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Genome Research

Claudia Rita Catacchio, Flavia Angela Maria Maggiolini, Pietro D'Addabbo, Miriana Bitonto, Oronzo Capozzi, Martina Lepore Signorile, Mattia Miroballo, Nicoletta Archidiacono, Evan E Eichler, Mario Ventura, Francesca Antonacci
For many years, inversions have been proposed to be a direct driving force in speciation since they suppress recombination when heterozygous. Inversions are the most common large-scale differences among humans and great apes. Nevertheless, they represent large events easily distinguishable by classical cytogenetics, whose resolution, however, is limited. Here, we performed a genome-wide comparison between human, great ape, and macaque genomes using the net alignments for the most recent releases of genome assemblies...
May 18, 2018: Genome Research
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky
In a conventional view of the prokaryotic genome organization, promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS 2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred)...
May 17, 2018: Genome Research
Yu Kong, Esther R Berko, Anthony Marckette, Shahina B Maqbool, Claudia A Simões-Pires, David F Kronn, Qian K Ye, Masako Suzuki, Adam Auton, John Greally
Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe the mosaic aneuploidy detection by massively-parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins, and how the MADSEQ analytical approach can be applied to exome or whole genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples...
May 17, 2018: Genome Research
Shijia Zhu, John Beaulaurier, Gintaras Deikus, Tao Wu, Maya Strahl, Ziyang Hao, Guanzheng Luo, James A Gregory, Andrew Chess, Chuan He, Andrew Xiao, Robert Sebra, Eric E Schadt, Gang Fang
N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes...
May 15, 2018: Genome Research
Quan Nguyen, Samuel Lukowski, Han Chiu, Anne Senabouth, Timothy Bruxner, Angelika Christ, Nathan Palpant, Joseph Powell
Heterogeneity of cell states represented in pluripotent cultures have not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method, and through this identified four subpopulations distinguishable on the basis of their pluripotent state including: a core pluripotent population (48...
May 11, 2018: Genome Research
Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert
DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq)...
May 7, 2018: Genome Research
Alberto Gomez-Carballa, Jacobo Pardo-Seco, Stefania Brandini, Alessandro Achilli, Ugo A Perego, Michael D Coble, Toni M Diegoli, Vanesa Alvarez-Iglesias, Federico Martinon-Torres, Anna Olivieri, Antonio Torroni, Antonio Salas
Genetic and archaeological data indicate that the initial Paleoindian settlers of South America followed two entry routes separated by the Andes and the Amazon rainforest. The interactions between these paths and their impact on the peopling of South America remain unclear. Analysis of genetic variation in the Peruvian Andes and regions located South of the Amazon River might provide clues on this issue. We analyzed mitochondrial DNA variation at different Andean locations and >360,000 autosomal SNPs from 28 Native American ethnic groups to evaluate different trans-Andean demographic scenarios...
May 7, 2018: Genome Research
Lianrong Pu, Yu Lin, Pavel A Pevzner
Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6...
May 7, 2018: Genome Research
Luisa Robbez-Masson, Christopher H C Tie, Lucia Conde, Hale Tunbak, Connor Husovsky, Iva A Tchasovnikarova, Richard T Timms, Javier Herrero, Paul J Lehner, Helen M Rowe
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of a SVA retrotransposon reporter. By using naïve vs. primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development...
May 4, 2018: Genome Research
Kei Fukuda, Akihiko Okuda, Kosuke Yusa, Yoichi Shinkai
In mouse embryonic stem cells (mESCs), expression of provirus and endogenous retroelements is epigenetically repressed. Although many cellular factors involved in retroelement silencing have been identified, the complete molecular mechanism remains elusive. In this study, we performed a genome-wide CRISPR screen to advance our understanding of retroelement silencing in mESCs. The Moloney murine leukemia virus (MLV)-based retroviral vector MSCV-GFP, which is repressed by the SETDB1/KAP1 pathway in mESCs was used as a reporter provirus and we identified more than 80 genes involved in this process...
May 4, 2018: Genome Research
Yun-Hua Esther Hsiao, Jae Hoon Bahn, Yun Yang, Xianzhi Lin, Stephen Tran, Ei-Wen Yang, Giovanni Quinones-Valdez, Xinshu Xiao
In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood...
May 3, 2018: Genome Research
Giovanni Iacono, Elisabetta Mereu, Amy Guillaumet-Adkins, Roser Corominas, Ivon Cuscó, Gustavo Rodríguez-Esteban, Marta Gut, Luis Alberto Pérez-Jurado, Ivo Gut, Holger Heyn
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers of cells, however, generates extremely large data sets, extending processing time and challenging computing resources. Current scRNA-seq analysis tools are not designed to interrogate large data sets and often lack sensitivity to identify marker genes. With bigSCale, we provide a scalable analytical framework to analyze millions of cells, which addresses the challenges associated with large data sets...
May 3, 2018: Genome Research
Bo Wang, Michael Regulski, Elizabeth Tseng, Andrew Olson, Sara Goodwin, W Richard McCombie, Doreen Ware
Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues and usually had fewer isoforms than old genes...
April 30, 2018: Genome Research
Heon Seok Kim, Kyungjin Lee, Seong-Jun Kim, Sungchan Cho, Hye Jin Shin, Chonsaeng Kim, Jin-Soo Kim
Pooled CRISPR screens based on lentiviral systems have been widely applied to identify the effect of gene knockout on cellular phenotype. Although many screens were successful, they also have the limitation that genes conferring mild phenotypes or those essential for growth can be overlooked, as every genetic perturbation is incorporated in the same population. Arrayed screens, on the other hand, incorporate a single genetic perturbation in each well and could overcome these limitations. However, arrayed screens based on siRNA-mediated knockdown were recently criticized for low reproducibility caused by incomplete inhibition of gene expression...
April 30, 2018: Genome Research
Solomon G Nergadze, Francesca M Piras, Riccardo Gamba, Marco Corbo, Federico Cerutti, Joseph G W McCarter, Eleonora Cappelletti, Francesco Gozzo, Rebecca M Harman, Douglas F Antczak, Donald Miller, Maren Scharfe, Giulio Pavesi, Elena Raimondi, Kevin F Sullivan, Elena Giulotto
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Equus caballus Chromosome 11. Here, we investigated the satellite-free centromeres of Equus asinus by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31)...
April 30, 2018: Genome Research
Robert Kofler, Kirsten-André Senti, Viola Nolte, Ray Tobler, Christian Schlötterer
The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P - element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P - element spread rapidly for 20 generations, but no further spread was noted later on...
April 30, 2018: Genome Research
Brigid M O'Flaherty, Yan Li, Ying Tao, Clinton R Paden, Krista Queen, Jing Zhang, Darrell L Dinwiddie, Stephen M Gross, Gary P Schroth, Suxiang Tong
Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases...
April 27, 2018: Genome Research
Yuchun Guo, Kevin Tian, Haoyang Zeng, Xiaoyun Guo, David K Gifford
The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated non-coding genetic variants. We present a novel TF binding motif representation, the k-mer set memory (KSM), which consists of a set of aligned k-mers that are over-represented at TF binding sites, and a new method called KMAC for de novo discovery of KSMs. We find that KSMs more accurately predict in vivo binding sites than position weight matrix (PWM) models and other more complex motif models across a large set of ChIP-seq experiments...
April 13, 2018: Genome Research
Amel Ghouila, Geoffrey Henry Siwo, Jean-Baka Domelevo Entfellner, Sumir Panji, Katrina A Button-Simons, Sage Zenon Davis, Faisal M Fadlelmola, Michael T Ferdig, Nicola Mulder
Scientific research plays a key role in the advancement of human knowledge and pursuit of solutions to important societal challenges. Typically, research occurs within specific institutions where data are generated and subsequently analyzed. Although collaborative science bringing together multiple institutions is now common, in such collaborations the analytical processing of the data is often performed by individual researchers within the team, with only limited internal oversight and critical analysis of the workflow prior to publication...
April 12, 2018: Genome Research
Jonathan M Howard, Hai Lin, Andrew J Wallace, Garam Kim, Jolene M Draper, Maximilian Haeussler, Sol Katzman, Masoud Toloue, Yunlong Liu, Jeremy R Sanford
Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay of trans -acting RNA binding proteins (RBPs) with myriad cis -regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein-coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on noncoding regions (introns). One of the earliest events in this process is recognition of the 3' splice site (3'ss) by U2 small nuclear RNA auxiliary factor 2 (U2AF2)...
April 12, 2018: Genome Research
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