scholarly journals Chromatinization ofEscherichia coliwith archaeal histones

2019 ◽  
Author(s):  
Maria Rojec ◽  
Antoine Hocher ◽  
Matthias Merkenschlager ◽  
Tobias Warnecke
Keyword(s):  
Nucleosome Occupancy ◽  
Micrococcal Nuclease ◽  
Ancestral State ◽  
E Coli ◽  
Genome Wide ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Methanothermus Fervidus ◽  
Chromatin Proteins

ABSTRACTNucleosomes restrict DNA accessibility throughout eukaryotic genomes, with repercussions for replication, transcription, and other DNA-templated processes. How this globally restrictive organization emerged from a presumably more open ancestral state remains poorly understood. Here, to better understand the challenges associated with establishing globally restrictive chromatin, we express histones in a naïve bacterial system that has not evolved to deal with nucleosomal structures:Escherichia coli. We find that histone proteins from the archaeonMethanothermus fervidusassemble on theE. colichromosomein vivoand protect DNA from micrococcal nuclease digestion, allowing us to map binding footprints genome-wide. We provide evidence that nucleosome occupancy along theE. coligenome tracks intrinsic sequence preferences but is disturbed by ongoing transcription and replication. Notably, we show that higher nucleosome occupancy at promoters and across gene bodies is associated with lower transcript levels, consistent with local repressive effects. Surprisingly, however, this sudden enforced chromatinization has only mild repercussions for growth, suggesting that histones can become established as ubiquitous chromatin proteins without interfering critically with key DNA-templated processes. Our results have implications for the evolvability of transcriptional ground states and highlight chromatinization by archaeal histones as a potential avenue for controlling genome accessibility in synthetic prokaryotic systems.

scholarly journals Chromatinization of Escherichia coli with archaeal histones

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Maria Rojec ◽  
Antoine Hocher ◽  
Kathryn M Stevens ◽  
Matthias Merkenschlager ◽  
Tobias Warnecke
Keyword(s):  
Escherichia Coli ◽  
Nucleosome Occupancy ◽  
Micrococcal Nuclease ◽  
E Coli ◽  
Genome Wide ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Methanothermus Fervidus ◽  
Chromatin Proteins

Nucleosomes restrict DNA accessibility throughout eukaryotic genomes, with repercussions for replication, transcription, and other DNA-templated processes. How this globally restrictive organization emerged during evolution remains poorly understood. Here, to better understand the challenges associated with establishing globally restrictive chromatin, we express histones in a naive system that has not evolved to deal with nucleosomal structures: Escherichia coli. We find that histone proteins from the archaeon Methanothermus fervidus assemble on the E. coli chromosome in vivo and protect DNA from micrococcal nuclease digestion, allowing us to map binding footprints genome-wide. We show that higher nucleosome occupancy at promoters is associated with lower transcript levels, consistent with local repressive effects. Surprisingly, however, this sudden enforced chromatinization has only mild repercussions for growth unless cells experience topological stress. Our results suggest that histones can become established as ubiquitous chromatin proteins without interfering critically with key DNA-templated processes.

scholarly journals Slaying the last unicorn - discovery of histones in the microalga Nanochlorum eucaryotum

2020 ◽  
Author(s):  
Valerie WC Soo ◽  
Tobias Warnecke
Keyword(s):  
Exceptional Case ◽  
Micrococcal Nuclease ◽  
Histone Fold ◽  
Histone Mrnas ◽  
Micrococcal Nuclease Digestion ◽  
Eukaryotic Chromatin ◽  
Nuclease Digestion ◽  
Eukaryotic Gene ◽  
Core Histones

ABSTRACTHistones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3, and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum. If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologs to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo. We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, N. eucaryotum has histone-based chromatin characteristic of most eukaryotes.

scholarly journals CAM: a quality control pipeline for MNase-seq data

2017 ◽  
Author(s):  
Sheng’en Hu ◽  
Xiaolan Chen ◽  
Ji Liao ◽  
Yiqing Chen ◽  
Chengchen Zhao ◽  
...  
Keyword(s):  
Quality Control ◽  
High Throughput Sequencing ◽  
Micrococcal Nuclease ◽  
Functional Regions ◽  
Nucleosome Organization ◽  
Genome Wide ◽  
Micrococcal Nuclease Digestion ◽  
A Genome ◽  
Nuclease Digestion ◽  
Wide Scale

AbstractNucleosome organization affects the accessibility of cis-elements to trans-acting factors. Micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq) is the most popular technology used to profile nucleosome organization on a genome-wide scale. Evaluating the data quality of MNase-seq data remains challenging, especially in mammalian. There is a strong need for a convenient and comprehensive approach to obtain dedicated quality control (QC) for MNase-seq data analysis. Here we developed CAM, which is a comprehensive QC pipeline for MNase-seq data. The CAM pipeline provides multiple informative QC measurements and nucleosome organization profiles on different potentially functional regions for given MNase-seq data. CAM also includes 268 historical MNase-seq datasets from human and mouse as a reference atlas for unbiased assessment. CAM is freely available at: http://www.tongji.edu.cn/~zhanglab/CAM

scholarly journals Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum

2021 ◽  
Vol 8 (2) ◽  
pp. 202023
Author(s):  
Valerie W. C. Soo ◽  
Tobias Warnecke
Keyword(s):  
Exceptional Case ◽  
Micrococcal Nuclease ◽  
Histone Fold ◽  
Histone Mrnas ◽  
Micrococcal Nuclease Digestion ◽  
Eukaryotic Chromatin ◽  
Nuclease Digestion ◽  
Eukaryotic Gene ◽  
Core Histones

Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3 and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga Nanochlorum eucaryotum . If true, derived histone loss in this lineage would constitute an exceptional case that might help us further understand the principles governing eukaryotic gene regulation. To substantiate these earlier reports of histone loss in N. eucaryotum, we sequenced, assembled and quantified its transcriptome. Following a systematic search for histone-fold domains in the assembled transcriptome, we detect orthologues to all four core histones. We also find histone mRNAs to be highly expressed, comparable to the situation in other eukaryotes. Finally, we obtain characteristic protection patterns when N. eucaryotum chromatin is subjected to micrococcal nuclease digestion, indicating widespread formation of nucleosomal complexes in vivo . We conclude that previous reports of missing histones in N. eucaryotum were mistaken. By all indications, Nanochlorum eucaryotum has histone-based chromatin characteristic of most eukaryotes.

scholarly journals Polyamine depletion is associated with altered chromatin structure in HeLa cells

1989 ◽  
Vol 260 (3) ◽  
pp. 697-704 ◽  
Author(s):  
R D Snyder
Keyword(s):  
Hela Cells ◽  
Chromatin Structure ◽  
Chromatin Accessibility ◽  
Micrococcal Nuclease ◽  
Polyamine Biosynthesis ◽  
Treatment Groups ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Nucleosomal Structure

HeLa cells depleted of polyamines by treatment with alpha-difluoromethylornithine (DFMO), methylglyoxal bis(guanylhydrazone) (MGBG) or a combination of the two, were examined for sensitivity to micrococcal nuclease, DNAase I and DNAase II. The degrees of chromatin accessibility to DNAase I and II appeared enhanced somewhat in all three treatment groups, and the released digestion products differed from those in non-depleted cells. DNA released from MGBG- and DFMO/MGBG-treated cells by DNAase II digestion was enriched 4-7-fold for Mg2+-soluble species relative to controls. DNA released by micrococcal nuclease digestion from all three treatment groups was characterized as consisting of higher-order nucleosomal structure than was DNA released from untreated cells. At least some of the altered chromatin properties were abolished by a brief treatment of cells with polyamines, notably spermine. These studies provide the first demonstration in vivo of altered chromatin structure in cells treated with inhibitors of polyamine biosynthesis.

scholarly journals plot2DO: a tool to assess the quality and distribution of genomic data

2017 ◽  
Author(s):  
Răzvan V. Chereji
Keyword(s):  
Micrococcal Nuclease ◽  
Supplementary Information ◽  
Gene Promoters ◽  
Functional Regions ◽  
Genome Wide ◽  
Micrococcal Nuclease Digestion ◽  
A Genome ◽  
Nuclease Digestion ◽  
Wide Scale

AbstractSummaryMicrococcal nuclease digestion followed by deep sequencing (MNase-seq) is the most used method to investigate nucleosome organization on a genome-wide scale. We present plot2DO, a software package for creating 2D occupancy plots, which allows biologists to evaluate the quality of MNase-seq data and to visualize the distribution of nucleosomes near the functional regions of the genome (e.g. gene promoters, origins of replication, etc.).Availability And ImplementationThe plot2DO open source package is freely available on GitHub at https://github.com/rchereji/plot2DO under the MIT [email protected] InformationSupplementary data are available at Bioinformatics online.

scholarly journals Human SWI/SNF Generates Abundant, Structurally Altered Dinucleosomes on Polynucleosomal Templates

2005 ◽  
Vol 25 (24) ◽  
pp. 11156-11170 ◽  
Author(s):  
Natalia P. Ulyanova ◽  
Gavin R. Schnitzler
Keyword(s):  
Cell Cycle Control ◽  
Micrococcal Nuclease ◽  
Asymmetric Structures ◽  
Micrococcal Nuclease Digestion ◽  
Evolutionarily Conserved ◽  
Nuclease Digestion ◽  
Transcriptional Memory ◽  
Altered Form ◽  
Regulatory Functions ◽  
Negative Supercoils

ABSTRACT Human SWI/SNF (hSWI/SNF) is an evolutionarily conserved ATP-dependent chromatin remodeling complex required for transcriptional regulation and cell cycle control. The regulatory functions of hSWI/SNF are correlated with its ability to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. Our current studies indicate that this change in supercoiling is due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed “altosomes,” each composed of two histone octamers and bearing an asymmetrically located region of nuclease-accessible DNA. Altosomes can be formed on chromatin containing the abundant mammalian linker histone H1 and have a unique micrococcal nuclease digestion footprint that allows their position and abundance on any DNA sequence to be measured. Over time, altosomes spontaneously revert to structurally normal but improperly positioned nucleosomes, suggesting a novel mechanism for transcriptional attenuation as well as transcriptional memory following hSWI/SNF action.

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