4,373 results match your criteria Genome Biology [Journal]


Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

Genome Biol 2019 Feb 21;20(1):38. Epub 2019 Feb 21.

Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.

Background: The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.

Results: We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Read More

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http://dx.doi.org/10.1186/s13059-019-1650-2DOI Listing
February 2019

Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.

Genome Biol 2019 Feb 21;20(1):37. Epub 2019 Feb 21.

Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.

Background: Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes and macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Read More

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http://dx.doi.org/10.1186/s13059-019-1651-1DOI Listing
February 2019

dStruct: identifying differentially reactive regions from RNA structurome profiling data.

Genome Biol 2019 Feb 21;20(1):40. Epub 2019 Feb 21.

Department of Biomedical Engineering and Genome Center, University of California, Davis, One Shields Avenue, Davis, 95616, CA, USA.

RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not account for biological variation. Read More

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http://dx.doi.org/10.1186/s13059-019-1641-3DOI Listing
February 2019

Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history.

Genome Biol 2019 Feb 21;20(1):36. Epub 2019 Feb 21.

Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.

Background: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood.

Results: Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions. Read More

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http://dx.doi.org/10.1186/s13059-019-1648-9DOI Listing
February 2019

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm.

Genome Biol 2019 Feb 21;20(1):41. Epub 2019 Feb 21.

Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.

Background: Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.

Results: In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Read More

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http://dx.doi.org/10.1186/s13059-019-1652-0DOI Listing
February 2019

Fragile DNA contributes to repeated evolution.

Genome Biol 2019 Feb 21;20(1):39. Epub 2019 Feb 21.

Department of Biology, University of Konstanz, Konstanz, Germany.

Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots. Read More

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http://dx.doi.org/10.1186/s13059-019-1655-xDOI Listing
February 2019

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.

Genome Biol 2019 Feb 21;20(1):42. Epub 2019 Feb 21.

Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany.

Background: DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. Read More

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http://dx.doi.org/10.1186/s13059-019-1654-yDOI Listing
February 2019

Rapid turnover of life-cycle-related genes in the brown algae.

Genome Biol 2019 02 14;20(1):35. Epub 2019 Feb 14.

Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.

Background: Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. Read More

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http://dx.doi.org/10.1186/s13059-019-1630-6DOI Listing
February 2019

Skmer: assembly-free and alignment-free sample identification using genome skims.

Genome Biol 2019 02 13;20(1):34. Epub 2019 Feb 13.

Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093, CA, USA.

The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. Read More

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http://dx.doi.org/10.1186/s13059-019-1632-4DOI Listing
February 2019

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma.

Genome Biol 2019 02 13;20(1):33. Epub 2019 Feb 13.

RNA Editing Lab., Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo, 15 00146, Rome, Italy.

Background: Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.

Results: Here, we characterize the inosinome signature in normal brain and de novo glioblastoma (GBM) using new metrics that re-stratify GBM patients according to their editing profiles and indicate this post-transcriptional event as a possible molecular mechanism for sexual dimorphism in GBM. We find that over 85% of de novo GBMs carry a deletion involving the genomic locus of ADAR3, which is specifically expressed in the brain. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1647-xDOI Listing
February 2019
5 Reads

NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans.

Genome Biol 2019 02 11;20(1):32. Epub 2019 Feb 11.

Clinical Bioinformatics Lab, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, 75015, Paris, France.

State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogenic non-coding variants associated with monogenic Mendelian diseases. In addition to interspecies conservation, a comprehensive set of recent and ongoing purifying selection signals in humans is explored, accounting for lineage-specific regulatory elements. Read More

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http://dx.doi.org/10.1186/s13059-019-1634-2DOI Listing
February 2019

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.

Genome Biol 2019 02 11;20(1):31. Epub 2019 Feb 11.

Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, 351-0198, Japan.

Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Read More

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http://dx.doi.org/10.1186/s13059-019-1639-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371477PMC
February 2019

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

Genome Biol 2019 02 11;20(1):30. Epub 2019 Feb 11.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

Background: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically diverse populations. This has identified disease-relevant splicing events, as well as associations between splicing and genomic features, including sequence composition and conservation. Read More

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http://dx.doi.org/10.1186/s13059-019-1644-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371455PMC
February 2019

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.

Genome Biol 2019 02 11;20(1):29. Epub 2019 Feb 11.

INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.

How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Read More

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http://dx.doi.org/10.1186/s13059-019-1627-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369560PMC
February 2019

Modeling double strand break susceptibility to interrogate structural variation in cancer.

Genome Biol 2019 02 8;20(1):28. Epub 2019 Feb 8.

MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.

Background: Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs).

Results: We used experimentally quantified DSB frequencies in cell lines with matched chromatin and sequence features to derive the first quantitative genome-wide models of DSB susceptibility. Read More

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http://dx.doi.org/10.1186/s13059-019-1635-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368699PMC
February 2019

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Genome Biol 2019 02 5;20(1):27. Epub 2019 Feb 5.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

Background: CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed.

Results: Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. Read More

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http://dx.doi.org/10.1186/s13059-019-1637-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362594PMC
February 2019

A comparative evaluation of hybrid error correction methods for error-prone long reads.

Genome Biol 2019 02 4;20(1):26. Epub 2019 Feb 4.

Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA.

Background: Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been developed to date. Read More

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http://dx.doi.org/10.1186/s13059-018-1605-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362602PMC
February 2019

Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds.

Genome Biol 2019 02 5;20(1):15. Epub 2019 Feb 5.

State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.

CRISPR-Cas12a/Cpf1, a single RNA-guided endonuclease system, provides a promising tool for genome engineering. However, only three Cas12a orthologs have been employed for mammalian genome editing, and the editing efficiency as well as targeting coverage still requires improvements. Here, we harness six novel Cas12a orthologs for genome editing in human and mouse cells, some of which utilize simple protospacer adjacent motifs (PAMs) that remarkably increase the targeting range in the genomes. Read More

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http://dx.doi.org/10.1186/s13059-019-1620-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362571PMC
February 2019
1 Read

Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.

Genome Biol 2019 02 4;20(1):24. Epub 2019 Feb 4.

Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.

Background: Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed.

Results: Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as non-editable nucleotides in human. The occurrence of these recent gain and loss of RNA editing through DNA point mutation is significantly more prevalent than that expected for the nearby regions. Read More

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http://dx.doi.org/10.1186/s13059-019-1638-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360793PMC
February 2019

Graph genomes article collection.

Genome Biol 2019 02 1;20(1):25. Epub 2019 Feb 1.

Genome Biology, London, UK.

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http://dx.doi.org/10.1186/s13059-019-1636-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357451PMC
February 2019

Gene editing of the multi-copy H2A.B gene and its importance for fertility.

Genome Biol 2019 01 31;20(1):23. Epub 2019 Jan 31.

The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.

Background: Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1633-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357441PMC
January 2019
4 Reads

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication.

Genome Biol 2019 01 30;20(1):22. Epub 2019 Jan 30.

Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.

Background: Evidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood.

Results: We investigate the genomic landscape and evolution of putative crop-wild-relative introgression by analyzing the nuclear and chloroplast genomes from a panel of wild (Glycine soja) and domesticated (Glycine max) soybeans. Our data suggest that naturally occurring introgression between wild and domesticated soybeans was widespread and that introgressed variation in both wild and domesticated soybeans was selected against throughout the genomes and preferentially removed from the genomic regions underlying selective sweeps and domestication quantitative trait locus (QTL). Read More

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http://dx.doi.org/10.1186/s13059-019-1631-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354408PMC
January 2019

Multiple-gene targeting and mismatch tolerance can confound analysis of genome-wide pooled CRISPR screens.

Genome Biol 2019 01 25;20(1):21. Epub 2019 Jan 25.

Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, 94080, CA, USA.

Background: Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases associated with copy number alterations, the effects of sgRNAs co-targeting multiple genomic loci in CRISPR screens have not been discussed.

Results: In this work, we analyze CRISPR essentiality screen data from 391 cancer cell lines to characterize biases induced by multi-target sgRNAs. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1621-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346559PMC
January 2019
3 Reads

Guide RNAs with embedded barcodes boost CRISPR-pooled screens.

Genome Biol 2019 01 24;20(1):20. Epub 2019 Jan 24.

Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.

We report a new method using re-designed guide RNAs with internal barcodes (iBARs) embedded in their loop regions. Our iBAR approach outperforms the conventional method by producing screening results with much lower false-positive and false-negative rates especially with a high multiplicity of infection (MOI). Importantly, the iBAR approach reduces the starting cells at high MOI significantly with greatly improved efficiency and accuracy compared with the canonical CRISPR screens at a low MOI. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1628-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345036PMC
January 2019
5 Reads

Degradation of endogenous proteins and generation of a null-like phenotype in zebrafish using Trim-Away technology.

Genome Biol 2019 01 23;20(1):19. Epub 2019 Jan 23.

Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang, People's Republic of China.

Trim-Away is a recent technique to rapidly deplete a protein from any cell type. Guided by antibodies, TRIM21 selects proteins for destruction. However, the applicability of this method in model organisms has not been investigated. Read More

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http://dx.doi.org/10.1186/s13059-019-1624-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343325PMC
January 2019

Where is genomics going next?

Authors:
Barbara Cheifet

Genome Biol 2019 01 22;20(1):17. Epub 2019 Jan 22.

BioMed Central, New York, NY, USA.

We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. Read More

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http://dx.doi.org/10.1186/s13059-019-1626-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341733PMC
January 2019

Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data.

Genome Biol 2019 01 22;20(1):18. Epub 2019 Jan 22.

Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.

We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation. By integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide miRNA target prediction. Read More

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http://dx.doi.org/10.1186/s13059-019-1629-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341724PMC
January 2019

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.

Genome Biol 2019 01 22;20(1):16. Epub 2019 Jan 22.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Background: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region. Read More

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http://dx.doi.org/10.1186/s13059-018-1616-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341659PMC
January 2019
1 Read

iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.

Genome Biol 2019 01 17;20(1):14. Epub 2019 Jan 17.

Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.

Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we report an improvement of the GUIDE-seq method, iGUIDE, which allows filtering of mispriming events to clarify the true cleavage signal. Using iGUIDE, we specify the locations of Cas9-guided cleavage for four guide RNAs, characterize associated deletions, and show that naturally occurring background DNA double-strand breaks are associated with open chromatin, gene dense regions, and chromosomal fragile sites. Read More

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http://dx.doi.org/10.1186/s13059-019-1625-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337799PMC
January 2019
1 Read

Correction to: Applications and potential of genome editing in crop improvement.

Genome Biol 2019 01 16;20(1):13. Epub 2019 Jan 16.

The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

Following publication of the original article [1], the authors reported the following two errors. Read More

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http://dx.doi.org/10.1186/s13059-019-1622-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335730PMC
January 2019
1 Read

Exosomal miR-196a derived from cancer-associated fibroblasts confers cisplatin resistance in head and neck cancer through targeting CDKN1B and ING5.

Genome Biol 2019 01 14;20(1):12. Epub 2019 Jan 14.

Department of Oral and Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, People's Republic of China.

Background: Cisplatin resistance is a major challenge for advanced head and neck cancer (HNC). Understanding the underlying mechanisms and developing effective strategies against cisplatin resistance are highly desired in the clinic. However, how tumor stroma modulates HNC growth and chemoresistance is unclear. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13059-018-1604-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332863PMC
January 2019
6 Reads

Correction to: RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs.

Genome Biol 2019 01 11;20(1):11. Epub 2019 Jan 11.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

Following publication of the original article [1], the authors reported the following error in the name of the fourth author. Read More

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http://dx.doi.org/10.1186/s13059-019-1623-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329048PMC
January 2019
1 Read

Accurate prediction of cell type-specific transcription factor binding.

Genome Biol 2019 01 10;20(1). Epub 2019 Jan 10.

Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle (Saale), 06120, Germany.

Prediction of cell type-specific, in vivo transcription factor binding sites is one of the central challenges in regulatory genomics. Here, we present our approach that earned a shared first rank in the "ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge" in 2017. In post-challenge analyses, we benchmark the influence of different feature sets and find that chromatin accessibility and binding motifs are sufficient to yield state-of-the-art performance. Read More

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http://dx.doi.org/10.1186/s13059-018-1614-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327544PMC
January 2019
1 Read

Evolutionary genomics: the fruits of genomic approaches applied to evolutionary biology.

Authors:
Timothy R Sands

Genome Biol 2019 01 10;20(1):10. Epub 2019 Jan 10.

Genome Biology, BMC, London, UK.

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http://dx.doi.org/10.1186/s13059-018-1615-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329088PMC
January 2019
1 Read

Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants.

Genome Biol 2019 01 8;20(1). Epub 2019 Jan 8.

Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

Background: Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis elegans lincRNAs and evaluate their phenotypes.

Results: C. Read More

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http://dx.doi.org/10.1186/s13059-018-1619-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325887PMC
January 2019
1 Read

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

Genome Biol 2019 01 8;20(1). Epub 2019 Jan 8.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. Read More

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http://dx.doi.org/10.1186/s13059-018-1618-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325816PMC
January 2019
4 Reads

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Genome Biol 2019 01 7;20(1). Epub 2019 Jan 7.

Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.

Background: The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the d/d ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and d/d are apparently absent. Read More

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http://dx.doi.org/10.1186/s13059-018-1613-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322265PMC
January 2019
1 Read

Keen on the tenure track job, are you? Know these things, you should.

Genome Biol 2019 01 7;20(1). Epub 2019 Jan 7.

Department of Systems Pharmacology and Translational Therapeutics and Department of Genetics, University of Pennsylvania, Perelman School of Medicine, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA.

Success along the tenure track requires more than hard work and long hours. Here, the experiences of a recently tenured professor are distilled into a collection of tips to assist others along the path. Read More

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http://dx.doi.org/10.1186/s13059-018-1617-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324164PMC
January 2019
1 Read

plyranges: a grammar of genomic data transformation.

Genome Biol 2019 01 4;20(1). Epub 2019 Jan 4.

Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, USA.

Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows "tidy" data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1597-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320618PMC
January 2019
6 Reads

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease.

Genome Biol 2019 01 3;20(1). Epub 2019 Jan 3.

The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada.

Background: Maintenance of physiological circadian rhythm plays a crucial role in human health. Numerous studies have shown that disruption of circadian rhythm may increase risk for malignant, psychiatric, metabolic, and other diseases.

Results: Extending our recent findings of oscillating cytosine modifications (osc-modCs) in mice, in this study, we show that osc-modCs are also prevalent in human neutrophils. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1608-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317262PMC
January 2019
15 Reads

Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex.

Genome Biol 2019 01 3;20(1). Epub 2019 Jan 3.

Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., ESC 4041, Toronto, ON, M5S 3B2, Canada.

Background: Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 agricultural and environmental strains using whole-genome sequencing and evolutionary genomic analyses.

Results: We describe the phylogenetic distribution of all 77,728 orthologous gene families in the pan-genome, reconstruct the core genome phylogeny using the 2410 core genes, hierarchically cluster the accessory genome, identify the diversity and distribution of type III secretion systems and their effectors, predict ecologically and evolutionary relevant loci, and establish the molecular evolutionary processes operating on gene families. Read More

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http://dx.doi.org/10.1186/s13059-018-1606-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317194PMC
January 2019
1 Read

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.

Genome Biol 2019 01 3;20(1). Epub 2019 Jan 3.

Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.

The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1. Read More

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http://dx.doi.org/10.1186/s13059-018-1612-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317252PMC
January 2019
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RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs.

Genome Biol 2018 12 27;19(1):229. Epub 2018 Dec 27.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

Background: RNA secondary structures in the 5'-untranslated regions (5'-UTR) of mRNAs are key to the post-transcriptional regulation of gene expression. While it is evident that non-canonical Hoogsteen-paired G-quadruplex (rG4) structures somehow contribute to the regulation of translation initiation, the nature and extent of human mRNAs that are regulated by rG4s is not known. Here, we provide new insights into a mechanism by which rG4 formation modulates translation. Read More

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http://dx.doi.org/10.1186/s13059-018-1602-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307142PMC
December 2018
2 Reads

Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses.

Genome Biol 2018 12 27;19(1):228. Epub 2018 Dec 27.

The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY, 12222, USA.

Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. Read More

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http://dx.doi.org/10.1186/s13059-018-1611-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307160PMC
December 2018
1 Read

SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing.

Genome Biol 2018 12 24;19(1):227. Epub 2018 Dec 24.

Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.

Optically decodable beads link the identity of a sample to a measurement through an optical barcode, enabling libraries of biomolecules to be captured on beads in solution and decoded by fluorescence. This approach has been foundational to microarray, sequencing, and flow-based expression profiling technologies. We combine microfluidics with optically decodable beads and show that phenotypic analysis of living cells can be linked to single-cell sequencing. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1607-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305572PMC
December 2018
5 Reads

Illuminating the genome-wide activity of genome editors for safe and effective therapeutics.

Genome Biol 2018 12 22;19(1):226. Epub 2018 Dec 22.

Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.

Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss both important considerations for therapeutic genome editing and our understanding of the functional impact of undesired off-target mutations. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1610-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303961PMC
December 2018
6 Reads

Making supplemental information more accessible.

Authors:
Barbara Cheifet

Genome Biol 2018 12 21;19(1):225. Epub 2018 Dec 21.

, New York, USA.

Supplemental information is difficult to organize, review, and understand. Genome Biology has listed some new recommendations for the organization of supplemental data. Read More

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http://dx.doi.org/10.1186/s13059-018-1609-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302478PMC
December 2018
1 Read

Predicting age from the transcriptome of human dermal fibroblasts.

Genome Biol 2018 12 20;19(1):221. Epub 2018 Dec 20.

Integrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. Read More

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http://dx.doi.org/10.1186/s13059-018-1599-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300908PMC
December 2018
1 Read

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.

Genome Biol 2018 12 19;19(1):224. Epub 2018 Dec 19.

NYU Center for Genomics and Systems Biology, New York Genome Center, New York, NY, USA.

Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and "super-load" commercial droplet-based systems for significant cost reduction. Read More

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http://dx.doi.org/10.1186/s13059-018-1603-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300015PMC
December 2018
1 Read

Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation.

Genome Biol 2018 12 18;19(1):222. Epub 2018 Dec 18.

Unit of Human Evolutionary Genetics, Institut Pasteur, 75015, Paris, France.

Background: DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, their genetic determinants, and their respective causal impact on immune gene regulation remain elusive.

Results: We report extensive population differences in DNA methylation between 156 individuals of African and European descent, detected in primary monocytes that are used as a model of a major innate immunity cell type. Read More

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http://dx.doi.org/10.1186/s13059-018-1601-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299574PMC
December 2018
2 Reads