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This work reviews current theoretical approaches of biophysics and bioinformatics for the descrip tion of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from the molecular mechanistic and biologi cal points of view. In addition to classical problems in this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field.

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“…There are several factors influencing the bending rigidity of a chromosome. For human chromosomes the existence of nucleosomes and their distribution along the backbone of the chain imply a distribution of bending rigidity along the fiber. A further factor is the repulsion of the histone tails, that is, methylation .…”

Section: Introductionmentioning

confidence: 99%

The Effect of Bending Rigidity on Polymers

Jia

Hofmann

et al. 2019

Macro Theory & Simulations

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The conformations of chromatin are influenced by many factors. In the regulation of gene expression the bending rigidity of the chromatin polymer and its heterogeneity play an important role for the possible conformations. To elucidate this, the effect of bending rigidity as well as its heterogeneity on various polymer properties is investigated. In the context of chromatin organization, the contact probability is an important measure. It is analyzed whether there is any ambiguity in the definition of a contact. The results show that the contact probability does not depend on the range of contact in the limit of a large contour length between monomers. Further, the persistence length as a function of the bending rigidity is computed in the homogeneous and heterogeneous cases. The persistence length is systematically smaller in the heterogeneous case. Chromosomes are confined by each other in the nucleus and by looking at specific loci, the environment changes much more slowly than the local chromatin part. In conjunction with bending rigidity, polymers in rectangular confinements with several aspect ratios are simulated. Due to the spiraling behavior when the box size is small enough, an oscillation in the contact probability and the orientational correlation function is found.

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Chromatin Remodeling and Nucleosome Positioning

Cited by 6 publications

References 193 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

Nucleosomes in gene regulation: Theoretical approaches

The Effect of Bending Rigidity on Polymers

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