journal
MENU ▼
Read by QxMD icon Read
search

Genome Biology

journal
https://www.readbyqxmd.com/read/29458393/dominant-integration-locus-drives-continuous-diversification-of-plant-immune-receptors-with-exogenous-domain-fusions
#1
Paul C Bailey, Christian Schudoma, William Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew Moscou, Ksenia V Krasileva
BACKGROUND: The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. RESULTS: We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses...
February 19, 2018: Genome Biology
https://www.readbyqxmd.com/read/29452591/ageing-associated-dna-methylation-dynamics-are-a-molecular-readout-of-lifespan-variation-among-mammalian-species
#2
Robert Lowe, Carl Barton, Christopher A Jenkins, Christina Ernst, Oliver Forman, Denise S Fernandez-Twinn, Christoph Bock, Stephen J Rossiter, Chris G Faulkes, Susan E Ozanne, Lutz Walter, Duncan T Odom, Cathryn Mellersh, Vardhman K Rakyan
BACKGROUND: Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ageing-associated differentially methylated positions (aDMPs) in human and mouse. These are CpG sites at which DNA methylation dynamics show significant correlations with age. We hypothesise that aDMPs are pan-mammalian and are a dynamic molecular readout of lifespan variation among different mammalian species...
February 16, 2018: Genome Biology
https://www.readbyqxmd.com/read/29448949/a-standardized-framework-for-representation-of-ancestry-data-in-genomics-studies-with-application-to-the-nhgri-ebi-gwas-catalog
#3
LETTER
Joannella Morales, Danielle Welter, Emily H Bowler, Maria Cerezo, Laura W Harris, Aoife C McMahon, Peggy Hall, Heather A Junkins, Annalisa Milano, Emma Hastings, Cinzia Malangone, Annalisa Buniello, Tony Burdett, Paul Flicek, Helen Parkinson, Fiona Cunningham, Lucia A Hindorff, Jacqueline A L MacArthur
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations...
February 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29433568/the-peopling-of-the-last-green-sahara-revealed-by-high-coverage-resequencing-of-trans-saharan-patrilineages
#4
Eugenia D'Atanasio, Beniamino Trombetta, Maria Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth Watson, Alfredo Coppa, Paolo Anagnostou, Jean-Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto, Fulvio Cruciani
BACKGROUND: Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS: In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations...
February 12, 2018: Genome Biology
https://www.readbyqxmd.com/read/29426353/precise-genome-wide-mapping-of-single-nucleosomes-and-linkers-in-vivo
#5
Răzvan V Chereji, Srinivas Ramachandran, Terri D Bryson, Steven Henikoff
We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A...
February 9, 2018: Genome Biology
https://www.readbyqxmd.com/read/29422066/genome-wide-analyses-reveal-a-role-of-polycomb-in-promoting-hypomethylation-of-dna-methylation-valleys
#6
Yuanyuan Li, Hui Zheng, Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang, Wei Xie
BACKGROUND: Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large and extend well beyond proximal promoters, forming DNA methylation valleys (DMVs) or DNA methylation canyons. However, it remains elusive how most developmental genes can evade DNA methylation regardless of their transcriptional states. RESULTS: We show that DMVs are hypomethylated in development and are highly conserved across vertebrates...
February 8, 2018: Genome Biology
https://www.readbyqxmd.com/read/29415772/kourami-graph-guided-assembly-for-novel-human-leukocyte-antigen-allele-discovery
#7
Heewook Lee, Carl Kingsford
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching approaches and their outputs are inherently limited by the completeness of already known types, making them unsuitable for discovery of novel alleles. We have developed a graph-guided assembly technique for classical HLA genes, which can construct allele sequences given high-coverage whole-genome sequencing data...
February 7, 2018: Genome Biology
https://www.readbyqxmd.com/read/29415752/correction-to-a-statistical-framework-for-analyzing-deep-mutational-scanning-data
#8
Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler
After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an overestimation of the standard errors calculated using the Enrich2 random-effects model.
February 7, 2018: Genome Biology
https://www.readbyqxmd.com/read/29409532/scanpy-large-scale-single-cell-gene-expression-data-analysis
#9
F Alexander Wolf, Philipp Angerer, Fabian J Theis
SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells ( https://github.com/theislab/Scanpy ). Along with SCANPY, we present ANNDATA, a generic class for handling annotated data matrices ( https://github.com/theislab/anndata )...
February 6, 2018: Genome Biology
https://www.readbyqxmd.com/read/29409527/bystro-rapid-online-variant-annotation-and-natural-language-filtering-at-whole-genome-scale
#10
Alex V Kotlar, Cristina E Trevino, Michael E Zwick, David J Cutler, Thomas S Wingo
Accurately selecting relevant alleles in large sequencing experiments remains technically challenging. Bystro ( https://bystro.io/ ) is the first online, cloud-based application that makes variant annotation and filtering accessible to all researchers for terabyte-sized whole-genome experiments containing thousands of samples. Its key innovation is a general-purpose, natural-language search engine that enables users to identify and export alleles and samples of interest in milliseconds. The search engine dramatically simplifies complex filtering tasks that previously required programming experience or specialty command-line programs...
February 6, 2018: Genome Biology
https://www.readbyqxmd.com/read/29386055/focus-on-african-diversity-confirms-complexity-of-skin-pigmentation-genetics
#11
Tina Lasisi, Mark D Shriver
Renewed focus on African populations confirms the complexity of skin pigmentation genetics, and suggests future directions for pigmentation research.
January 31, 2018: Genome Biology
https://www.readbyqxmd.com/read/29386051/the-probam-and-probed-standard-formats-enabling-a-seamless-integration-of-genomics-and-proteomics-data
#12
LETTER
Gerben Menschaert, Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W Deutsch, Tobias Ternent, Juan Antonio Vizcaíno
On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data...
January 31, 2018: Genome Biology
https://www.readbyqxmd.com/read/29382368/a-panoramic-view-of-rna-modifications-exploring-new-frontiers
#13
Zijun Zhang, Eddie Park, Lan Lin, Yi Xing
Meeting report on the Cold Spring Harbor Asia conference on RNA Modifications and Epitranscriptomics, held in Suzhou, China, 13-17 November, 2017.
January 30, 2018: Genome Biology
https://www.readbyqxmd.com/read/29378643/a-reproducibility-based-computational-framework-identifies-an-inducible-enhanced-antiviral-state-in-dendritic-cells-from-hiv-1-elite-controllers
#14
Enrique Martin-Gayo, Michael B Cole, Kellie E Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D Walker, Nir Yosef, Alex K Shalek, Xu G Yu
BACKGROUND: Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. RESULTS: To overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification...
January 29, 2018: Genome Biology
https://www.readbyqxmd.com/read/29368664/extensive-epigenetic-reprogramming-during-the-life-cycle-of-marchantia-polymorpha
#15
Marc W Schmid, Alejandro Giraldo-Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L Bowman, Ueli Grossniklaus
BACKGROUND: In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles...
January 25, 2018: Genome Biology
https://www.readbyqxmd.com/read/29368663/developmental-dynamics-of-gene-expression-and-alternative-polyadenylation-in-the-caenorhabditis-elegans-germline
#16
Sean M West, Desirea Mecenas, Michelle Gutwein, David Aristizábal-Corrales, Fabio Piano, Kristin C Gunsalus
BACKGROUND: The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation...
January 24, 2018: Genome Biology
https://www.readbyqxmd.com/read/29361968/an-obesity-associated-gut-microbiome-reprograms-the-intestinal-epigenome-and-leads-to-altered-colonic-gene-expression
#17
Yufeng Qin, John D Roberts, Sara A Grimm, Fred B Lih, Leesa J Deterding, Ruifang Li, Kaliopi Chrysovergis, Paul A Wade
BACKGROUND: The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli through alterations in chromatin features and, ultimately, gene expression. How the host mediates epigenomic responses to gut microbiota is an emerging area of interest. Here, we profile the gut microbiome and chromatin characteristics in colon epithelium from mice fed either an obesogenic or control diet, followed by an analysis of the resultant changes in gene expression...
January 23, 2018: Genome Biology
https://www.readbyqxmd.com/read/29351814/setdb1-prevents-tet2-dependent-activation-of-iap-retroelements-in-na%C3%A3-ve-embryonic-stem-cells
#18
Özgen Deniz, Lorenzo de la Rica, Kevin C L Cheng, Dominik Spensberger, Miguel R Branco
BACKGROUND: Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos...
January 19, 2018: Genome Biology
https://www.readbyqxmd.com/read/29343290/finemav-prioritizing-candidate-genetic-variants-driving-local-adaptations-in-human-populations
#19
Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue, Chris Tyler-Smith
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data...
January 17, 2018: Genome Biology
https://www.readbyqxmd.com/read/29334995/antisense-suppression-of-the-nonsense-mediated-decay-factor-upf3b-as-a-potential-treatment-for-diseases-caused-by-nonsense-mutations
#20
Lulu Huang, Audrey Low, Sagar S Damle, Melissa M Keenan, Steven Kuntz, Susan F Murray, Brett P Monia, Shuling Guo
BACKGROUND: About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncated proteins, but also often result in  decreased mRNA abundance due to  nonsense-mediated mRNA decay (NMD). Although pharmacological inhibition of NMD could be an attractive therapeutic approach for the treatment of diseases caused by nonsense mutations, NMD also regulates the expression of 10-20% of the normal transcriptome...
January 15, 2018: Genome Biology
journal
journal
35114
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"