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Genome Biology

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https://www.readbyqxmd.com/read/28724393/methicillin-resistant-staphylococcus-aureus-emerged-long-before-the-introduction-of-methicillin-into-clinical-practice
#1
Catriona P Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D Bentley, Angela M Kearns, Matthew T G Holden
BACKGROUND: The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the emergence of resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after the introduction of this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence has always suggested that resistance arose around this period, when the mecA gene encoding methicillin resistance carried on an SCCmec element, was horizontally transferred to an intrinsically sensitive strain of S...
July 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28687088/canonical-mrna-is-the-exception-rather-than-the-rule
#2
Jun-An Chen, Simon Conn
A report on the Second Aegean International Conference on the Long and the Short of Non-Coding RNAs, held in Heraklion, Greece, 9-14 June 2017.
July 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/28687080/inhibition-of-rna-polymerase-ii-allows-controlled-mobilisation-of-retrotransposons-for-plant-breeding
#3
Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze, Etienne Bucher
BACKGROUND: Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity...
July 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/28683804/mapk-triggered-chromatin-reprogramming-by-histone-deacetylase-in-plant-innate-immunity
#4
David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling, Moussa Benhamed, Heribert Hirt
BACKGROUND: Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we determine whether microbial-associated molecular pattern-triggered gene expression involves modifications at the chromatin level. RESULTS: Histone acetylation and deacetylation are major regulators of microbial-associated molecular pattern-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defence gene expression and innate immunity...
July 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28683755/plant-epigenomics-deciphering-the-mechanisms-of-epigenetic-inheritance-and-plasticity-in-plants
#5
EDITORIAL
Claudia Köhler, Nathan Springer
No abstract text is available yet for this article.
July 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28679434/benchmarking-contexts-and-details-matter
#6
Siyuan Zheng
Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Biology.Please see related Li et al. and Newman et al. correspondence articles: www.dx.doi.org/10.1186/s13059-017-1256-5 and www.dx.doi.org/10.1186/s13059-017-1257-4.
July 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28679399/data-normalization-considerations-for-digital-tumor-dissection
#7
Aaron M Newman, Andrew J Gentles, Chih Long Liu, Maximilian Diehn, Ash A Alizadeh
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The Cancer Genome Atlas. Methods to characterize TIL biology are increasingly important, and the authors offer several arguments in favor of their strategy. Several of these claims warrant further discussion and highlight the critical importance of data normalization in gene expression deconvolution applications...
July 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28679386/revisit-linear-regression-based-deconvolution-methods-for-tumor-gene-expression-data
#8
Bo Li, Jun S Liu, X Shirley Liu
No abstract text is available yet for this article.
July 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28673357/strong-epistatic-and-additive-effects-of-linked-candidate-snps-for-drosophila-pigmentation-have-implications-for-analysis-of-genome-wide-association-studies-results
#9
Jean-Michel Gibert, Jorge Blanco, Marlies Dolezal, Viola Nolte, Frédérique Peronnet, Christian Schlötterer
BACKGROUND: The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how many of the SNPs in the block, and which ones, are causative. Drosophila pigmentation is a powerful model to dissect the genetic basis of intra-specific and inter-specific phenotypic variation. Three tightly linked SNPs in the t-MSE enhancer have been identified in three D...
July 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28655330/nice-seq-high-resolution-open-chromatin-profiling
#10
V K Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-Yong Xu, Touati Benoukraf, Sriharsa Pradhan
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seq captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden...
June 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28655341/hi-c-as-a-tool-for-precise-detection-and-characterisation-of-chromosomal-rearrangements-and-copy-number-variation-in-human-tumours
#11
Louise Harewood, Kamal Kishore, Matthew D Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V Peter Collins, Peter Fraser
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution...
June 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28655331/brie-transcriptome-wide-splicing-quantification-in-single-cells
#12
Yuanhua Huang, Guido Sanguinetti
Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA processing events such as splicing. Here, we present BRIE (Bayesian regression for isoform estimation), a Bayesian hierarchical model that resolves these problems by learning an informative prior distribution from sequence features. We show that BRIE yields reproducible estimates of exon inclusion ratios in single cells and provides an effective tool for differential isoform quantification between scRNA-seq data sets...
June 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28655328/epigenetic-and-chromatin-based-mechanisms-in-environmental-stress-adaptation-and-stress-memory-in-plants
#13
REVIEW
Jörn Lämke, Isabel Bäurle
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults...
June 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28637491/stable-centromere-positioning-in-diverse-sequence-contexts-of-complex-and-satellite-centromeres-of-maize-and-wild-relatives
#14
Jonathan I Gent, Na Wang, R Kelly Dawe
BACKGROUND: Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3)...
June 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629478/genetic-epigenetic-interactions-in-cis-a-major-focus-in-the-post-gwas-era
#15
REVIEW
Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M Greally, Benjamin Tycko
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS)...
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629467/chromatin-marks-and-ambient-temperature-dependent-flowering-strike-up-a-novel-liaison
#16
Alexander Steffen, Dorothee Staiger
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629446/increasing-mapping-precision-of-genome-wide-association-studies-to-genotype-and-impute-sequence-or-both
#17
Zhaoming Wang, Nilanjan Chatterjee
Fine-mapping to identify causal variants in genome-wide association studies remains challenging. A recent study provides guidance for future research.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629399/epigenomics-dissecting-hybridization-and-polyploidization
#18
Scott A Jackson
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28622766/translational-contributions-to-tissue-specificity-in-rhythmic-and-constitutive-gene-expression
#19
Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield
BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney and contrasted our findings with liver data available from the same mice. RESULTS: Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largely non-overlapping transcript sets with distinct phase clustering in the two organs...
June 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28619099/differentiated-demographic-histories-and-local-adaptations-between-sherpas-and-tibetans
#20
Chao Zhang, Yan Lu, Qidi Feng, Xiaoji Wang, Haiyi Lou, Jiaojiao Liu, Zhilin Ning, Kai Yuan, Yuchen Wang, Ying Zhou, Lian Deng, Lijun Liu, Yajun Yang, Shilin Li, Lifeng Ma, Zhiying Zhang, Li Jin, Bing Su, Longli Kang, Shuhua Xu
BACKGROUND: The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two groups, we analyzed genome-wide data in 111 Sherpas (Tibet and Nepal) and 177 Tibetans (Tibet and Qinghai), together with available data from present-day human populations. RESULTS: Sherpas and Tibetans show considerable genetic differences and can be distinguished as two distinct groups, even though the divergence between them (~3200-11,300 years ago) is much later than that between Han Chinese and either of the two groups (~6200-16,000 years ago)...
June 15, 2017: Genome Biology
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