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Open Access
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The status of the human gene catalogue
Although the catalogue of human protein-coding genes is nearing completion, the number of non-coding RNA genes remains highly uncertain, and for all genes much work remains to be done to understand their functions.
- Paulo Amaral
- , Silvia Carbonell-Sala
- & Steven L. Salzberg
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Article |
A spatially resolved single-cell genomic atlas of the adult human breast
The Human Breast Cell Atlas identifies 12 major breast cell types and 58 biological cell states, revealing abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states.
- Tapsi Kumar
- , Kevin Nee
- & Nicholas Navin
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Article
| Open Access
Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) arises from clonal (premalignant) haematopoietic precursors in the bone marrow, and BPDCN skin tumours first develop at sun-exposed anatomical sites and are distinguished by clonally expanded mutations induced by ultraviolet radiation.
- Gabriel K. Griffin
- , Christopher A. G. Booth
- & Andrew A. Lane
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Article
| Open Access
Spatial epigenome–transcriptome co-profiling of mammalian tissues
The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.
- Di Zhang
- , Yanxiang Deng
- & Rong Fan
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Perspective |
The Human Pangenome Project: a global resource to map genomic diversity
The Human Pangenome Reference Consortium aims to offer the highest quality and most complete human pangenome reference that provides diverse genomic representation across human populations.
- Ting Wang
- , Lucinda Antonacci-Fulton
- & David Haussler
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Article |
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques for analysis of complex cellular phenotypes.
- Tongtong Zhao
- , Zachary D. Chiang
- & Fei Chen
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Article
| Open Access
A chickpea genetic variation map based on the sequencing of 3,366 genomes
Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.
- Rajeev K. Varshney
- , Manish Roorkiwal
- & Xin Liu
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Article |
Single-cell Ribo-seq reveals cell cycle-dependent translational pausing
Highly sensitive ribosome profiling of single cells at single-codon resolution enables identification of distinct cell cycle-dependent translational dynamic states in individual cells.
- Michael VanInsberghe
- , Jeroen van den Berg
- & Alexander van Oudenaarden
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Article |
Spo11 generates gaps through concerted cuts at sites of topological stress
Meiotic recombination in yeast is not only initiated by single break sites, but also caused by closely spaced Spo11-dependent double-stranded DNA breaks that create chromosomal gaps.
- Silvia Prieler
- , Doris Chen
- & Franz Klein
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Article |
Neuronal diversity and convergence in a visual system developmental atlas
The neuronal diversity of the Drosophila optic lobe is described throughout pupal development by single-cell sequencing, leading to the discovery of transient extrinsic neurons and a dorsoventral asymmetry of the visual circuits.
- Mehmet Neset Özel
- , Félix Simon
- & Claude Desplan
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Article |
Conformation of sister chromatids in the replicated human genome
Modified chromosome conformation capture (Hi-C) technology is used to characterize the interactions between sister chromatids, despite their identical DNA sequences.
- Michael Mitter
- , Catherina Gasser
- & Daniel W. Gerlich
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Article
| Open Access
Landscape of cohesin-mediated chromatin loops in the human genome
A map of cohesin-mediated chromatin loops in 24 types of human cells identifies loops that show cell-type-specific variation, indicating that chromatin loops may help to specify cell-specific gene expression programs and functions.
- Fabian Grubert
- , Rohith Srivas
- & Michael Snyder
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Article |
Resolving the fibrotic niche of human liver cirrhosis at single-cell level
Single-cell RNA sequencing is used to characterize and compare the functional diversity of cells from liver biopsies of human scarred and normal liver, and identifies markers for scar-associated macrophages and endothelial cells.
- P. Ramachandran
- , R. Dobie
- & N. C. Henderson
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Letter |
Tracking tumour evolution in glioma through liquid biopsies of cerebrospinal fluid
Identification and sequencing of circulating tumour DNA in the cerebrospinal fluid of patients with glioma.
- Alexandra M. Miller
- , Ronak H. Shah
- & Ingo K. Mellinghoff
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Article |
Somatic APP gene recombination in Alzheimer’s disease and normal neurons
The gene for the amyloid precursor protein (APP) shows somatic gene recombination in neurons, and the abundance and diversity of APP variants is increased in neurons from individuals with Alzheimer’s disease.
- Ming-Hsiang Lee
- , Benjamin Siddoway
- & Jerold Chun
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Letter |
The cis-regulatory dynamics of embryonic development at single-cell resolution
An improved assay for chromatin accessibility at single-cell resolution in Drosophila melanogaster embryos enables identification of developmental-stage- and cell-lineage-specific patterns of chromatin-level transcriptional regulation.
- Darren A. Cusanovich
- , James P. Reddington
- & Eileen E. M. Furlong
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Article
| Open Access
The axolotl genome and the evolution of key tissue formation regulators
Sequencing and assembly of the 32-Gb genome of the Mexican axolotl reveals that it lacks the developmental gene Pax3, which is essential in other vertebrates; the genome sequence could improve our understanding of the evolution of the axolotl’s remarkable regenerative capabilities.
- Sergej Nowoshilow
- , Siegfried Schloissnig
- & Eugene W. Myers
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Letter |
Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing
Lipolysis declines with age because NLRP3 inflammasome-activated adipose tissue macrophages reduce levels of noradrenaline by upregulating genes that control its degradation, such as GDF3 and MAOA.
- Christina D. Camell
- , Jil Sander
- & Vishwa Deep Dixit
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Letter |
Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites
Highly parallel single-cell transcriptome profiling of Plasmodium falciparum blood stages provides insight into the role AP2-G plays in early sexual development of this eukaryotic pathogen.
- Asaf Poran
- , Christopher Nötzel
- & Björn F. C. Kafsack
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Outlook |
Genetics: Clues in the code
Gene exploration is providing unexpected insights into inflammatory bowel disease, and getting scientists closer to finding treatments that target the biological mechanisms.
- Sarah DeWeerdt
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Letter |
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
The transcriptome changes driving the conversion of fibroblasts to neurons at the single-cell level are reported, revealing that early neuronal reprogramming steps are homogenous, driven by the proneural pioneer factor Ascl1; the expression of myogenic genes then has a dampening effect on efficiency, which needs to be counteracted by the neuronal factors Myt1l and Brn2 for more efficient reprogramming.
- Barbara Treutlein
- , Qian Yi Lee
- & Stephen R. Quake
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Article |
Synchronized mitochondrial and cytosolic translation programs
The genes encoding the subunits of oxidative phosphorylation complexes are split between the nuclear and mitochondrial genomes, but their translation is synchronized by signalling from the cytosol to the mitochondria.
- Mary T. Couvillion
- , Iliana C. Soto
- & L. Stirling Churchman
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Article |
Active medulloblastoma enhancers reveal subgroup-specific cellular origins
Genomic studies of the paediatric brain tumour medulloblastoma have revealed four clinically distinct molecular subgroups; here active gene regulatory elements in 28 primary medulloblastoma tissues are mapped to reveal differentially regulated enhancers across the different subgroups, allowing insights into the transcription factors that characterize subgroup divergence and the cellular origin of the poorly characterized Group 3 and 4 subgroups.
- Charles Y. Lin
- , Serap Erkek
- & Paul A. Northcott
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Letter |
Single-cell chromatin accessibility reveals principles of regulatory variation
A single-cell method for probing genome-wide chromatin accessibility has been developed; the results provide insight into the relationship between cell-to-cell variation associated with specific trans-factors and cis-elements, as well insights into the relationship between chromatin accessibility and three-dimensional genome organization.
- Jason D. Buenrostro
- , Beijing Wu
- & William J. Greenleaf
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Brief Communications Arising |
Universality of core promoter elements?
- Matthias Siebert
- & Johannes Söding
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Outlook |
Comparative biology: Naked ambition
A subterranean species that seems to be cancer-proof is providing promising clues on how we might prevent the disease in humans.
- Sarah Deweerdt
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Letter |
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.
- Alex K. Shalek
- , Rahul Satija
- & Aviv Regev
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Article |
A metagenome-wide association study of gut microbiota in type 2 diabetes
The authors have developed a new method, metagenome-wide association study (MGWAS), to compare the combined genetic content of the faecal microbiota of healthy people versus patients with type 2 diabetes; they identify multiple microbial species and metabolic pathways that are associated with either cohort and show that some of these may be used as biomarkers.
- Junjie Qin
- , Yingrui Li
- & Jun Wang
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Article |
Genomic analysis of a key innovation in an experimental Escherichia coli population
By combining full-genome sequencing and ‘evolutionary replay’ experiments to dissect the origin of aerobic citrate use in an experimental Escherichia coli population over 40,000 generations and 2 decades, the authors unveil a 3-step process in which potentiation makes a trait possible, actualization makes the trait manifest and refinement makes it effective.
- Zachary D. Blount
- , Jeffrey E. Barrick
- & Richard E. Lenski
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Letter
| Open Access
Dissecting the genomic complexity underlying medulloblastoma
Medulloblastoma is the most common brain tumour in children; using whole-genome sequencing of tumour samples the authors show that the clinically challenging Group 3 and 4 tumours can be tetraploid, and reveal the expression of the first medulloblastoma fusion genes identified.
- David T. W. Jones
- , Natalie Jäger
- & Peter Lichter
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Research Highlights |
Tracking Taz's transmissible cancer
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News & Views |
Transcription initiation unwrapped
A genome-wide, high-resolution study of DNA-binding sites for proteins that transcribe DNA into RNA reveals details about how this process occurs in vivo. See Article p.295
- Stephen Buratowski
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Outlook |
Perspective: A model disease
Despite its rarity, multiple myeloma is an ideal testing ground for cancer biology, says William Matsui.
- William Matsui
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Letter |
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk
- Georg B. Ehret
- , Patricia B. Munroe
- & Toby Johnson
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Letter
| Open Access
The genome of the green anole lizard and a comparative analysis with birds and mammals
- Jessica Alföldi
- , Federica Di Palma
- & Kerstin Lindblad-Toh
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Research Highlights |
A map of gene copy numbers
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Letter |
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
- Stephen Sawcer
- , Garrett Hellenthal
- & Alastair Compston
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News |
Gene pool offers way to save Mexican oasis
Commercializing genetic wealth will test biodiversity treaty.
- Nicola Jones
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Article
| Open Access
Genome sequence and analysis of the tuber crop potato
- Xun Xu
- , Shengkai Pan
- & Richard G. F. Visser
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Article |
Genomic island variability facilitates Prochlorococcus–virus coexistence
- Sarit Avrani
- , Omri Wurtzel
- & Debbie Lindell
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Letter |
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
- William A. Pastor
- , Utz J. Pape
- & Anjana Rao
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News |
Out of southern Africa
A genetic study challenges the idea that modern humans evolved in eastern Africa.
- Matt Kaplan
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News |
Water flea genome offers revolution in toxicity testing
DNA sequence of Daphnia could help scientists to probe the environment and test chemicals.
- Virginia Gewin
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Technology Feature |
Seeing more SNPs
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Technology Feature |
The search for association
The list of human genetic variations is expanding; but an understanding of how they contribute to disease is still patchy.
- Monya Baker
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Article
| Open Access
A map of human genome variation from population-scale sequencing
The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.
- Richard M. Durbin
- , David Altshuler (Co-Chair)
- & Gil A. McVean
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News |
Poisonous platypuses confirm convergent evolution
Genome analysis shows that the monotremes and snakes have similar venoms.
- Ewen Callaway
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News & Views |
Variations in blood lipids
What is the new gold standard for genome-wide association studies? As exemplified by analyses of blood lipids, it is collaboration to amass huge sample sizes and functional studies of the genes identified.
- Alan R. Shuldiner
- & Toni I. Pollin
Deciphering cell states and genealogies of human haematopoiesis
Integrated genomic analyses of ovarian carcinoma