Genetics articles within Nature Communications

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  • Article
    | Open Access

    A proportion of neurodevelopmental disorder and congenital anomaly cases remain without a genetic diagnosis. Here, the authors study aberrations of DNA methylation in such cases and find that epivariations might provide an explanation for some of these undiagnosed patients.

    • Mafalda Barbosa
    • , Ricky S. Joshi
    •  & Andrew J. Sharp

  • Article
    | Open Access

    The distinct genomic and epidemiological features of Chinese lung cancer patients suggest the presence of alternative causal mechanisms. Here, the authors present the genomic landscape of 149 Chinese NSCLC patients and reveal distinct mutational signatures associated with inflammatory microenvironments.

    • Cheng Wang
    • , Rong Yin
    •  & Hongbing Shen

  • Article
    | Open Access

    Historical acute promyelocytic leukemia patients treated with retinoic acid and chemotherapy sometimes did relapse. Here the authors performed exome sequencing on 64 patient's samples from diagnosis/relapse/remission and show relapse associates either with cooperating oncogenes at diagnosis, or with unexpected persistence of ancestral pre-leukemic clones.

    • Jacqueline Lehmann-Che
    • , Cécile Bally
    •  & Hugues de Thé

  • Article
    | Open Access

    The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.

    • Zhouqing Luo
    • , Lihui Wang
    •  & Junbiao Dai

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Article
    | Open Access

    Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.

    • Rebecca E. O’Connor
    • , Michael N. Romanov
    •  & Darren K. Griffin

  • Article
    | Open Access

    Supergenes result from beneficial linkage and recombination suppression between two or more genes. Giraud and colleagues use whole genome sequencing data to show convergent evolution of supergenes on mating-type chromosomes in multiple closely-related fungal lineages.

    • Sara Branco
    • , Fantin Carpentier
    •  & Tatiana Giraud

  • Article
    | Open Access

    Nephrotic syndrome is the second most common chronic kidney disease but there are no targeted treatment strategies available. Here the authors identify mutations of six genes codifying for proteins involved in cytoskeleton remodelling and modulation of small GTPases in 17 families with nephrotic syndrome.

    • Shazia Ashraf
    • , Hiroki Kudo
    •  & Friedhelm Hildebrandt

  • Article
    | Open Access

    Pancreatic ductal adenocarcinoma (PDAC) is a complex disease and its underlying epigenomic heterogeneity is not fully understood. Here, the authors utilize patient-derived PDAC xenografts to define the epigenomic landscape of PDAC, highlighting chromatin states linked to differing disease aggressiveness and survival.

    • Gwen Lomberk
    • , Yuna Blum
    •  & Raul Urrutia

  • Article
    | Open Access

    The timing of female reproductive capacity is influenced by genetic and environmental factors. Here, in genome-wide association studies, the authors identify genetic loci for age at menarche and onset of menopause in Japanese women, and highlight differences with European populations.

    • Momoko Horikoshi
    • , Felix R. Day
    •  & John. R. B. Perry

  • Article
    | Open Access

    Efficient gene targeting in higher plants remains challenging. Here, the authors develop a sequential transformation method for CRISPR/Cas9-mediated gene targeting in Arabidopsis and demonstrate its functionality at five genomic sites in two endogenous loci.

    • Daisuke Miki
    • , Wenxin Zhang
    •  & Jian-Kang Zhu

  • Article
    | Open Access

    Genome-wide association studies have identified multiple loci for resting heart rate (HR) but the genetic factors associated with HR increase during and HR recovery after exercise are less well studied. Here, the authors examine both traits in a two-stage GWAS design in up to 67,257 individuals from UK Biobank.

    • Julia Ramírez
    • , Stefan van Duijvenboden
    •  & Patricia B. Munroe

  • Article
    | Open Access

    Neuromyelitis optica (NMO) is a rare autoimmune condition characterized by inflammation and demyelination of the optic nerve and the spinal cord. Here, Estrada et al. identify NMO susceptibility variants in the MHC region and find that autoantibody-positive NMO genetically overlaps with lupus.

    • Karol Estrada
    • , Christopher W. Whelan
    •  & Daniel G. MacArthur

  • Article
    | Open Access

    CRISPR interference (CRISPRi) is a method for targeted silencing of transcription that requires the coexpression of protein dCas9 and a customized guide RNA. Here, Cui et al. show that certain guide RNAs induce toxicity in E. coli, and provide design rules to minimize off-target effects.

    • Lun Cui
    • , Antoine Vigouroux
    •  & David Bikard

  • Article
    | Open Access

    Fibroblast-like synoviocytes (FLS) in the intimal layer of the synovium can become invasive and destroy cartilage in patients with rheumatoid arthritis (RA). Here the authors integrate a variety of epigenomic data to map the epigenome of FLS in RA and identify potential therapeutic targets.

    • Rizi Ai
    • , Teresina Laragione
    •  & Gary S. Firestein

  • Article
    | Open Access

    The development of malaria parasites is controlled by coordinated changes in gene expression. Here, the authors show that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycles of Plasmodium falciparum and Plasmodium vivax parasites.

    • Evelien M. Bunnik
    • , Kate B. Cook
    •  & Karine G. Le Roch

  • Article
    | Open Access

    Polycomb-group proteins are key regulators of transcriptional programs that maintain cell identity. Here the authors provide evidence that PCGF5, a subunit of Polycomb Repressor Complex 1, is important for the differentiation of mouse embryonic stem cells towards a neural cell fate.

    • Mingze Yao
    • , Xueke Zhou
    •  & Hongjie Yao

  • Article
    | Open Access

    DNA methylation is known to contribute to B cell differentiation, but de novo methylation has not been studied in this context. Here the authors use a conditional Dnmt3a/b knockout mouse to map the function of de novo DNA methylation in B cell differentiation and the development of humoral immunity.

    • Benjamin G. Barwick
    • , Christopher D. Scharer
    •  & Jeremy M. Boss

  • Article
    | Open Access

    The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.

    • Tadeusz Krassowski
    • , Aisling Y. Coughlan
    •  & Kenneth H. Wolfe

  • Article
    | Open Access

    Reduced central corneal thickness (CCT) is observed in common eye diseases as well as in rare Mendelian disorders. Here, in a cross-ancestry GWAS, the authors identify 19 novel genetic loci associated with CCT, a subset of which is involved in rare corneal or connective tissue disorders.

    • Adriana I. Iglesias
    • , Aniket Mishra
    •  & Stuart MacGregor

  • Article
    | Open Access

    Human complex traits and disorders often show differentiation among populations. Here, the authors analyze SNPs associated with 10 complex traits using data of large sample size from African, East Asian and European populations, and find significant genetic differentiation among global populations shaped by natural selection.

    • Jing Guo
    • , Yang Wu
    •  & Jian Yang

  • Article
    | Open Access

    In mammalian female germ cells, parent-specific epigenetic marks are erased and the X chromosome reactivated before entry into meiosis. Here, by combining parental haplotype reconstruction with single-cell transcriptomics of human female embryonic germ cells, the authors demonstrate that epigenetic reprogramming occurs in a heterogeneous fashion and during a broad time window up to week 14.

    • Ábel Vértesy
    • , Wibowo Arindrarto
    •  & Susana M. Chuva de Sousa Lopes

  • Article
    | Open Access

    The mechanisms of PARP inhibitor (PARPi) resistance are poorly understood. Here the authors employ a CRISPR mutagenesis approach to identify PARP1 mutants causing PARPi resistance and find that PARP1 mutations are tolerated in BRCA1 mutated cells, suggesting alternative resistance mechanisms.

    • Stephen J. Pettitt
    • , Dragomir B. Krastev
    •  & Christopher J. Lord

  • Article
    | Open Access

    Adenomyoepithelioma is a rare tumor of the breast with an unknown genetic basis. Here the authors perform a genomic analysis of adenomyoepitheliomas revealing that their repertoire of somatic mutations vary according to the estrogen receptor (ER) status, and that ER-negative tumors harbor recurrent mutations in HRAS and PI3K pathway genes.

    • Felipe C. Geyer
    • , Anqi Li
    •  & Jorge S. Reis-Filho

  • Article
    | Open Access

    Phenotypic variation and diseases are influenced by factors such as genetic variants and gene expression. Here, Barbeira et al. develop S-PrediXcan to compute PrediXcan results using summary data, and investigate the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes.

    • Alvaro N. Barbeira
    • , Scott P. Dickinson
    •  & Hae Kyung Im

  • Article
    | Open Access

    Myopic maculopathy is a complication of myopia that often progresses to blindness. Here, in a genome-wide association study, Hosoda et al. find that rs11873439 intronic to CCDC102B is associated with myopic maculopathy, but not with myopia, thus representing a risk factor independent of myopia.

    • Yoshikatsu Hosoda
    • , Munemitsu Yoshikawa
    •  & Kenji Yamashiro

  • Article
    | Open Access

    In acute leukemia with KMT2A rearrangements (KMT2A-R), activating signaling mutations are common. Here, the authors use a retroviral acute myeloid mouse leukemia model to show that subclonal de novo activating mutations drive clonal evolution in acute leukemia with KMT2A-R and enhance clonal fitness.

    • Axel Hyrenius-Wittsten
    • , Mattias Pilheden
    •  & Anna K. Hagström-Andersson

  • Article
    | Open Access

    Leprosy, caused by infection with Mycobacterium leprae, was common in Europe in the Middle Ages. Here, Krause-Kyora et al. analyze ancient DNA from a medieval Danish leprosarium to assemble 10 complete bacterial genomes and perform association analysis of the DRB1*15:01 allele with risk of leprosy infection.

    • Ben Krause-Kyora
    • , Marcel Nutsua
    •  & Almut Nebel

  • Article
    | Open Access

    As cells evolve towards malignancy, somatic mutations arise from defects in DNA damage and repair processes which are each associated with individual mutation signatures. Here the authors show it is possible to recreate cancer mutational signatures in vitro using gene editing experiments in an isogenic human-cell system.

    • Xueqing Zou
    • , Michel Owusu
    •  & Serena Nik-Zainal

  • Article
    | Open Access

    Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.

    • Jordi Paps
    •  & Peter W. H. Holland

  • Article
    | Open Access

    Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) enables characterization of a patient’s cancer. Here, the authors analyse CTCs, cfDNA, and tumor biopsies from multiple myeloma patients to show these approaches are complementary for mutation detection, together enabling a greater fraction of patient tumors to be profiled.

    • S. Manier
    • , J. Park
    •  & I. M. Ghobrial

  • Article
    | Open Access

    Hutchinson-Gilford Progeria Syndrome is characterized by premature aging with cardiovascular disease being the main cause of death. Here the authors show that inhibition of the NAT10 enzyme enhances cardiac function and fitness, and reduces age-related phenotypes in a mouse model of premature aging.

    • Gabriel Balmus
    • , Delphine Larrieu
    •  & Stephen P. Jackson

  • Article
    | Open Access

    Previous studies suggest that DNA methylation is the main mechanism to silence endogenous retroviruses (ERVs) in somatic cells. Here the authors provide evidence that distinctive sets of ERVs are silenced by Setdb1 in different types of somatic cells, suggesting a general function in ERV silencing.

    • Masaki Kato
    • , Keiko Takemoto
    •  & Yoichi Shinkai

  • Article
    | Open Access

    Mei (Prunus mume) is a woody tree that produces ornamental blossoms which symbolize spring in East Asia. Here, Zhang et al. resequence wild and domesticated mei to reveal considerable admixture and introgression from other Prunus species and identify loci associated with floral traits.

    • Qixiang Zhang
    • , He Zhang
    •  & Tangren Cheng

  • Article
    | Open Access

    ELL2 was recently discovered as a susceptibility gene for multiple myeloma (MM). Here, they show that the MM risk allele lowers ELL2 expression in plasma cells, that it also upregulates gene sets related to ribosome biogenesis, and that one of the linked variants reduces binding of MAFF/G/K family transcription factors.

    • Mina Ali
    • , Ram Ajore
    •  & Björn Nilsson

  • Article
    | Open Access

    Many SNPs associated with inflammatory bowel disease are located in non-coding genomic regions. Here, the authors perform CAGE-sequencing on descending colon biopsies of Crohn’s disease and ulcerative colitis patients to map transcription start sites and enhancer activity for analysis of regulatory regions.

    • Mette Boyd
    • , Malte Thodberg
    •  & Albin Sandelin

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