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Genome Research

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https://www.readbyqxmd.com/read/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#1
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29118011/comparative-genome-analysis-of-programmed-dna-elimination-in-nematodes
#2
Jianbin Wang, Shenghan Gao, Yulia Mostovoy, Yuanyuan Kang, Maxim Zagoskin, Yongqiao Sun, Bing Zhang, Laura K White, Alice Easton, Thomas B Nutman, Pui-Yan Kwok, Songnian Hu, Martin K Nielsen, Richard E Davis
Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens...
November 8, 2017: Genome Research
https://www.readbyqxmd.com/read/29113982/nanopore-sequencing-of-complex-genomic-rearrangements-in-yeast-reveals-mechanisms-of-repeat-mediated-double-strand-break-repair
#3
Ryan J McGinty, Rachel G Rubinstein, Alexander J Neil, Margaret Dominska, Denis Kiktev, Thomas D Petes, Sergei M Mirkin
Improper DNA double-strand break (DSB) repair results in complex genomic rearrangements (CGRs) in many cancers and various congenital disorders in humans. Trinucleotide repeat sequences, such as (GAA)n repeats in Friedreich's ataxia, (CTG)n repeats in myotonic dystrophy and (CGG)n repeats in fragile X syndrome, are also subject to double strand breaks within the repetitive tract followed by DNA repair. Mapping the outcomes of CGRs is important for understanding their causes and potential phenotypic effects...
November 7, 2017: Genome Research
https://www.readbyqxmd.com/read/29097404/deep-learning-of-the-regulatory-grammar-of-yeast-5-untranslated-regions-from-500-000-random-sequences
#4
Josh T Cuperus, Benjamin Groves, Anna Kuchina, Alexander B Rosenberg, Nebojsa Jojic, Stanley Fields, Georg Seelig
Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the 5' untranslated region (UTR) of mRNAs in the yeast Saccharomyces cerevisiae. We constructed a library of half a million 50-nucleotide-long random 5' UTRs and assayed their activity in a massively parallel growth selection experiment...
November 2, 2017: Genome Research
https://www.readbyqxmd.com/read/29097403/gridss-sensitive-and-specific-genomic-rearrangement-detection-using-positional-de-bruijn-graph-assembly
#5
Daniel L Cameron, Jan Schröder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss
The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler...
November 2, 2017: Genome Research
https://www.readbyqxmd.com/read/29089372/quantitative-rna-seq-meta-analysis-of-alternative-exon-usage-in-c-elegans
#6
Nicolas J Tourasse, Jonathan R M Millet, Denis Dupuy
Almost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated. Here we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event...
October 31, 2017: Genome Research
https://www.readbyqxmd.com/read/29079676/sex-biased-microrna-expression-in-mammals-and-birds-reveals-underlying-regulatory-mechanisms-and-a-role-in-dosage-compensation
#7
Maria Warnefors, Katharina Mössinger, Jean Halbert, Tania Studer, John L VandeBerg, Isa Lindgren, Amir Fallahshahroudi, Per Jensen, Henrik Kaessmann
Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set to analyze male and female miRNA expression profiles in mouse, opossum, and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, with the largest proportion found in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes...
October 27, 2017: Genome Research
https://www.readbyqxmd.com/read/29079675/deep-sequencing-of-natural-and-experimental-populations-of-drosophila-melanogaster-reveals-biases-in-the-spectrum-of-new-mutations
#8
Zoe June Assaf, Jane Park, Susanne Tilk, Mark L Siegal, Dmitri Petrov
Mutations provide the raw material of evolution, and thus our ability to study evolution fundamentally depends on having precise measurements of mutational rates and patterns. We generate a dataset for this purpose using i) de novo mutations from mutation accumulation experiments and ii) extremely rare polymorphisms from natural populations. The first, mutation accumulation (MA) lines, are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome...
October 27, 2017: Genome Research
https://www.readbyqxmd.com/read/29074739/genome-wide-discovery-of-active-regulatory-elements-and-transcription-factor-footprints-in-caenorhabditis-elegans-using-dnase-seq
#9
Paul Sternberg, Margaret Ho, Porfirio Quintero-Cadena
Deep sequencing of size-selected DNase I-treated chromatin (DNase-seq) allows high resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters and 28% in introns, with similar statistics observed in L1 arrest larvae...
October 26, 2017: Genome Research
https://www.readbyqxmd.com/read/29066617/a-novel-approach-for-data-integration-and-disease-subtyping
#10
Tin Nguyen, Rebecca Tagett, Diana Diaz, Sorin Draghici
Advances in high-throughput technologies allow for measurements of many types of omics data, yet the meaningful integration of several different data types remains a significant challenge. Another important and difficult problem is the discovery of molecular disease subtypes characterized by relevant clinical differences, such as survival. Here we present a novel approach, called Perturbation clustering for data INtegration and disease Subtyping (PINS), which is able to address both challenges. The framework has been validated on thousands of cancer samples, using gene expression, DNA methylation, non-coding microRNA, and copy number variation data available from the Gene Expression Omnibus, the Broad Institute, The Cancer Genome Atlas (TCGA), and the European Genome-Phenome Archive...
October 24, 2017: Genome Research
https://www.readbyqxmd.com/read/29030470/single-cell-sequencing-data-reveal-widespread-recurrence-and-loss-of-mutational-hits-in-the-life-histories-of-tumors
#11
Jack Kuipers, Katharina Jahn, Benjamin J Raphael, Niko Beerenwinkel
Intra-tumor heterogeneity poses substantial challenges for cancer treatment. A tumor's composition can be deduced by reconstructing its mutational history. Central to current approaches is the infinite sites assumption that every genomic position can only mutate once over the lifetime of a tumor. The validity of this assumption has never been quantitatively assessed. We developed a rigorous statistical framework to test the infinite sites assumption with single-cell sequencing data. Our framework accounts for the high noise and contamination present in such data...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29030469/single-cell-gene-expression-analysis-reveals-regulators-of-distinct-cell-subpopulations-among-developing-human-neurons
#12
Jiaxu Wang, Piroon Jenjaroenpun, Akshay Bhinge, Vladimir Espinosa Angarica, Antonio Del Sol, Intawat Nookaew, Vladimir A Kuznetsov, Lawrence W Stanton
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29030468/assessing-the-reliability-of-spike-in-normalization-for-analyses-of-single-cell-rna-sequencing-data
#13
Aaron T L Lun, Fernando J Calero-Nieto, Liora Haim-Vilmovsky, Berthold Göttgens, John C Marioni
By profiling the transcriptomes of individual cells, single-cell RNA sequencing provides unparalleled resolution to study cellular heterogeneity. However, this comes at the cost of high technical noise, including cell-specific biases in capture efficiency and library generation. One strategy for removing these biases is to add a constant amount of spike-in RNA to each cell and to scale the observed expression values so that the coverage of spike-in transcripts is constant across cells. This approach has previously been criticized as its accuracy depends on the precise addition of spike-in RNA to each sample...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29025896/high-throughput-single-molecule-telomere-characterization
#14
Jennifer McCaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao
We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG)n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7-bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG)n tract length at the end of each large telomere-terminal DNA segment...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29025895/accounting-for-gc-content-bias-reduces-systematic-errors-and-batch-effects-in-chip-seq-data
#15
Mingxiang Teng, Rafael A Irizarry
The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics' public catalogs is based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance, as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-seq experiments and that this variability leads to false-positive peak calls...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29025894/nascent-rna-sequencing-reveals-a-dynamic-global-transcriptional-response-at-genes-and-enhancers-to-the-natural-medicinal-compound-celastrol
#16
Noah Dukler, Gregory T Booth, Yi-Fei Huang, Nathaniel Tippens, Colin T Waters, Charles G Danko, John T Lis, Adam Siepel
Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory, and obesity-controlling effects...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#17
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29021291/a-genome-wide-interactome-of-dna-associated-proteins-in-the-human-liver
#18
Ryne C Ramaker, Daniel Savic, Andrew A Hardigan, Kimberly Newberry, Gregory M Cooper, Richard M Myers, Sara J Cooper
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29021290/identifying-cis-mediators-for-trans-eqtls-across-many-human-tissues-using-genomic-mediation-analysis
#19
Fan Yang, Jiebiao Wang, Brandon L Pierce, Lin S Chen
The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is "mediation" by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are "cis-mediators" of trans-eQTLs, including those "cis-hubs" involved in regulation of many trans-genes...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29021289/quantifying-the-regulatory-effect-size-of-cis-acting-genetic-variation-using-allelic-fold-change
#20
Pejman Mohammadi, Stephane E Castel, Andrew A Brown, Tuuli Lappalainen
Mapping cis-acting expression quantitative trait loci (cis-eQTL) has become a popular approach for characterizing proximal genetic regulatory variants. In this paper, we describe and characterize log allelic fold change (aFC), the magnitude of expression change associated with a given genetic variant, as a biologically interpretable unit for quantifying the effect size of cis-eQTLs and a mathematically convenient approach for systematic modeling of cis-regulation. This measure is mathematically independent from expression level and allele frequency, additive, applicable to multiallelic variants, and generalizable to multiple independent variants...
November 2017: Genome Research
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