Sequencing

  • Article
    | Open Access

    Protein phosphatase1 (PP1), a signalling and transcriptional regulator, and epigenetic modulator is known to be a memory suppressor. Here the authors show that memory control by PP1 involves the microRNA cluster miR-183/96/182, and that this cluster is selectively regulated during memory formation in mice.

    • Bisrat T. Woldemichael
    • , Ali Jawaid
    •  & Isabelle M. Mansuy
  • Article
    | Open Access

    In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.

    • Dana C. Nadler
    • , Stacy-Anne Morgan
    •  & David F. Savage
  • Article
    | Open Access

    RNA editing rate detected from bulk RNA-seq data can vary widely. Here, by constructing a hierarchical Bayesian model, the authors report substantial variance in editing signatures detected by RNA-seq data from both single cells and a cognate bulk sample.

    • Dewi Harjanto
    • , Theodore Papamarkou
    •  & Anastasia Papavasiliou
  • Article
    | Open Access

    Next generation sequencing has been pivotal in identifying somatic mutations in cancer samples. In this study, the authors analyse whole exome sequencing data using a variety of bioinformatic methods to identify mutations in known cancer genes and find that many cancer genes are not detected by these methods.

    • Matan Hofree
    • , Hannah Carter
    •  & Trey Ideker
  • Article
    | Open Access

    Chromosomal aberrations can be detected by global gene expression analysis. Here, the authors report eSNP-Karyotyping, a new method that can detect chromosomal aberrations by measuring the ratio of expression between the two alleles without comparison to a matched diploid sample.

    • Uri Weissbein
    • , Maya Schachter
    •  & Nissim Benvenisty
  • Article
    | Open Access

    Short-read sequencing has inherent limitations in the characterisation of long repeat elements. Shi and Guo et al.combine single-molecule real-time sequencing and IrysChip to construct a Chinese reference genome that fills many gaps in the reference genome, and identify novel spliced genes.

    • Lingling Shi
    • , Yunfei Guo
    •  & Kai Wang
  • Article
    | Open Access

    The ability to accurately sequence long DNA molecules is important across biology. Here, Lan et al. report a droplet-based method that barcodes single DNA molecules, allowing the full-length molecules to be sequenced with multi-fold coverage using short-read next-generation sequencing.

    • Freeman Lan
    • , John R. Haliburton
    •  & Adam R. Abate
  • Article
    | Open Access

    The gut microbiome has been implicated in several autoimmune disorders. Here, the authors study the gut microbiome of patients with multiple sclerosis, and find correlations between altered abundance of certain gut microorganisms and changes in expression of immune defence genes.

    • Sushrut Jangi
    • , Roopali Gandhi
    •  & Howard L. Weiner
  • Article
    | Open Access

    Here, Libertini and colleagues devise a computation tool that can analyze whole-genome bisulfite sequencing (WGBS) data to recover of 30% of the lost differential methylation position information. They use COMETgazer and COMETvintage to analyze 13 diffferent methylome data to demonstrate their performance.

    • Emanuele Libertini
    • , Simon C. Heath
    •  & Stephan Beck
  • Article
    | Open Access

    Alternative splicing and alternative polyadenylation (APA) contribute to mRNA diversity but are difficult to assess using short read RNA-seq data. Here, the authors use single molecule long-read isoform sequencing and develop a computational pipeline to identify full-length splice isoforms and APA sites in sorghum.

    • Salah E. Abdel-Ghany
    • , Michael Hamilton
    •  & Anireddy S. N. Reddy
  • Article
    | Open Access

    Zea mays is an important crop species and genetic model but uncertainties remain regarding the structure of the transcriptome. Here Wang et al. use single-molecule sequencing and size-fractionated libraries to identify novel transcripts and isoforms illustrating the complexity of maize mRNA.

    • Bo Wang
    • , Elizabeth Tseng
    •  & Doreen Ware
  • Article
    | Open Access

    Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novogenome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation.

    • Morris Agaba
    • , Edson Ishengoma
    •  & Douglas R. Cavener
  • Article
    | Open Access

    The zinc finger transcriptional repressor Prdm1/Blimp1 is essential for remodelling maternal blood vessels in a subset of trophoblast cells. Here, the authors perform single-cell RNA-seq analysis on this Blimp1+ lineage, identifying functionally distinct cell types present at the maternal–foetal interface.

    • Andrew C. Nelson
    • , Arne W. Mould
    •  & Elizabeth J. Robertson
  • Article
    | Open Access

    The molecular dynamics associated with neuronal activation patterns in vivo are unclear. Lacar et al. perform single-nuclei RNA-sequencing of hippocampal neurons from mice exposed to a novel environment, and identify large-scale transcriptome changes in individual neurons associated with the experience.

    • Benjamin Lacar
    • , Sara B. Linker
    •  & Fred H. Gage
  • Article
    | Open Access

    DNA N6-methyladenine is prevalent in prokaryotes, and is recently also detected in eukaryotes such as roundworm and fly. Here, Luo et al. report a DpnI-assisted base resolution method that detects 6mA genome-wide with nanograms of input DNA and lower sequencing depth than the previous restriction enzyme-based approach.

    • Guan-Zheng Luo
    • , Fang Wang
    •  & Chuan He
  • Article
    | Open Access

    Read mapping and alignment tools are critical for many applications based on MinION sequencers. Here, the authors present GraphMap, a mapping algorithm designed to analyze nanopore sequencing reads, that progressively refines candidate alignments to handle potentially high error rates to align long reads.

    • Ivan Sović
    • , Mile Šikić
    •  & Niranjan Nagarajan
  • Article
    | Open Access

    With age, haematopoietic stem cells (HSCs) produce more myeloid than lymphoid cells, affecting adaptive immunity. By combining HSC single cell transcriptomics with functional studies, Grover et al. find that platelet production is also increased in old murine HSCs and show that the FOG-1 transcription factor contributes to the age-dependent platelet bias.

    • Amit Grover
    • , Alejandra Sanjuan-Pla
    •  & Claus Nerlov
  • Article
    | Open Access

    Existing single-cell RNA-seq methods provide the transcriptome of a cellular phenotype at a single time point. Here, Kimmerlinget al. present a microfluidic platform that enables off-chip single-cell RNA-seq after multigenerational lineage tracking under controlled culture conditions.

    • Robert J. Kimmerling
    • , Gregory Lee Szeto
    •  & Scott R. Manalis
  • Article
    | Open Access

    Based on whole genome resequencing of more than 80 wild and domestic yaks from high-altitude Qinghai-Tibet Plateau, this study recovers demographic and genetic processes underlying the domestication of this animal. Qiu et al.also identify genes and associated pathways as candidates for selection during the domestication process.

    • Qiang Qiu
    • , Lizhong Wang
    •  & Jianquan Liu
  • Article
    | Open Access

    The clinical application of new sequencing techniques is expected to accelerate pathogen identification. Here, Bradley et al. present a clinician-friendly software package that uses sequencing data for quick and accurate prediction of antibiotic resistance profiles for S. aureus and M. tuberculosis.

    • Phelim Bradley
    • , N. Claire Gordon
    •  & Zamin Iqbal
  • Article
    | Open Access

    Cancer genetics has benefited from the advent of next generation sequencing, yet a comparison of sequencing and analysis techniques is lacking. Here, the authors sequence a normal-tumour pair and perform data analysis at multiple institutes and highlight some of the pitfalls associated with the different methods.

    • Tyler S. Alioto
    • , Ivo Buchhalter
    •  & Ivo G. Gut
  • Article
    | Open Access

    The oncogenic events driving indolent chronic lymphocytic leukaemia are relatively unknown. Here, the authors perform whole genome sequencing on 30 such tumours and identify recurrent mutations in IGLL5and two activation induced cytidine deaminase signatures that are operative at different stages of CLL evolution.

    • S. Kasar
    • , J. Kim
    •  & J. R. Brown
  • Article
    | Open Access

    Osteosarcomas are a heterogenous group of tumours and little is known about how these tumours evolve. Here, Kovac et al. use exome sequencing and discover that although no driver gene explains the majority of these tumours, they are characterized by specific mutation signatures and genomic instability typical of BRCA1/2-deficient tumours.

    • Michal Kovac
    • , Claudia Blattmann
    •  & Daniel Baumhoer
  • Article
    | Open Access

    Date palm is a perennial fruit tree crop that thrives in arid environments of North Africa and the Middle East. Here Hazzouriet al. analyze the date palm germplasm by re-sequencing 62 different varieties and uncover selection signatures and candidate genes associated with important agronomic traits.

    • Khaled M. Hazzouri
    • , Jonathan M. Flowers
    •  & Michael D. Purugganan
  • Article
    | Open Access

    Roifman Syndrome is a rare disorder whose disease manifestations include growth retardation, spondyloepiphyseal dysplasia and immunodeficiency. Here, the authors use whole-genome sequencing to discover that rare compound heterozygous variants disrupting the small nuclear RNA gene RNU4ATACcause Roifman Syndrome.

    • Daniele Merico
    • , Maian Roifman
    •  & Stephen W. Scherer
  • Article
    | Open Access

    Single-cell RNA-sequencing (scRNA-seq) can be applied to dissect the kinetics of gene expression and patterns of allele-specific expression. Here, Kim et al.report a generative statistical model that can separate biological variability from technical noise by quantifying technical noise using external RNA spike-ins.

    • Jong Kyoung Kim
    • , Aleksandra A. Kolodziejczyk
    •  & John C. Marioni
  • Article
    | Open Access

    This paper described a new and efficient method for de novoassembly of multiple DNA sequence information from mutagenized clone libraries. Using codon-barcoded libraries and calling the method JigsawSeq, the authors overcome limitations of short-read sequencing assembly from next-generation sequencing.

    • Namjin Cho
    • , Byungjin Hwang
    •  & Duhee Bang
  • Article
    | Open Access

    Atypical adenomatous hyperplasia is thought to be a precursor lesion for lung adenocarcinoma. Here, using targeted deep sequencing, the authors demonstrate that hyperplastic lesions contain somatic mutations associated with malignant disease and that these can be detected in circulating tumour cells.

    • Evgeny Izumchenko
    • , Xiaofei Chang
    •  & David Sidransky
  • Article
    | Open Access

    Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods.

    • Jie Huang
    • , Bryan Howie
    •  & Nicole Soranzo
  • Article
    | Open Access

    Butterflies are a promising system to study the genetics and evolution of morphological diversification, yet genomic and technological resources are limited. Here, the authors sequence genomes of two Papiliobutterflies and develop a CRISPR/Cas9 gene editing method for these species.

    • Xueyan Li
    • , Dingding Fan
    •  & Wen Wang
  • Article
    | Open Access

    Immune system diversity is generated by V(D)J recombination, leading to clonal T-cell lineages. Here the authors investigate the events leading to T-cell diversity through the use of a modified PCR technique combined with deep sequencing.

    • Eliana Ruggiero
    • , Jan P. Nicolay
    •  & Christof von Kalle
  • Article
    | Open Access

    The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.

    • Masao Nagasaki
    • , Jun Yasuda
    •  & Masayuki Yamamoto
  • Article
    | Open Access

    With the rapid increase in the volume of publically available RNA-seq data, quality control is an increasingly important consideration. Here Feng et al. develop mRIN, a method to directly assess mRNA integrity, and show that RNA degradation in post-mortem samples has a strong impact on global expression profiles.

    • Huijuan Feng
    • , Xuegong Zhang
    •  & Chaolin Zhang
  • Article
    | Open Access

    Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novodetection of epigenetic heterogeneity.

    • John Beaulaurier
    • , Xue-Song Zhang
    •  & Gang Fang
  • Article
    | Open Access

    Anaplastic oligodendrogliomas are rare and incurable primary brain tumours with few treatment options. Here Labrecheet al. perform whole-exome sequencing and identify recurring mutations in transcription factor TCF12, which are associated with aggressive tumours.

    • Karim Labreche
    • , Iva Simeonova
    •  & Michel Wager
  • Article
    | Open Access

    DNA phasing information — the determination of which specific sequences belong to the same DNA molecule—is not easily obtained from sequencing applications that rely on short reads. Here the authors develop a phasing method based on massively parallel barcoding of single DNA molecules.

    • Erik Borgström
    • , David Redin
    •  & Afshin Ahmadian
  • Article
    | Open Access

    To what extent translational control can contribute to global gene expression patterns in the disease state is poorly defined. Here the authors conduct genome-wide RNA-seq and ribosome profiling in a rat model of hypertension and uncover altered translation patterns in disease associated genes.

    • Sebastian Schafer
    • , Eleonora Adami
    •  & Norbert Hubner
  • Article
    | Open Access

    Herpes simplex virus 1 (HSV-1) efficiently shuts down host gene expression in infected cells. Here Rutkowski et al. analyse the genome-wide changes in transcription and translation in infected cells, and show that HSV-1 triggers an extensive disruption of transcription termination of cellular genes.

    • Andrzej J. Rutkowski
    • , Florian Erhard
    •  & Lars Dölken
  • Article |

    Artifacts caused by whole-genome amplification bias are a recurrent challenge in single-cell sequencing analysis. Here, the authors develop statistical models and demonstrate an efficient strategy for controlling amplification errors by a joint analysis of single cell genomes.

    • Cheng-Zhong Zhang
    • , Viktor A. Adalsteinsson
    •  & J. Christopher Love