Genome Biology最新文献_第9页

The utility of transposon mutagenesis for cancer studies in the era of genome editing. 在基因组编辑时代，转座子突变在癌症研究中的应用。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-19 DOI: 10.1186/s13059-015-0794-y

Gina M DeNicola, Florian A Karreth, David J Adams, Chi C Wong

引用次数: 2

Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. 全基因组图谱揭示了真核微生物利什曼原虫的单源染色体复制。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-19 DOI: 10.1186/s13059-015-0788-9

Catarina A Marques, Nicholas J Dickens, Daniel Paape, Samantha J Campbell, Richard McCulloch

{"title":"Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.","authors":"Catarina A Marques, Nicholas J Dickens, Daniel Paape, Samantha J Campbell, Richard McCulloch","doi":"10.1186/s13059-015-0788-9","DOIUrl":"10.1186/s13059-015-0788-9","url":null,"abstract":"Background: DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania.Results: Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins.Conclusions: The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"230"},"PeriodicalIF":12.3,"publicationDate":"2015-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34099797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Erratum to: Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. 对小鼠伏隔核慢性可卡因调节的表观基因组变化的勘误。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-14 DOI: 10.1186/s13059-015-0789-8

Jian Feng, Matthew Wilkinson, Xiaochuan Liu, Immanuel Purushothaman, Deveroux Ferguson, Vincent Vialou, Ian Maze, Ningyi Shao, Pamela Kennedy, JaWook Koo, Caroline Dias, Benjamin Laitman, Victoria Stockman, Quincey LaPlant, Michael E Cahill, Eric J Nestler, Li Shen

引用次数: 3

Erratum to: Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases. 全面的基因面板提供了优于孟德尔疾病临床外显子组测序的优势。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-13 DOI: 10.1186/s13059-015-0798-7

引用次数: 8

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Schmutzi:估计污染和内源性线粒体共识呼吁古代DNA。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-12 DOI: 10.1186/s13059-015-0776-0

Gabriel Renaud, Viviane Slon, Ana T Duggan, Janet Kelso

引用次数: 289

Do count-based differential expression methods perform poorly when genes are expressed in only one condition? 当基因仅在一种情况下表达时，基于计数的差异表达方法是否表现不佳?

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-08 DOI: 10.1186/s13059-015-0781-3

Xiaobei Zhou, Mark D Robinson

引用次数: 4

PfAlba1: master regulator of translation in the malaria parasite. PfAlba1:疟原虫翻译的主调控因子。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-08 DOI: 10.1186/s13059-015-0795-x

Evelien M Bunnik, Karine G Le Roch

引用次数: 4

Response to Zhou and Robinson. 对周和罗宾逊的回应。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-08 DOI: 10.1186/s13059-015-0782-2

Doron Betel, Nicholas D Socci, Raya Khanin, Christopher E Mason, Franck Rapaport

引用次数: 0

gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. 用于反卷积脱靶混淆RNA干扰筛选的统计模型。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-07 DOI: 10.1186/s13059-015-0783-1

Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Rämö, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio, Niko Beerenwinkel

{"title":"gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.","authors":"Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Rämö, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio, Niko Beerenwinkel","doi":"10.1186/s13059-015-0783-1","DOIUrl":"https://doi.org/10.1186/s13059-015-0783-1","url":null,"abstract":"Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package. ","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"220"},"PeriodicalIF":12.3,"publicationDate":"2015-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0783-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34069744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 34

Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST. 侧翼染色体序列对人类非编码RNA XIST定位和沉默的影响。

IF 12.3 1区生物学

Genome Biology Pub Date : 2015-10-02 DOI: 10.1186/s13059-015-0774-2

Angela D Kelsey, Christine Yang, Danny Leung, Jakub Minks, Thomas Dixon-McDougall, Sarah E L Baldry, Aaron B Bogutz, Louis Lefebvre, Carolyn J Brown

{"title":"Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST.","authors":"Angela D Kelsey, Christine Yang, Danny Leung, Jakub Minks, Thomas Dixon-McDougall, Sarah E L Baldry, Aaron B Bogutz, Louis Lefebvre, Carolyn J Brown","doi":"10.1186/s13059-015-0774-2","DOIUrl":"https://doi.org/10.1186/s13059-015-0774-2","url":null,"abstract":"Background: X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosomes in mammalian females. To understand how the RNA can establish silencing across millions of basepairs of DNA we have modelled the process by inducing expression of XIST from nine different locations in human HT1080 cells.Results: Localization of XIST, depletion of Cot-1 RNA, perinuclear localization, and ubiquitination of H2A occurs at all sites examined, while recruitment of H3K9me3 was not observed. Recruitment of the heterochromatic features SMCHD1, macroH2A, H3K27me3, and H4K20me1 occurs independently of each other in an integration site-dependent manner. Silencing of flanking reporter genes occurs at all sites, but the spread of silencing to flanking endogenous human genes is variable in extent of silencing as well as extent of spread, with silencing able to skip regions. The spread of H3K27me3 and loss of H3K27ac correlates with the pre-existing levels of the modifications, and overall the extent of silencing correlates with the ability to recruit additional heterochromatic features.Conclusions: The non-coding RNA XIST functions as a cis-acting silencer when expressed from nine different locations throughout the genome. A hierarchy among the features of heterochromatin reveals the importance of interaction with the local chromatin neighborhood for optimal spread of silencing, as well as the independent yet cooperative nature of the establishment of heterochromatin by the non-coding XIST RNA.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"208"},"PeriodicalIF":12.3,"publicationDate":"2015-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0774-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34056785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3