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Genome Biology

Maja P Mattle-Greminger, Tugce Bilgin Sonay, Alexander Nater, Marc Pybus, Tariq Desai, Guillem de Valles, Ferran Casals, Aylwyn Scally, Jaume Bertranpetit, Tomas Marques-Bonet, Carel P van Schaik, Maria Anisimova, Michael Krützen
BACKGROUND: Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene...
November 15, 2018: Genome Biology
Michelle S Kim, Kane P Patel, Andrew K Teng, Ali J Berens, Joseph Lachance
BACKGROUND: Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. Here, we integrate whole genome sequence data from global populations, results from thousands of genome-wide association studies (GWAS), and extensive computer simulations to identify how genetic disease risks can be misestimated. RESULTS: In contrast to null expectations, we find that risk allele frequencies at known disease loci are significantly different for African populations compared to other continents...
November 14, 2018: Genome Biology
Mengjie Chen, Xiang Zhou
We develop a method, VIPER, to impute the zero values in single-cell RNA sequencing studies to facilitate accurate transcriptome quantification at the single-cell level. VIPER is based on nonnegative sparse regression models and is capable of progressively inferring a sparse set of local neighborhood cells that are most predictive of the expression levels of the cell of interest for imputation. A key feature of our method is its ability to preserve gene expression variability across cells after imputation. We illustrate the advantages of our method through several well-designed real data-based analytical experiments...
November 12, 2018: Genome Biology
Heath E O'Brien, Eilis Hannon, Matthew J Hill, Carolina C Toste, Matthew J Robertson, Joanne E Morgan, Gemma McLaughlin, Cathryn M Lewis, Leonard C Schalkwyk, Lynsey S Hall, Antonio F Pardiñas, Michael J Owen, Michael C O'Donovan, Jonathan Mill, Nicholas J Bray
BACKGROUND: Genetic influences on gene expression in the human fetal brain plausibly impact upon a variety of postnatal brain-related traits, including susceptibility to neuropsychiatric disorders. However, to date, there have been no studies that have mapped genome-wide expression quantitative trait loci (eQTL) specifically in the human prenatal brain. RESULTS: We performed deep RNA sequencing and genome-wide genotyping on a unique collection of 120 human brains from the second trimester of gestation to provide the first eQTL dataset derived exclusively from the human fetal brain...
November 12, 2018: Genome Biology
Ting Zhao, Xiaoyuan Tao, Shouli Feng, Luyao Wang, Hui Hong, Wei Ma, Guandong Shang, Shisong Guo, Yuxin He, Baoliang Zhou, Xueying Guan
BACKGROUND: Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding portion of the genome in particular remains largely unknown. In this study, we examine the profile of long non-coding RNAs (lncRNAs), comparing them with that of coding genes in allotetraploid cotton (Gossypium hirsutum), its putative diploid ancestors (G. arboreum; G...
November 12, 2018: Genome Biology
Jinzhi Duan, Guangqing Lu, Yu Hong, Qingtao Hu, Xueying Mai, Jing Guo, Xiaofang Si, Fengchao Wang, Yu Zhang
CRISPR/dCas9 is a versatile tool that can be used to recruit various effectors and fluorescent molecules to defined genome regions where it can modulate genetic and epigenetic markers, or track the chromatin dynamics in live cells. In vivo applications of CRISPR/dCas9 in animals have been challenged by delivery issues. We generate and characterize a mouse strain with dCas9-EGFP ubiquitously expressed in various tissues. Studying telomere dynamics in these animals reveals surprising results different from those observed in cultured cell lines...
November 8, 2018: Genome Biology
Jennifer Westoby, Marcela Sjöberg Herrera, Anne C Ferguson-Smith, Martin Hemberg
Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data. The reduction in performance compared with bulk RNA-seq is small. An important biological insight comes from our analysis of real data which shows that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells...
November 7, 2018: Genome Biology
Ani Grigoryan, Novella Guidi, Katharina Senger, Thomas Liehr, Karin Soller, Gina Marka, Angelika Vollmer, Yolanda Markaki, Heinrich Leonhardt, Christian Buske, Daniel B Lipka, Christoph Plass, Yi Zheng, Medhanie A Mulaw, Hartmut Geiger, Maria Carolina Florian
BACKGROUND: The decline of hematopoietic stem cell (HSC) function upon aging contributes to aging-associated immune remodeling and leukemia pathogenesis. Aged HSCs show changes to their epigenome, such as alterations in DNA methylation and histone methylation and acetylation landscapes. We previously showed a correlation between high Cdc42 activity in aged HSCs and the loss of intranuclear epigenetic polarity, or epipolarity, as indicated by the specific distribution of H4K16ac. RESULTS: Here, we show that not all histone modifications display a polar localization and that a reduction in H4K16ac amount and loss of epipolarity are specific to aged HSCs...
November 7, 2018: Genome Biology
Jiekun Yang, Xiaolong Wei, Turan Tufan, Cem Kuscu, Hayrunnisa Unlu, Saadia Farooq, Elif Demirtas, Bryce M Paschal, Mazhar Adli
BACKGROUND: The mutational processes underlying non-coding cancer mutations and their biological significance in tumor evolution are poorly understood. To get better insights into the biological mechanisms of mutational processes in breast cancer, we integrate whole-genome level somatic mutations from breast cancer patients with chromatin states and transcription factor binding events. RESULTS: We discover that a large fraction of non-coding somatic mutations in estrogen receptor (ER)-positive breast cancers are confined to ER binding sites...
November 7, 2018: Genome Biology
Xiang Guo, Ann Dean
A recent study used CRISPR/Cas9 to reveal long-range looping between disease-related genes and their regulatory elements that is mediated by the CCCTC-binding factor (CTCF) in prostate cancer.
November 6, 2018: Genome Biology
Yong Lei, Yung-Hsin Huang, Margaret A Goodell
DNA methylation plays important roles in determining cellular identity, disease, and environmental responses, but little is known about the mechanisms that drive methylation changes during cellular differentiation and tumorigenesis. Meanwhile, the causal relationship between DNA methylation and transcription remains incompletely understood. Recently developed targeted DNA methylation manipulation tools can address these gaps in knowledge, leading to new insights into how methylation governs gene expression...
November 6, 2018: Genome Biology
Yixin Yao
No abstract text is available yet for this article.
November 6, 2018: Genome Biology
Anna Y Lee, Adam D Ewing, Kyle Ellrott, Yin Hu, Kathleen E Houlahan, J Christopher Bare, Shadrielle Melijah G Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N Yamaguchi, Michael R Kellen, Ken Chen, Thea C Norman, Stephen H Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A Margolin, Joshua M Stuart, Paul C Boutros
BACKGROUND: The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel mutagenic mechanisms. A plethora of somatic structural variant detection algorithms have been created to enable these discoveries; however, there are no systematic benchmarks of them...
November 6, 2018: Genome Biology
Jordan L Smith, Haiwei Mou, Wen Xue
Two new studies refine our understanding of CRISPR-associated exon skipping and redefine its utility in engineering alternative splicing.
November 6, 2018: Genome Biology
Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C Hayward, Yurong Tang, Gavin Huttley, Eldon E Ball, Sylvain Forêt, David J Miller
BACKGROUND: Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. RESULTS: Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp...
November 2, 2018: Genome Biology
Philipp Drewe-Boss, Hans-Hermann Wessels, Uwe Ohler
CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein - RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays...
November 1, 2018: Genome Biology
Han Chen, Haidong Shu, Liyuan Wang, Fan Zhang, Xi Li, Sylvans Ochieng Ochola, Fei Mao, Hongyu Ma, Wenwu Ye, Tingting Gu, Lubin Jiang, Yufeng Wu, Yuanchao Wang, Sophien Kamoun, Suomeng Dong
BACKGROUND: Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome architecture is associated with genome-wide DNA modifications is unknown. RESULTS: We show that the oomycetes Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome...
October 31, 2018: Genome Biology
Stella Maxouri, Stavros Taraviras, Zoi Lygerou
Histone variants constitute a fundamental feature of the epigenome. However, their dynamics during normal and challenged DNA replication and their distribution in the three-dimensional space of the nucleus remain poorly characterized. A recent study employed stochastic optical reconstruction microscopy (STORM) to obtain a high-resolution view of the spatial distribution of H3 histone variants in the nucleus and related this to the timing of DNA replication.
October 31, 2018: Genome Biology
Daniel J Nasko, Sergey Koren, Adam M Phillippy, Todd J Treangen
In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes...
October 30, 2018: Genome Biology
Emily Perry, Kristin Tessmar-Raible, Florian Raible
As part of our Q&A series, Genome Biology spoke to four scientists about their personal experiences as parents in their careers to highlight the challenges of researchers having children and the support they need in this regard. Our participants also included a couple (Kristin Tessmar-Raible and Florian Raible), as we were interested to know whether both parents being active researchers can have an impact. One of our participants wishes to remain anonymous.
October 29, 2018: Genome Biology
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