The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning

<div><p>Similar to regularly spaced nucleosomes in chromatin, long tandem DNA arrays are composed of regularly alternating monomers that have almost identical primary DNA structures. Such a similarity in the structural organization makes these arrays especially interesting for studying the role of intrinsic DNA preferences in nucleosome positioning. We have studied the nucleosome formation potential of DNA tandem repeat families with different monomer lengths (ML). In total, 165 plant tandem repeat families from the PlantSat database (<a href="http://w3lamc.umbr.cas.cz/PlantSat/" target="_blank">http://w3lamc.umbr.cas.cz/PlantSat/</a>) were divided into two classes based on the number of nucleosome repeats in one DNA monomer. For predicting nucleosome formation potential, we developed the Phase method, which combines the advantages of multiple bioinformatics models. The Phase method was able to distinguish interfamily differences and intrafamily monomer variation and identify the influence of nucleotide context on nucleosome formation potential. Three main types of nucleosome arrangement in DNA tandem repeat arrays – regular, partially regular (partial), and flexible – were distinguished among a great variety of Phase profiles. The regular type, in which all nucleosomes of the monomer array are positioned in a context-dependent manner, is the most representative type of the class 1 families, with ML equal to or a multiple of the nucleosome repeat length (NRL). In the partially regular type, nucleotide context influences the positioning of only a subset of nucleosomes. The influence of the nucleotide context on nucleosome positioning has the least effect in the flexible type, which contains the greatest number of families (65). The majority of these families belong to class 2 and have nonmultiple ML to NRL ratios.</p></div

Accession numbers of chromosome proteins.

<p>*modENCODE data used (<a href="http://www.modencode.org/Genomes.shtml" target="_blank">http://www.modencode.org/Genomes.shtml</a>).</p><p>**GEO data used (<a href="http://www.ncbi.nlm.nih.gov/gds/" target="_blank">http://www.ncbi.nlm.nih.gov/gds/</a>).</p

DNA compaction ratio of the bands in the 9F13 -10B3 region.

a<p>– estimated on electron microscope sections of 50 polytene chromosomes.</p><p>Notes: IB-interband; B-band.</p><p>Data of release FB2011_03 were used.</p

Localization of proteins and DNA elements in 9F13 – 10B3 region of nonpolytene chromosomes (according to data of modENCODE).

<p>The positions of proteins were located as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#s4" target="_blank">Material and Methods</a>. <b>A</b> - physical map of DNA; positions of <i>v</i> and <i>sev</i> genes are taken from FlyBase, arrows 1–4 indicate position of probes for FISH on physical map. <b>B</b> - <i>P</i>-elements density in the region calculated as number of insertions per 1 kb in 10 kb interval (data on insertions are taken from FlyBase) <b>C</b> - interband specific and active chromatin specific proteins in S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a>, <b>D</b> - DNase I hypersensitivity sites (DHS) in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>E</b> - ORC2-binding sites in S2, BG3 and Kc cultural and salivary gland cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Eaton1" target="_blank">[59] </a><b>F</b> - histone H1 dips localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Braunschweig1" target="_blank">[45] </a><b>G</b> - histone H3.3 localization in S2 cells (modENCODE, Henikoff group) <b>H</b> - 30 chromatin states in BG3 and S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a>, and 5 chromatin types in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47] </a><b>I</b> - nucleosome turnover dynamics in S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Deal1" target="_blank">[60]</a>, <b>J</b> - D1 localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47]</a>, <b>K</b> - SUUR localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47]</a>, <b>L</b> - Lamin localization in Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Filion1" target="_blank">[47] </a><b>M</b> - early (up) and late (down) replication in S2, Kc and BG3 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Schwaiger1" target="_blank">[61] </a><b>N</b> - gene density (number of genes per 10 kb of DNA) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Belyakin2" target="_blank">[54]</a>.</p

Relation of genetic map, and band/interband pattern in the region 9F13 – 10B3.

<p><b>A</b> - predicted bands <b>B</b> - FlyBase genes <b>C</b> – 30 chromatin states in BG3 and S2 cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>D</b> - DNase I hypersensitivity sites (DHS) in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48] </a><b>E</b> - ORC-binding sites in S2, BG3 and Kc cells <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Eaton1" target="_blank">[59] </a><b>F</b> – Nucleosome Density (modENCODE, Henikoff group) <b>G</b> - active chromatin specific <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Kharchenko1" target="_blank">[48]</a> and - interbands specific proteins. Predicted interbands (dotted vertical lines are according to peaks in distribution of corresponding elements, solid lines reflect the edges of distributions of different characteristics).</p

Colocalization of DNA probes limiting the band 10B1–2, and Chriz/CHRO protein.

<p>Banding pattern in the region 10A–B (DAPI) (<b>A</b>), immunostaining of Chriz/CHRO and FISH of the DNA probe (<b>A</b>), immunostaining of Chriz/CHRO, FISH of the DNA probe and DAPI (<b>C</b>). Bar represents 5 µm.</p

Comparison of extents of band/interbands in polytene chromosomes according to Flybase r5.25 (A, B) and to the data of this study (C).

<p>Physical DNA map is situated between 10792800 and 11220400 positions of the map of Flybase.</p

Localization in polytene chromosomes of DNA fragments, which according to modEncode data are located in the predicted interbands flanking the 10A1–2 and 10B1–2 bands of the nonpolytene chromosomes.

<p>Banding pattern in the region under phase contrast microscope (<b>A, D</b>), pairwise FISH mapping of DNA fragments, limiting the bands 10A1–2 (probes CG15208 and Vago) (<b>B, C</b>) and 10B1–2 (CG32668 and l(1)10Bb) (<b>E, F</b>).</p

Comparison of several Electron Microscope sections of the region 9F11-12 – 10B (A, B) with revised Bridges map

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025960#pone.0025960-Bridges1" target="_blank">[<b>56</b>] </a><b>(C).</b> Vertical lines connect homologous bands. Scale represents 1 µm.</p

Coordinates and sizes of bands and interbands on physical map of the 9F13 – 10B3 region.

<p>Notes: IB-interband; B-band.</p><p>Data of release FB2011_03 were used.</p