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Genome Biology

Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue, Erik J Sontheimer
BACKGROUND: Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) has been extensively used for genome editing. Currently, three Cas9 orthologs have been adapted for in vivo genome engineering applications: Streptococcus pyogenes Cas9 (SpyCas9), Staphylococcus aureus Cas9 (SauCas9), and Campylobacter jejuni (CjeCas9). However, additional in vivo editing platforms are needed, in part to enable a greater range of sequences to be accessed via viral vectors, especially those in which Cas9 and sgRNA are combined into a single vector genome...
September 19, 2018: Genome Biology
Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki, Kenta Nakai
BACKGROUND: The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. RESULTS: Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns...
September 19, 2018: Genome Biology
Xavier Grau-Bové, Iñaki Ruiz-Trillo, Manuel Irimia
BACKGROUND: Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode across non-animal eukaryotes, animals have unusually high rates of exon skipping. However, when and how this high prevalence of exon skipping evolved is unknown. Since exon skipping can greatly expand proteomes, answering these questions sheds light on the evolution of higher organismal complexity in metazoans...
September 17, 2018: Genome Biology
Chaorui Duan, Qing Huan, Xiaoshu Chen, Shaohuan Wu, Lucas B Carey, Xionglei He, Wenfeng Qian
BACKGROUND: Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis. RESULTS: Here, we use a combination of synthetic genes and sequences of thousands of isolated yeast colonies to show that intrinsic DNA curvature is a major cis determinant of mutation rate...
September 14, 2018: Genome Biology
Yungang Xu, Weiling Zhao, Scott D Olson, Karthik S Prabhakara, Xiaobo Zhou
BACKGROUND: Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. However, their intricate interrelations and joint contributions to ESC fate decision remain unclear. RESULTS: We analyze the transcriptomes and epigenomes of human ESC and five types of differentiated cells...
September 14, 2018: Genome Biology
Weronika E Borek, Adele L Marston
A meeting report on the 14th Gordon Research Conference on Meiosis, held at Colby Sawyer College, New London, NH, USA, 9-15 June 2018, chaired by Monica Colaiacovo, Harvard Medical School.
September 14, 2018: Genome Biology
Megan A Supple, Beth Shapiro
"Conservation genomics" encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, it has only recently become tractable to generate genome-wide data at a scale that is useful for conservation. In this Review, we discuss how genome-scale data can inform species delineation in the face of admixture, facilitate evolution through the identification of adaptive alleles, and enhance evolutionary rescue based on genomic patterns of inbreeding...
September 11, 2018: Genome Biology
Paul Geeleher, Aritro Nath, Fan Wang, Zhenyu Zhang, Alvaro N Barbeira, Jessica Fessler, Robert L Grossman, Cathal Seoighe, R Stephanie Huang
Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts...
September 11, 2018: Genome Biology
Marketa Tomkova, Jakub Tomek, Skirmantas Kriaucionis, Benjamin Schuster-Böckler
BACKGROUND: DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS: We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication...
September 10, 2018: Genome Biology
Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo, Zhixi Tian
BACKGROUND: In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. RESULTS: To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars...
September 10, 2018: Genome Biology
Hashem Koohy, Daniel J Bolland, Louise S Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jeremy Denizot, Raquel Manzano Garcia, Steven W Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip Hawkins, Len Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E Corcoran, Patrick D Varga-Weisz
BACKGROUND: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS: Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice...
September 5, 2018: Genome Biology
Seunghoon Baek, Kyung Choi, Goon-Bo Kim, Hee-Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kae Sun Chang, Joo-Hwan Kim, Jeong-Hwan Mun
BACKGROUND: Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. RESULTS: We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis...
September 4, 2018: Genome Biology
Sergio Barberán-Soler, Jenny M Vo, Ryan E Hogans, Anne Dallas, Brian H Johnston, Sergei A Kazakov
The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq®-AC provides greatly reduced miRNA sequencing bias and allows the identification of the largest variety of miRNAs in biological samples...
September 3, 2018: Genome Biology
K Leigh Greathouse, James R White, Ashely J Vargas, Valery V Bliskovsky, Jessica A Beck, Natalia von Muhlinen, Eric C Polley, Elise D Bowman, Mohammed A Khan, Ana I Robles, Tomer Cooks, Bríd M Ryan, Noah Padgett, Amiran H Dzutsev, Giorgio Trinchieri, Marbin A Pineda, Sven Bilke, Paul S Meltzer, Alexis N Hokenstad, Tricia M Stickrod, Marina R Walther-Antonio, Joshua P Earl, Joshua C Mell, Jaroslaw E Krol, Sergey V Balashov, Archana S Bhat, Garth D Ehrlich, Alex Valm, Clayton Deming, Sean Conlan, Julia Oh, Julie A Segre, Curtis C Harris
BACKGROUND: Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort...
August 24, 2018: Genome Biology
Lakshmipuram Seshadri Swapna, Alyssa M Molinaro, Nicole Lindsay-Mosher, Bret J Pearson, John Parkinson
BACKGROUND: In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations...
August 24, 2018: Genome Biology
Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M Luber, Scott B Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H Alver, Hanspeter Pfister, Leonid A Mirny, Peter J Park, Nils Gehlenborg
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public...
August 24, 2018: Genome Biology
Lin Li, Steven R Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Antony M Chettoor, Scott A Givan, Rex A Cole, John E Fowler, Matthew M S Evans, Michael J Scanlon, Jianming Yu, Patrick S Schnable, Marja C P Timmermans, Nathan M Springer, Gary J Muehlbauer
The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effects should have been B73, rather than Mo17, due to the original coding of biallele SNPs as "0s" and "1s". Going through the entire analysis procedure, it was determined that the mistake was made while tabulating the eQTL results from QTL Cartographer.
August 23, 2018: Genome Biology
Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S Clayton, Nigel G Laing, Daniel G MacArthur, Alicia Oshlack
Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read length and so are unable to detect the majority of pathogenic expansions. Here we present STRetch, a new genome-wide method to scan for STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting STR expansions using short-read whole-genome sequencing data at known pathogenic loci as well as novel STR loci...
August 21, 2018: Genome Biology
Razib Khan, David Mittelman
With more than 10 million genotyped customers, the consumer genomics industry is maturing and becoming a mainstream phenomenon. At last, innovations and applications, some unforeseen, are being brought to the masses.
August 20, 2018: Genome Biology
François Mallard, Viola Nolte, Ray Tobler, Martin Kapun, Christian Schlötterer
BACKGROUND: Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS: To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements reveal extensive metabolic rewiring after only approximately 60 generations in a hot environment...
August 20, 2018: Genome Biology
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