Sequencing

  • Article
    | Open Access

    Aging skeletal muscle shows declining numbers and activity of satellite cells. Here, Franco et al. show that in satellite cells of the human leg muscle vastus lateralis, somatic mutations accumulate with age and that these mutations become enriched in exons and promoters of genes involved in muscle function.

    • Irene Franco
    • , Anna Johansson
    •  & Maria Eriksson
  • Article
    | Open Access

    Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

    • Todd P. Michael
    • , Florian Jupe
    •  & Joseph R. Ecker
  • Article
    | Open Access

    Influenza A virus packaging depends on interactions between nucleoprotein (NP) and viral RNA (vRNA), but the pattern of NP binding is unclear. Using PAR-CLIP, Williams et al. here show that NP binds vRNA non-uniformly and that RNA structures in low-NP binding regions are important for packaging.

    • Graham D. Williams
    • , Dana Townsend
    •  & Adrianus C. M. Boon
  • Article
    | Open Access

    A large number of RNA binding proteins (RBPs) and miRNAs bind to the 3′ untranslated regions of mRNA, but methods to dissect their function and interactions are lacking. Here the authors introduce post-transcriptional regulatory element sequencing (PTRE-seq) to dissect sequence preferences, interactions and consequences of RBP and miRNA binding.

    • Kyle A. Cottrell
    • , Hemangi G. Chaudhari
    •  & Sergej Djuranovic
  • Article
    | Open Access

    Selaginella lepidophylla is a clubmoss with extreme desiccation tolerance. Here, the authors assemble its highly heterozygotic haplotypes and examine gene expression changes during desiccation, which shed light on the mechanisms for maintaining a small genome size and adaptation to extreme drying.

    • Robert VanBuren
    • , Ching Man Wai
    •  & Todd P. Michael
  • Article
    | Open Access

    Regeneration capable flatworms have emerged as powerful models for studying stem cell biology and patterning, however their study has been hindered by the lack of transgenesis methods. Here, the authors describe a transgenesis method for Macrostomum lignano, as well as a new annotated genome sequence.

    • Jakub Wudarski
    • , Daniil Simanov
    •  & Eugene Berezikov
  • Article
    | Open Access

    Crassulacean acid metabolism (CAM) is a metabolic adaptation of photosynthesis that enhances water use efficiency. Here, via genomic analysis of Kalanchoë, the authors provide evidence for convergent evolution of protein sequence and temporal gene expression underpinning the multiple independent emergences of CAM.

    • Xiaohan Yang
    • , Rongbin Hu
    •  & Gerald A. Tuskan
  • Article
    | Open Access

    Bivalve molluscs have evolved various characteristics to adapt to benthic filter-feeding. Here, Li et al investigate the genome, transcriptomes and proteomes of scallop Chlamys farreri, revealing evidences of molecular adaptations to semi-sessile life and neurotoxins.

    • Yuli Li
    • , Xiaoqing Sun
    •  & Zhenmin Bao
  • Article
    | Open Access

    Mutations in potassium and calcium channel genes have been associated with cardiac arrhythmias. Here, Jensen et al. show that an anion transporter chloride-bicarbonate exchanger AE3 is also responsible for the genetically-induced mechanism of cardiac arrhythmia, suggesting new therapeutic targets for this disease

    • Kasper Thorsen
    • , Vibeke S. Dam
    •  & Henrik K. Jensen
  • Article
    | Open Access

    High-throughput sequencing is used to identify somatic variants in cancer patients. Here, the authors perform panel-based profiling of 5095 clinical samples and demonstrate that many clinically-actionable variants have low variant allele fractions, requiring assays with high detection sensitivity.

    • Hyun-Tae Shin
    • , Yoon-La Choi
    •  & Woong-Yang Park
  • Article
    | Open Access

    Wing pattern mimicry in the butterfly Papilio polytes is controlled by a single Mendelian locus, the mimicry supergene doublesex. Here, Zhang and colleagues reconstruct the complex evolutionary history of the doublesex supergene and mimicry in the Papilio polytes species group.

    • Wei Zhang
    • , Erica Westerman
    •  & Marcus R. Kronforst
  • Article
    | Open Access

    The detection of structural variants can be difficult with short-read sequencing technology, especially when variants are highly complex. Here, the authors use a MinION nanopore sequencer to analyse two patient genomes and develop NanoSV to map known and novel structural variants in long read data.

    • Mircea Cretu Stancu
    • , Markus J. van Roosmalen
    •  & Wigard P. Kloosterman
  • Article
    | Open Access

    Haplotype information is important in investigating many biological phenomena. Here, Porubsky et al. combine Strand-seq with long-read or linked-read sequencing to obtain complete and genome-wide haplotypes of a single individual genome at manageable costs.

    • David Porubsky
    • , Shilpa Garg
    •  & Tobias Marschall
  • Article
    | Open Access

    While circulating DNA has been extensively explored as a potential cancer biomarker, RNA potential has been overlooked so far. Here the authors present a comprehensive analysis of extracellular RNA secreted by glioblastoma cells that could prove a valuable resource for biomarker discovery and a means of intercellular communication.

    • Zhiyun Wei
    • , Arsen O. Batagov
    •  & Anna M. Krichevsky
  • Article
    | Open Access

    Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.

    • Matteo D′Antonio
    • , Donate Weghorn
    •  & Kelly A Frazer
  • Article
    | Open Access

    While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

    • Sahar Gelfman
    • , Quanli Wang
    •  & David B. Goldstein
  • Article
    | Open Access

    Single cell RNA sequencing is a powerful tool for understanding cellular diversity but is limited by cost, throughput and sample preparation. Here the authors use nanogrid technology with integrated imaging to sequence thousands of cancer nuclei in parallel from fresh or frozen tissue.

    • Ruli Gao
    • , Charissa Kim
    •  & Nicholas Navin
  • Article
    | Open Access

    Viruses play an important role in microbial communities but, due to limitations of available techniques, our understanding of viral diversity is limited. Here, the authors use SVGs and identify highly abundant viruses in marine communities that have been previously overlooked.

    • Francisco Martinez-Hernandez
    • , Oscar Fornas
    •  & Manuel Martinez-Garcia
  • Article
    | Open Access

    In single-cell RNA sequencing data of heterogeneous cell populations, cell cycle stage of individual cells would often be informative. Here, the authors introduce a computational model to reconstruct a pseudo-time series from single cell transcriptome data, identify the cell cycle stages, identify candidate cell cycle-regulated genes and recover the methylome changes during the cell cycle.

    • Zehua Liu
    • , Huazhe Lou
    •  & Ting Chen
  • Article
    | Open Access

    Genome sequencing alone fails to provide a genetic diagnosis for many Mendelian disorder patients. Here, the authors utilize RNA sequencing to complement genotyping of patients with a rare mitochondrial disease by detecting aberrant RNA expression, splicing and allele-specific expression.

    • Laura S. Kremer
    • , Daniel M. Bader
    •  & Holger Prokisch
  • Article
    | Open Access

    Human T-cell leukaemia virus type-1 and bovine leukaemia virus infect T and B lymphocytes and lead to aggressive leukaemia. Here, the authors show these proviruses integrate near cancer drivers perturbing transcription termination or antisense RNA-dependent interaction, suggesting post-transcriptional mechanisms in some cases.

    • Nicolas Rosewick
    • , Keith Durkin
    •  & Anne Van den Broeke
  • Article
    | Open Access

    Detection ofde novo, low frequency mutations is important for characterising heterogeneous cell populations, such as those found in cancer cell populations. Here the authors present o2n-seq, an ultrasensitive method with highly efficient data usage for detection of rare mutations.

    • Kaile Wang
    • , Shujuan Lai
    •  & Jue Ruan
  • Article
    | Open Access

    Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.

    • Coen M. Adema
    • , LaDeana W. Hillier
    •  & Richard K. Wilson
  • Article
    | Open Access

    High-quality reference genomes facilitate analysis of genome structure and variation. Here Duet al. create a near-complete assembly of the indicarice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.

    • Huilong Du
    • , Ying Yu
    •  & Chengzhi Liang
  • Article
    | Open Access

    Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors usein vitroproximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.

    • Sebastian Reyes-Chin-Wo
    • , Zhiwen Wang
    •  & Richard W. Michelmore
  • Article
    | Open Access

    Techniques for structural characterization and quantification of DNA origami are still poorly developed, despite advances in other aspects of DNA nanotechnology. Here, the authors combine barcoding and next generation sequencing to simultaneously image and quantify self-assembled DNA nanostructures.

    • Cameron Myhrvold
    • , Michael Baym
    •  & Peng Yin
  • Article
    | Open Access

    Alternative splicing of mRNAs occurs in tissue specific manners and may be modulated by genetic variations. Here, Takata and colleagues perform splicing quantitative trait loci analysis (sQTL) of human brain and show significant enrichment of sQTLs among neurological disease-associated loci.

    • Atsushi Takata
    • , Naomichi Matsumoto
    •  & Tadafumi Kato
  • Article
    | Open Access

    Shotgun DNA sequencing experiments for microbial genomic analysis are often impractical due to minimum sample input requirements. Here the authors develop a microfluidic sample preparation platform that reduces sample input requirements 100-fold and enables high throughput sequencing from low numbers of cells.

    • Soohong Kim
    • , Joachim De Jonghe
    •  & Paul C. Blainey
  • Article
    | Open Access

    On-site diagnostics technologies allow for rapid, cost-effective diagnosis with a particular importance for remote communities. Here the authors demonstrate the use of mobile phone based microscopy for targeted DNA sequencing andin situpoint mutation detection in tumours.

    • Malte Kühnemund
    • , Qingshan Wei
    •  & Mats Nilsson
  • Article
    | Open Access

    Knockout collections provide a valuable tool to explore gene function, yet are expensive and technically challenging to produce at a genome-wide scale. Here Baym et al. devise a cost-effective transposon-based method to quickly develop a knockout collection for the electroactive microbe Shewanella oneidensis.

    • Michael Baym
    • , Lev Shaket
    •  & Buz Barstow
  • Article
    | Open Access

    Recurrent sporadic mutations are important risk factors for autism spectrum disorders (ASDs) but have been primarily investigated in European cohorts. Here, Eichler, Xia and colleagues analyse risk genes in a large Chinese ASD cohort and find novel recurrences of potential pathogenic significance.

    • Tianyun Wang
    • , Hui Guo
    •  & Evan E. Eichler
  • Article
    | Open Access

    Currently available single-cell transcriptomic analyses are expensive and low throughput. Here, Vickovicet al. describe a new method called MASC-seq that is based on microarray barcoding of expression pattern and of low cost with high robustness.

    • Sanja Vickovic
    • , Patrik L. Ståhl
    •  & Joakim Lundeberg
  • Article
    | Open Access

    The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) aims to better understand population genetics of the African diaspora. Here, it uses deeply sequenced whole-genomes to describe the impact of admixture and potential disease burden of deleterious variants.

    • Rasika Ann Mathias
    • , Margaret A. Taub
    •  & Kathleen C. Barnes