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 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.

Whole human exome capture for high-throughput sequencing

Genome ◽  
2010 ◽  
Vol 53 (7) ◽  
pp. 568-574 ◽  
Author(s):  
Dae-Won Kim ◽  
Seong-Hyeuk Nam ◽  
Ryong Nam Kim ◽  
Sang-Haeng Choi ◽  
Hong-Seog Park
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Exome Capture ◽  
Microarray Design ◽  
Genome Wide ◽  
Human Genes ◽  
Practical Usefulness ◽  
A Genome ◽  
Wide Scale ◽  
Total Base

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.

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 Nucleosome repeat structure is present in native salivary chromosomes of Drosophila melanogaster.

1982 ◽  
Vol 95 (1) ◽  
pp. 262-266 ◽  
Author(s):  
R J Hill ◽  
M R Mott ◽  
E J Burnett ◽  
S M Abmayr ◽  
K Lowenhaupt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Electron Microscope ◽  
Micrococcal Nuclease ◽  
Dna Fragments ◽  
Repeat Structure ◽  
Nucleosome Organization ◽  
Micrococcal Nuclease Digestion ◽  
Nuclease Digestion ◽  
Microsurgical Procedure ◽  
5S Gene

The regularly repeating periodic nucleosome organization is clearly resolved in the chromatin of the isolated salivary chromosomes of Drosophila melanogaster. A new microsurgical procedure of isolation in buffer A of Hewish and Burgoyne (1973, Biochem. Biophys. Res. Commun., 52:504-510) yielded native Drosophila salivary chromosomes. These chromosomes were then swollen and spread by a modified Miller procedure, stained or shadowed, and examined in the electron microscope. Individual nucleoprotein fibers were resolved with regularly repeated nucleosomes of approximately 10 nm diameter. Micrococcal nuclease digestion of isolated salivary nuclei gave a family of DNA fragments characteristic of nucleosomes for total chromatin, 5S gene, and simple satellite (rho = 1.688 g/cm3) sequences.

scholarly journals Epigenetic regulation and epigenomic landscape in rice

2016 ◽  
Vol 3 (3) ◽  
pp. 309-327 ◽  
Author(s):  
Xian Deng ◽  
Xianwei Song ◽  
Liya Wei ◽  
Chunyan Liu ◽  
Xiaofeng Cao
Keyword(s):  
Epigenetic Regulation ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Food Crop ◽  
Recent Advances ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Epigenetic Regulators ◽  
Complex Genome

Abstract Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.

scholarly journals F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1154
Author(s):  
Min Jeong Hong ◽  
Jin-Baek Kim ◽  
Yong Weon Seo ◽  
Dae Yeon Kim
Keyword(s):  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Post Translational Modification ◽  
Genome Wide ◽  
A Genome ◽  
High Sequence Homology ◽  
Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

scholarly journals Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

2014 ◽  
Vol 42 (15) ◽  
pp. 9838-9853 ◽  
Author(s):  
Saeed Kaboli ◽  
Takuya Yamakawa ◽  
Keisuke Sunada ◽  
Tao Takagaki ◽  
Yu Sasano ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Interaction ◽  
Interaction Network ◽  
Essential Genes ◽  
Genetic Interactions ◽  
Lethal Gene ◽  
Synthetic Lethal ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

Abstract Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

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