Repository logo

Scholarly Works - Genetics


Recent Submissions

Now showing 1 - 20 of 194
  • ItemOpen AccessPublished version Peer-reviewed
    Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.
    (Springer Science and Business Media LLC, 2017-06-23) Xue, Yali; Mezzavilla, Massimo; Haber, Marc; McCarthy, Shane; Chen, Yuan; Narasimhan, Vagheesh; Gilly, Arthur; Ayub, Qasim; Colonna, Vincenza; Southam, Lorraine; Finan, Christopher; Massaia, Andrea; Chheda, Himanshu; Palta, Priit; Ritchie, Graham; Asimit, Jennifer; Dedoussis, George; Gasparini, Paolo; Palotie, Aarno; Ripatti, Samuli; Soranzo, Nicole; Toniolo, Daniela; Wilson, James F; Durbin, Richard; Tyler-Smith, Chris; Zeggini, Eleftheria; Haber, Marc [0000-0003-1000-1448]; McCarthy, Shane [0000-0002-2715-4187]; Narasimhan, Vagheesh [0000-0001-8651-8844]; Ayub, Qasim [0000-0003-3291-0917]; Southam, Lorraine [0000-0002-7546-9650]; Palta, Priit [0000-0001-9320-7008]; Soranzo, Nicole [0000-0003-1095-3852]; Wilson, James F [0000-0001-5751-9178]; Durbin, Richard [0000-0002-9130-1006]; Zeggini, Eleftheria [0000-0003-4238-659X]
    The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully. We demonstrate relaxation of purifying selection in the isolates, leading to enrichment of rare and low-frequency functional variants, using novel statistics, DVxy and SVxy. We also develop an isolation-index (Isx) that predicts the overall level of such key genetic characteristics and can thus help guide population choice in future complex-trait association studies.
  • ItemOpen AccessPublished version Peer-reviewed
    Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.
    (Springer Science and Business Media LLC, 2016-12-22) Aranda, M; Li, Y; Liew, YJ; Baumgarten, S; Simakov, O; Wilson, MC; Piel, J; Ashoor, H; Bougouffa, S; Bajic, VB; Ryu, T; Ravasi, T; Bayer, T; Micklem, G; Kim, H; Bhak, J; LaJeunesse, TC; Voolstra, CR; Micklem, Gos [0000-0002-6883-6168]
    Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium.
  • ItemOpen AccessPublished version Peer-reviewed
    The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
    (Oxford University Press (OUP), 2011) Washington, Nicole L; Stinson, EO; Perry, Marc D; Ruzanov, Peter; Contrino, Sergio; Smith, Richard; Zha, Zheng; Lyne, Rachel; Carr, Adrian; Lloyd, Paul; Kephart, Ellen; McKay, Sheldon J; Micklem, Gos; Stein, Lincoln D; Lewis, Suzanna E; Lyne, Rachel [0000-0001-8050-402X]; Micklem, Gos [0000-0002-6883-6168]
    The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at
  • ItemOpen AccessPublished version Peer-reviewed
    modMine: flexible access to modENCODE data.
    (Oxford University Press (OUP), 2012-01) Contrino, Sergio; Smith, Richard N; Butano, Daniela; Carr, Adrian; Hu, Fengyuan; Lyne, Rachel; Rutherford, Kim; Kalderimis, Alex; Sullivan, Julie; Carbon, Seth; Kephart, Ellen T; Lloyd, Paul; Stinson, EO; Washington, Nicole L; Perry, Marc D; Ruzanov, Peter; Zha, Zheng; Lewis, Suzanna E; Stein, Lincoln D; Micklem, Gos; Lyne, Rachel [0000-0001-8050-402X]; Micklem, Gos [0000-0002-6883-6168]
    In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database ( described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.
  • ItemOpen AccessPublished version Peer-reviewed
    YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit.
    (Oxford University Press (OUP), 2012) Balakrishnan, Rama; Park, Julie; Karra, Kalpana; Hitz, Benjamin C; Binkley, Gail; Hong, Eurie L; Sullivan, Julie; Micklem, Gos; Cherry, J Michael; Micklem, Gos [0000-0002-6883-6168]
    The Saccharomyces Genome Database (SGD; provides high-quality curated genomic, genetic, and molecular information on the genes and their products of the budding yeast Saccharomyces cerevisiae. To accommodate the increasingly complex, diverse needs of researchers for searching and comparing data, SGD has implemented InterMine (, an open source data warehouse system with a sophisticated querying interface, to create YeastMine ( YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types. YeastMine offers multiple scenarios in which it can be used such as a powerful search interface, a discovery tool, a curation aid and also a complex database presentation format. DATABASE URL:
  • ItemOpen AccessPublished version Peer-reviewed
    Host shifts result in parallel genetic changes when viruses evolve in closely related species.
    (Public Library of Science (PLoS), 2018-04) Longdon, Ben; Day, Jonathan P; Alves, Joel M; Smith, Sophia CL; Houslay, Thomas M; McGonigle, John E; Tagliaferri, Lucia; Jiggins, Francis M; Longdon, Ben [0000-0001-6936-1697]; Alves, Joel M [0000-0001-6138-9134]; McGonigle, John E [0000-0001-8390-2867]; Jiggins, Francis M [0000-0001-7470-8157]
    Host shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease.
  • ItemOpen AccessAccepted version Peer-reviewed
    A reference panel of 64,976 haplotypes for genotype imputation.
    (Springer Science and Business Media LLC, 2016-10) McCarthy, Shane; Das, Sayantan; Kretzschmar, Warren; Delaneau, Olivier; Wood, Andrew R; Teumer, Alexander; Kang, Hyun Min; Fuchsberger, Christian; Danecek, Petr; Sharp, Kevin; Luo, Yang; Sidore, Carlo; Kwong, Alan; Timpson, Nicholas; Koskinen, Seppo; Vrieze, Scott; Scott, Laura J; Zhang, He; Mahajan, Anubha; Veldink, Jan; Peters, Ulrike; Pato, Carlos; van Duijn, Cornelia M; Gillies, Christopher E; Gandin, Ilaria; Mezzavilla, Massimo; Gilly, Arthur; Cocca, Massimiliano; Traglia, Michela; Angius, Andrea; Barrett, Jeffrey C; Boomsma, Dorrett; Branham, Kari; Breen, Gerome; Brummett, Chad M; Busonero, Fabio; Campbell, Harry; Chan, Andrew; Chen, Sai; Chew, Emily; Collins, Francis S; Corbin, Laura J; Smith, George Davey; Dedoussis, George; Dorr, Marcus; Farmaki, Aliki-Eleni; Ferrucci, Luigi; Forer, Lukas; Fraser, Ross M; Gabriel, Stacey; Levy, Shawn; Groop, Leif; Harrison, Tabitha; Hattersley, Andrew; Holmen, Oddgeir L; Hveem, Kristian; Kretzler, Matthias; Lee, James C; McGue, Matt; Meitinger, Thomas; Melzer, David; Min, Josine L; Mohlke, Karen L; Vincent, John B; Nauck, Matthias; Nickerson, Deborah; Palotie, Aarno; Pato, Michele; Pirastu, Nicola; McInnis, Melvin; Richards, J Brent; Sala, Cinzia; Salomaa, Veikko; Schlessinger, David; Schoenherr, Sebastian; Slagboom, P Eline; Small, Kerrin; Spector, Timothy; Stambolian, Dwight; Tuke, Marcus; Tuomilehto, Jaakko; Van den Berg, Leonard H; Van Rheenen, Wouter; Volker, Uwe; Wijmenga, Cisca; Toniolo, Daniela; Zeggini, Eleftheria; Gasparini, Paolo; Sampson, Matthew G; Wilson, James F; Frayling, Timothy; de Bakker, Paul IW; Swertz, Morris A; McCarroll, Steven; Kooperberg, Charles; Dekker, Annelot; Altshuler, David; Willer, Cristen; Iacono, William; Ripatti, Samuli; Soranzo, Nicole; Walter, Klaudia; Swaroop, Anand; Cucca, Francesco; Anderson, Carl A; Myers, Richard M; Boehnke, Michael; McCarthy, Mark I; Durbin, Richard; Haplotype Reference Consortium; McCarthy, Shane [0000-0002-2715-4187]; Das, Sayantan [0000-0001-6346-1590]; Kretzschmar, Warren [0000-0002-2575-0807]; Durbin, Richard [0000-0002-9130-1006]
    We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.
  • ItemOpen AccessAccepted version Peer-reviewed
    piRNA-mediated regulation of transposon alternative splicing in the soma and germ line
    (Nature Research, 2017-12-14) Karam Teixeira, FA; Okuniewska, M; Malone, CD; Coux, RX; Rio, DC; Lehmann, R; Karam Teixeira, Felipe [0000-0001-7651-1657]
    Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated1. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs2. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce transcript levels of the P-element transposon during P–M hybrid dysgenesis, a syndrome that affects germline development in Drosophila3,4. Instead, splicing regulation is mechanistically achieved together with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi–piRNA complex proteins Asterix (also known as Gtsf1)5,6,7 and Panoramix (Silencio)8,9, as well as Heterochromatin protein 1a (HP1a; encoded by Su(var)205). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster10, not only controls the accumulation of Gypsy retrotransposon transcripts11 but also regulates the splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events12,13. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.
  • ItemOpen AccessPublished version Peer-reviewed
    Repressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function.
    (Oxford University Press (OUP), 2018-02) Ahringer, Julie; Gasser, Susan M; Ahringer, Julie [0000-0002-7074-4051]; Gasser, Susan M [0000-0003-3610-9123]
    Chromatin is organized and compacted in the nucleus through the association of histones and other proteins, which together control genomic activity. Two broad types of chromatin can be distinguished: euchromatin, which is generally transcriptionally active, and heterochromatin, which is repressed. Here we examine the current state of our understanding of repressed chromatin in Caenorhabditis elegans, focusing on roles of histone modifications associated with repression, such as methylation of histone H3 lysine 9 (H3K9me2/3) or the Polycomb Repressive Complex 2 (MES-2/3/6)-deposited modification H3K27me3, and on proteins that recognize these modifications. Proteins involved in chromatin repression are important for development, and have demonstrated roles in nuclear organization, repetitive element silencing, genome integrity, and the regulation of euchromatin. Additionally, chromatin factors participate in repression with small RNA pathways. Recent findings shed light on heterochromatin function and regulation in C. elegans, and should inform our understanding of repressed chromatin in other animals.
  • ItemOpen AccessPublished version Peer-reviewed
    The UK10K project identifies rare variants in health and disease.
    (Springer Science and Business Media LLC, 2015-10-01) UK10K Consortium; Walter, Klaudia; Min, Josine L; Huang, Jie; Crooks, Lucy; Memari, Yasin; McCarthy, Shane; Perry, John RB; Xu, ChangJiang; Futema, Marta; Lawson, Daniel; Iotchkova, Valentina; Schiffels, Stephan; Hendricks, Audrey E; Danecek, Petr; Li, Rui; Floyd, James; Wain, Louise V; Barroso, Inês; Humphries, Steve E; Hurles, Matthew E; Zeggini, Eleftheria; Barrett, Jeffrey C; Plagnol, Vincent; Richards, J Brent; Greenwood, Celia MT; Timpson, Nicholas J; Durbin, Richard; Soranzo, Nicole; McCarthy, Shane [0000-0002-2715-4187]; Durbin, Richard [0000-0002-9130-1006]
    The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results.
  • ItemOpen AccessPublished version Peer-reviewed
    TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.
    (Springer Science and Business Media LLC, 2015-06-05) Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R; Mans, Dorus A; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia EC; Yap, Zhi Min; Letteboer, Stef JF; Taylor, S Paige; Herridge, Warren; Johnson, Colin A; Scambler, Peter J; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M; UK10K; Beales, Philip L; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M; Witman, George B; Raymond, Lucy [0000-0003-2652-3355]
    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions.
  • ItemOpen AccessPublished version Peer-reviewed
    Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
    (Springer Science and Business Media LLC, 2015-09-14) Huang, Jie; Howie, Bryan; McCarthy, Shane; Memari, Yasin; Walter, Klaudia; Min, Josine L; Danecek, Petr; Malerba, Giovanni; Trabetti, Elisabetta; Zheng, Hou-Feng; UK10K Consortium; Gambaro, Giovanni; Richards, J Brent; Durbin, Richard; Timpson, Nicholas J; Marchini, Jonathan; Soranzo, Nicole; Durbin, Richard [0000-0002-9130-1006]; Marchini, Jonathan [0000-0003-0610-8322]; Soranzo, Nicole [0000-0003-1095-3852]
    Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.
  • ItemOpen AccessPublished version Peer-reviewed
    Estimating telomere length from whole genome sequence data.
    (Oxford University Press (OUP), 2014-05) Ding, Zhihao; Mangino, Massimo; Aviv, Abraham; Spector, Tim; Durbin, Richard; UK10K Consortium; Ding, Zhihao [0000-0003-0961-2284]; Mangino, Massimo [0000-0002-2167-7470]
    Telomeres play a key role in replicative ageing and undergo age-dependent attrition in vivo. Here, we report a novel method, TelSeq, to measure average telomere length from whole genome or exome shotgun sequence data. In 260 leukocyte samples, we show that TelSeq results correlate with Southern blot measurements of the mean length of terminal restriction fragments (mTRFs) and display age-dependent attrition comparably well as mTRFs.
  • ItemOpen AccessAccepted version Peer-reviewed
    Obituary: Denise Barlow (1950-2017).
    (The Company of Biologists, 2018-03-14) Ferguson-Smith, Anne C; Bartolomei, Marisa S; Ferguson-Smith, Anne C [0000-0002-7608-5894]; Bartolomei, Marisa S [0000-0001-9410-5222]
    Anne Ferguson-Smith and Marisa Bartolomei look back at the life and science of Denise Barlow, a pioneer in genomic imprinting and epigenetics.
  • ItemOpen AccessPublished version Peer-reviewed
    L(3)mbt and the LINT complex safeguard cellular identity in the Drosophila ovary.
    (The Company of Biologists, 2018-04-04) Coux, Rémi-Xavier; Teixeira, Felipe Karam; Lehmann, Ruth; Coux, Rémi-Xavier [0000-0002-6114-2585]; Teixeira, Felipe Karam [0000-0001-7651-1657]; Lehmann, Ruth [0000-0002-8454-5651]
    Maintenance of cellular identity is essential for tissue development and homeostasis. At the molecular level, cell identity is determined by the coordinated activation and repression of defined sets of genes. The tumor suppressor L(3)mbt has been shown to secure cellular identity in Drosophila larval brains by repressing germline-specific genes. Here, we interrogate the temporal and spatial requirements for L(3)mbt in the Drosophila ovary, and show that it safeguards the integrity of both somatic and germline tissues. l(3)mbt mutant ovaries exhibit multiple developmental defects, which we find to be largely caused by the inappropriate expression of a single gene, nanos, a key regulator of germline fate, in the somatic ovarian cells. In the female germline, we find that L(3)mbt represses testis-specific and neuronal genes. At the molecular level, we show that L(3)mbt function in the ovary is mediated through its co-factor Lint-1 but independently of the dREAM complex. Together, our work uncovers a more complex role for L(3)mbt than previously understood and demonstrates that L(3)mbt secures tissue identity by preventing the simultaneous expression of original identity markers and tissue-specific misexpression signatures.
  • ItemOpen AccessAccepted version Peer-reviewed
    Efficient 3‐Hydroxybutyrate Production by Quiescent Escherichia coli Microbial Cell Factories is Facilitated by Indole‐Induced Proteomic and Metabolomic Changes
    (Wiley-Blackwell, 2018-05) Thomson, Nicholas M; Shirai, Tomokazu; Chiapello, Marco; Kondo, Akihiko; Mukherjee, Krishna J; Sivaniah, Easan; Numata, Keiji; Summers, David K; Thomson, Nicholas [0000-0003-1168-9010]; Summers, David [0000-0002-8243-9521]
    The authors show that quiescent (Q‐Cell) Escherichia coli cultures can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater specific productivity of a model metabolite, 3‐hydroxybutyrate (3HB), than a control. Q‐cells can be created by using the proton ionophore indole to halt cell division of an hns mutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks because less metabolic effort is diverted to surplus biomass production. However, the reason for the increased productivity of cells in the quiescent state was previously unknown. In this study, proteome expression patterns between wild‐type and Q‐cell cultures show that Q‐cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Metabolomic data reveal the accumulation of acetyl‐coenzyme A and phosphoenolpyruvate: excellent starting points for high‐value chemical production. We demonstrate the exploitation of these accumulated metabolites by engineering a simple pathway for 3HB production from acetyl‐coenzyme A. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g L−1 of 3HB compared to 18.6 g L−1 in the control. Q‐cells therefore have great potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals.
  • ItemOpen AccessPublished version Peer-reviewed
    bicoid mRNA localises to the Drosophila oocyte anterior by random Dynein-mediated transport and anchoring.
    (eLife Sciences Publications, Ltd, 2016-10-28) Trovisco, Vítor; Belaya, Katsiaryna; Nashchekin, Dmitry; Irion, Uwe; Sirinakis, George; Butler, Richard; Lee, Jack J; Gavis, Elizabeth R; St Johnston, Daniel; Trovisco, Vítor [0000-0002-8728-0281]; Irion, Uwe [0000-0003-2823-5840]; St Johnston, Daniel [0000-0001-5582-3301]
    bicoid mRNA localises to the Drosophila oocyte anterior from stage 9 of oogenesis onwards to provide a local source for Bicoid protein for embryonic patterning. Live imaging at stage 9 reveals that bicoid mRNA particles undergo rapid Dynein-dependent movements near the oocyte anterior, but with no directional bias. Furthermore, bicoid mRNA localises normally in shot2A2, which abolishes the polarised microtubule organisation. FRAP and photo-conversion experiments demonstrate that the RNA is stably anchored at the anterior, independently of microtubules. Thus, bicoid mRNA is localised by random active transport and anterior anchoring. Super-resolution imaging reveals that bicoid mRNA forms 110-120 nm particles with variable RNA content, but constant size. These particles appear to be well-defined structures that package the RNA for transport and anchoring.
  • ItemOpen AccessPublished version Peer-reviewed
  • ItemOpen AccessPublished version Peer-reviewed
    Studying vertebrate topoisomerase 2 function using a conditional knockdown system in DT40 cells.
    (Oxford University Press (OUP), 2009-08) Johnson, Mark; Phua, Hui Hui; Bennett, Sophia C; Spence, Jennifer M; Farr, Christine J; Farr, Christine [0000-0002-5357-5962]
    DT40 is a B-cell lymphoma-derived avian cell line widely used to study cell autonomous gene function because of the high rates with which DNA constructs are homologously recombined into its genome. Here, we demonstrate that the power of the DT40 system can be extended yet further through the use of RNA interference as an alternative to gene targeting. We have generated and characterized stable DT40 transfectants in which both topo 2 genes have been in situ tagged using gene targeting, and from which the mRNA of both topoisomerase 2 isoforms can be conditionally depleted through the tetracycline-induced expression of short hairpin RNAs. The cell cycle phenotype of topo 2-depleted DT40 cells has been compared with that previously reported for other vertebrate cells depleted either of topo 2alpha through gene targeting, or depleted of both isoforms simultaneously by transient RNAi. In addition, the DT40 knockdown system has been used to explore whether excess catenation arising through topo 2 depletion is sufficient to trigger the G2 catenation (or decatenation) checkpoint, proposed to exist in differentiated vertebrate cells.
  • ItemOpen AccessPublished version Peer-reviewed
    The α isoform of topoisomerase II is required for hypercompaction of mitotic chromosomes in human cells.
    (Oxford University Press (OUP), 2014-04) Farr, Christine J; Antoniou-Kourounioti, Melissa; Mimmack, Michael L; Volkov, Arsen; Porter, Andrew CG; Farr, Christine [0000-0002-5357-5962]
    As proliferating cells transit from interphase into M-phase, chromatin undergoes extensive reorganization, and topoisomerase (topo) IIα, the major isoform of this enzyme present in cycling vertebrate cells, plays a key role in this process. In this study, a human cell line conditional null mutant for topo IIα and a derivative expressing an auxin-inducible degron (AID)-tagged version of the protein have been used to distinguish real mitotic chromosome functions of topo IIα from its more general role in DNA metabolism and to investigate whether topo IIβ makes any contribution to mitotic chromosome formation. We show that topo IIβ does contribute, with endogenous levels being sufficient for the initial stages of axial shortening. However, a significant effect of topo IIα depletion, seen with or without the co-depletion of topo IIβ, is the failure of chromosomes to hypercompact when delayed in M-phase. This requires much higher levels of topo II protein and is impaired by drugs or mutations that affect enzyme activity. A prolonged delay at the G2/M border results in hyperefficient axial shortening, a process that is topo IIα-dependent. Rapid depletion of topo IIα has allowed us to show that its function during late G2 and M-phase is truly required for shaping mitotic chromosomes.