Apoptotic cleavage of DNA in human lymphocyte chromatin shows high sequence specificity

Bettecken, Thomas; Frenkel, Zakharia M.; Altmüller, Janine; Nürnberg, Peter; Trifonov, Edward N.

doi:10.1080/07391102.2012.677772

Cited by 6 publications

(22 citation statements)

References 18 publications

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“…Blue and red lines correspond to promoters of the first group with normal occupancy of nucleosomes, apoptotic lymphocytes and CD4 + cells respectively. These promoters have the similar average occupancy of nucleosomes, position of +1 nucleosome from set of apoptotic lymphocytes [14] is shifted 50–60 bp downstream. Black and orange lines correspond to promoters with low occupancy of nucleosomes during apoptosis, apoptotic lymphocytes and normal CD4+ cells respectively.…”

Section: Resultsmentioning

confidence: 93%

“…With that nucleosome occupancy in GC-rich (group 2) promoters obtained from [13] has intermediate value between nucleosome occupancy in normal CD4+ cells obtained from [8] and nucleosome occupancy in the apoptotic lymphocytes obtained from [14]. (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 97%

“…( A ) Distribution of nucleosomes around transcription start sites; blue line corresponds to apoptotic lymphocytes [14]; black line corresponds to normal CD4 + cells [8]. ( B ) Distribution of nucleosomes around transcription start sites; 32,038 promoters were divided into two groups by nucleosome occupancy in apoptotic lymphocytes [14], K-means clustering method: blue line corresponds to the first group of 16670 promoters with normal occurrence (one nucleosome per 250 bp) of nucleosomes; black line corresponds to the second group of 15368 promoters with low occurrence (one nucleosome per 1000 bp) of nucleosomes around TSS.…”

Section: Resultsmentioning

confidence: 99%

“…( B ) Distribution of nucleosomes around transcription start sites; 32,038 promoters were divided into two groups by nucleosome occupancy in apoptotic lymphocytes [14], K-means clustering method: blue line corresponds to the first group of 16670 promoters with normal occurrence (one nucleosome per 250 bp) of nucleosomes; black line corresponds to the second group of 15368 promoters with low occurrence (one nucleosome per 1000 bp) of nucleosomes around TSS. ( C ) Distribution of nucleosomes around transcription start sites.…”

Section: Resultsmentioning

confidence: 99%

“…Two sets of nucleosome sequences, the first from [8] and the second from [14] were obtained using different methods. They had different length and number of flanking sequences of each DNA fragment.…”

Section: Resultsmentioning

confidence: 99%

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Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Hosid

Ioshikhes

2014

PLoS Comput Biol

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We analyzed two sets of human CD4+ nucleosomal DNA directly sequenced by Illumina (Solexa) high throughput sequencing method. The first set has ∼40 M sequences and was produced from the normal CD4+ T lymphocytes by micrococcal nuclease. The second set has ∼44 M sequences and was obtained from peripheral blood lymphocytes by apoptotic nucleases. The different nucleosome sets showed similar dinucleotide positioning AA/TT, GG/CC, and RR/YY (R is purine, Y - pyrimidine) patterns with periods of 10–10.4 bp. Peaks of GG/CC and AA/TT patterns were shifted by 5 bp from each other. Two types of promoters in H. sapiens: AT and GC-rich were identified. AT-rich promoters in apoptotic cell had +1 nucleosome shifts 50–60 bp downstream from those in normal lymphocytes. GC-rich promoters in apoptotic cells lost 80% of nucleosomes around transcription start sites as well as in total DNA. Nucleosome positioning was predicted by combination of {AA, TT}, {GG, CC}, {WW, SS} and {RR, YY} patterns. In our study we found that the combinations of {AA, TT} and {GG, CC} provide the best results and successfully mapped 33% of nucleosomes 147 bp long with precision ±15 bp (only 31/147 or 21% is expected).

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Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 3 more Smart Citations

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Hosid

Ioshikhes

2014

PLoS Comput Biol

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Nucleosome positioning: resources and tools online

Teif¹

2015

Brief Bioinform

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Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely to provide a guide to the multitude of nucleosome positioning resources available online.These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info. 2

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Nucleosome positioning sequence patterns as packing or regulatory

Pranckevičienė

Hosid

Liang

et al. 2019

Preprint

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Nucleosome positioning DNA sequence patterns (NPS) -usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA -at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene expression. Statistically, NPS are defined as oscillations of the dinucleotide periodicity with about 10 base pairs (bp) which reflects the double helix period. We compared the nucleosomal DNA patterns in mouse, human and yeast organisms and observed few distinctive patterns that can be termed as packing and regulatory referring to distinctive modes of chromatin function. For the first time the NPS patterns in nucleus accumbens cells (NAC) in mouse brain were characterized and compared to the patterns in human CD4+ and apoptotic lymphocyte cells and well studied patterns in August 28, 2019 1/23 yeast. The NPS patterns in human CD4+ cells and mouse brain cells had very high positive correlation. However, there was no correlation between them and patterns in human apoptotic lymphocyte cells and yeast, but the latter two were highly correlated with each other. By their dinucleotide arrangements the analyzed NPS patterns classified into stable canonical WW/SS (W=A or T and S=C or G dinucleotide) and less stable RR/YY (R=A or G and Y =C or T dinucleotide) patterns and anti-patterns.In the anti-patterns positioning of the dinucleotides is flipped compared to those in the regular patterns. Stable canonical WW/SS patterns and anti-patterns are ubiquitously observed in many organisms and they had high resemblance between yeast and human apoptotic cells. Less stable RR/YY patterns had higher positive correlation between mouse and normal human cells. Our analysis and evidence from scientific literature lead to idea that various distinct patterns in nucleosomal DNA can be related to the two roles of the chromatin: packing (WW/SS) and regulatory (RR/YY and "anti"). Author summaryPrecise positioning of nucleosomes on DNA sequence is essential for gene regulatory processes. Two main classes of nucleosome positioning sequence (NPS) patterns with a periodicity of 10bp for their sequence elements were previously described. In the 1st class AA,TT and other WW dinucleotides (W= A or T) tend to occur together in the major groove of DNA closest to the histone octamer, while SS dinucleotides (S= G or C) are primarily positioned in the major groove facing outward. In the 2nd class AA and TT are structurally separated (AA backbone near the histone octamer, and TT backbone further away), but grouped with other RR (R is purine A or G) and YY (Y is pyrimidine C or T) dinucleotides. In [8] we also described novel anti-NPS patterns, inverse to the conventional NPS patterns: WW runs inverse to SS, RR inverse to YY.We demonstrated that Yeast nucleosomes in promoters show higher correlation to the RR/YY pattern whereas novel anti-NPS patterns are viable for nucleosomes in the promoters of stress associated genes related to active chromatin remodeling. In the present study we attribute different ...

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Apoptotic cleavage of DNA in human lymphocyte chromatin shows high sequence specificity

Cited by 6 publications

References 18 publications

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Nucleosome positioning: resources and tools online

Nucleosome positioning sequence patterns as packing or regulatory

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