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  • Microbial Genetics: Stress Management
    Trends Genet. (IF 11.333) Pub Date : 2020-11-27
    Shankar Iyer; Sonia Muliyil

    Microbes constitute the very core of our existence. Long believed to be a nuisance and proponents of various disease, latest research point toward their functions in processes that can prove beneficial for human survival and afford long-term protection from disease. The wide range of functions exhibited by a host of microbes implies diversity and heterogeneity at the level of the molecular machinery

  • Using Genetics to dissect out SARS-Cov-2 infection
    Trends Genet. (IF 11.333) Pub Date : 2020-11-26
    Patrick Brest; Baharia Mograbi; Paul Hofman; Gerard Milano

    To uncover the host key-cellular pathways associated with SARS-CoV-2 infectiousness, Daniloski and coworkers have used CRISPR-based whole genome screening. Their results could lead to propose new or repositioned drugs for the continuous fight against COVID-19.

  • Closing the Gaps in Genomic Research
    Trends Genet. (IF 11.333) Pub Date : 2020-11-24
    Cesar Fortes-Lima; Carina Schlebusch

    Despite Africa’s central role in the origin of our species, our knowledge of the genomic diversity in Africa is remarkably sparse. A recent publication by Choudhury et al. underscores the scientific imperative for a broader characterisation of African genomic diversity to better understand demographic history and improve global human health.

  • Noncoding RNA, Intragenomic Conflict, and Rodent SRY Evolution
    Trends Genet. (IF 11.333) Pub Date : 2020-11-23
    Scott William Roy

    The sex-determining gene SRY has undergone rapid evolution in rodents. Curiously, a new study by Miyawaki et al. reveals that a recently evolved SRY gene sequence antagonizes SRY protein stability, necessitating splicing of a novel intron. Other data suggest that this troublesome gene region has noncoding RNA functions, possibly related to conflict between sex chromosomes.

  • Autosomal Clonal Monoallelic Expression: Natural or Artifactual?
    Trends Genet. (IF 11.333) Pub Date : 2020-11-21
    P. RV; A. Sundaresh; M. Karunyaa; A. Arun; S. Gayen

    The prevalence of mitotically heritable clonal random monoallelic expression of autosomal genes (aRME) remains controversial. Specifically, presence of clonal aRME is well supported in vitro but remains elusive in vivo. Here, we provide critical insights into this matter and discuss whether prevalent clonal aRME is natural or artifactual.

  • Uncertainty in Genomics Impacts Precision Medicine
    Trends Genet. (IF 11.333) Pub Date : 2020-11-18
    Reed E. Pyeritz

    As exacting as genetic and genomic testing have become, health professionals continue to encounter uncertainty in their applications to medical practice. As examining the human genome at more refined levels increases, so is the likelihood of encountering uncertainty about the meaning of the information. The history of this concept informs how we might confront and deal with uncertainty, and what the

  • Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation
    Trends Genet. (IF 11.333) Pub Date : 2020-11-15
    Niels H. Gehring; Jean-Yves Roignant

    Splicing of precursor mRNAs (pre-mRNA) is an important step during eukaryotic gene expression. The identification of the actual splice sites and the proper removal of introns are essential for the production of the desired mRNA isoforms and their encoded proteins. While the basic mechanisms of splicing regulation are well understood, recent work has uncovered a growing number of noncanonical splicing

  • Germline Variants That Affect Tumor Progression
    Trends Genet. (IF 11.333) Pub Date : 2020-11-14
    Ajay Chatrath; Aakrosh Ratan; Anindya Dutta

    Germline variants have a rich history of being studied in the context of cancer risk. Emerging studies now suggest that germline variants contribute not only to cancer risk but to tumor progression as well. In this opinion article, we discuss the initial discoveries associating germline variants with patient outcome and the mechanisms by which germline variants affect molecular pathways. Germline variants

  • A TAD Skeptic: Is 3D Genome Topology Conserved?
    Trends Genet. (IF 11.333) Pub Date : 2020-11-14
    Ittai E. Eres; Yoav Gilad

    The notion that topologically associating domains (TADs) are highly conserved across species is prevalent in the field of 3D genomics. However, what exactly is meant by ‘highly conserved’ and what are the actual comparative data that support this notion? To address these questions, we performed a historical review of the relevant literature and retraced numerous citation chains to reveal the primary

  • Metabolic Microenvironments Drive Microbial Differentiation and Antibiotic Resistance
    Trends Genet. (IF 11.333) Pub Date : 2020-11-14
    Tatyana L. Povolotsky; Alona Keren-Paz; Ilana Kolodkin-Gal

    For bacteria, the transition from unicellular entities to multicellular biofilm communities generates distinct metabolic microenvironments. Dynamic and programmed metabolic responses allow the biofilms to react to local changes in nutrient levels. Moreover, metabolic adaptations contribute to phenotypic antibiotic resistance of the community, suggesting novel therapeutic approaches to target biofilms

  • RNA Editing in Mitochondria and Plastids: Weird and Widespread
    Trends Genet. (IF 11.333) Pub Date : 2020-11-14
    Julius Lukeš; Binnypreet Kaur; Dave Speijer

    Though widespread, RNA editing is rare, except in endosymbiotic organelles. A combination of higher mutation rates, relaxation of energetic constraints, and high genetic drift is found within plastids and mitochondria and is conducive for evolution and expansion of editing processes, possibly starting as repair mechanisms. To illustrate this, we present an exhaustive phylogenetic overview of editing

  • Hotspots of Human Mutation
    Trends Genet. (IF 11.333) Pub Date : 2020-11-13
    Alex V. Nesta; Denisse Tafur; Christine R. Beck

    Mutation of the human genome results in three classes of genomic variation: single nucleotide variants; short insertions or deletions; and large structural variants (SVs). Some mutations occur during normal processes, such as meiotic recombination or B cell development, and others result from DNA replication or aberrant repair of breaks in sequence-specific contexts. Regardless of mechanism, mutations

  • Impact of Parental Exposure on Offspring Health in Humans
    Trends Genet. (IF 11.333) Pub Date : 2020-11-11
    Ali Jawaid; Katherina-Lynn Jehle; Isabelle M. Mansuy

    The possibility that parental life experiences and environmental exposures influence mental and physical health across generations is an important concept in biology and medicine. Evidence from animal models has established the existence of a non-genetic mode of inheritance. This form of heredity involves transmission of the effects of parental exposure to the offspring through epigenetic changes in

  • Current Techniques for Complex Phenotypes: GWAS of the Electrocardiogram.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-23
    Eric B Fauman

    By sampling 500 time points of an electrocardiogram (ECG) trace in a genome-wide association study (GWAS), Verweig et al. identified novel correlates for cardiac dysfunction. Clustering of SNPs based on their impact at all time points revealed natural sets of SNPs with similar effects and mechanisms. Similar approaches may be applicable to other quantitative, time-ordered traits.

  • Base Editing Landscape Extends to Perform Transversion Mutation.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-18
    Kutubuddin A Molla,Yiping Qi,Subhasis Karmakar,Mirza J Baig

    Base editors have drawn considerable academic and industrial attention in recent years because of their ability to alter single DNA bases with precision. However, the existing cytosine and adenine base editors can only install transition mutations. Three recent studies (Kurt et al., Zhao et al., and Chen et al.) expand the base editing toolbox by developing cytosine transversion base editors.

  • SWEET Genes for Disease Resistance in Plants.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-04
    Pushpendra K Gupta

    Sugar transporters called SWEETs are utilized by plants for a variety of functions. Invading pathogens utilize them for the supply of nutrition, thus rendering the host susceptible, as shown in several plant species. Therefore, naturally occurring and genetically manipulated SWEET gene variants are being deployed for the development of resistant crop cultivars.

  • Anticipating and Identifying Collateral Damage in Genome Editing
    Trends Genet. (IF 11.333) Pub Date : 2020-10-08
    Gaëtan Burgio; Lydia Teboul

    Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion

  • Horizontal Gene Transfer in Eukaryotes: Not if, but How Much?
    Trends Genet. (IF 11.333) Pub Date : 2020-10-01
    Julia Van Etten; Debashish Bhattacharya

    Horizontal gene transfer (HGT), the movement of genetic material across branches of the tree of life, is well established in prokaryotes and uncontroversial. This is explained in part by relatively compact prokaryote genomes that facilitate assembly and gene prediction, resulting in thousands of complete genomes for analysis. By contrast, their large and often complex genome structure have thwarted

  • Genetics in Light of Transcriptional Adaptation.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-11
    Zacharias Kontarakis,Didier Y R Stainier

    Genetics has recently benefited from the genome engineering revolution: genes can be knocked out, knocked down, or activated more easily than ever before. This range of genetic manipulations has also provided a range of outcomes, sometimes contradictory. But how much interesting biology hides within these discrepancies? Recent studies have shown that genetic compensation can be activated by some gene

  • Self-Peptidome Variation Shapes Individual Immune Responses
    Trends Genet. (IF 11.333) Pub Date : 2020-10-21
    Pierre Pontarotti; Laurent Abi-Rached; Jung-Hua Yeh; Julien Paganini

    The relationship between human genetic variation and disease has not been fully elucidated. According to the present view on infectious diseases pathogen resistance is linked to human leukocyte antigen (HLA) class I/II variants and their individual capacity to present pathogen-derived peptides. Yet, T cell education in the thymus occurs through negative and positive selection, and both processes are

  • Epigenetic Regulators as the Gatekeepers of Hematopoiesis
    Trends Genet. (IF 11.333) Pub Date : 2020-10-21
    Cecilia Pessoa Rodrigues; Maria Shvedunova; Asifa Akhtar

    Hematopoiesis is the process by which both fetal and adult organisms derive the full repertoire of blood cells from a single multipotent progenitor cell type, the hematopoietic stem cells (HSCs). Correct enactment of this process relies on a synergistic interplay between genetically encoded differentiation programs and a host of cell-intrinsic and cell-extrinsic factors. These include the influence

  • All Creatures Great and Small: New Approaches for Understanding Down Syndrome Genetics
    Trends Genet. (IF 11.333) Pub Date : 2020-10-20
    Anna J. Moyer; Katheleen Gardiner; Roger H. Reeves

    Human chromosome 21 (Hsa21) contains more than 500 genes, making trisomy 21 one of the most complex genetic perturbations compatible with life. The ultimate goal of Down syndrome (DS) research is to design therapies that improve quality of life for individuals with DS by understanding which subsets of Hsa21 genes contribute to DS-associated phenotypes throughout the lifetime. However, the complexity

  • Gene Regulation and Cellular Metabolism: An Essential Partnership
    Trends Genet. (IF 11.333) Pub Date : 2020-10-19
    Richard W. Carthew

    It is recognized that cell metabolism is tightly connected to other cellular processes such as regulation of gene expression. Metabolic pathways not only provide the precursor molecules necessary for gene expression, but they also provide ATP, the primary fuel driving gene expression. However, metabolic conditions are highly variable since nutrient uptake is not a uniform process. Thus, cells must

  • Unbelievable but True: Epigenetics and Chromatin in Fungi
    Trends Genet. (IF 11.333) Pub Date : 2020-10-19
    Hiten D. Madhani

    Evolutionary innovations in chromatin biology have been recently discovered through the study of fungi. In Saccharomyces cerevisiae, a prion form of a deacetylase complex assembles over subtelomeric domains that produces a heritable gene expression state that enables resistance to stress. In Candida albicans, stress triggers adaptive chromosome destabilization via erasure a centromeric histone H3,

  • Keeping Up with RNA-Based Regulation in Bacteria: New Roles for RNA Binding Proteins
    Trends Genet. (IF 11.333) Pub Date : 2020-10-16
    Evelyne Ng Kwan Lim; Charles Sasseville; Marie-Claude Carrier; Eric Massé

    RNA binding proteins (RBPs) are ubiquitously found in all kingdoms of life. They are involved in a plethora of regulatory events, ranging from direct regulation of gene expression to guiding modification of RNA molecules. As bacterial regulators, RBPs can act alone or in concert with RNA-based regulators, such as small regulatory RNAs (sRNAs), riboswitches, or clustered regularly interspaced short

  • Editing the Mitochondrial Genome: No CRISPR Required.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-17
    Joey Riepsaame

    Precise gene editing of mitochondrial DNA (mtDNA) is essential for the generation of model systems to study rare mitochondrial diseases but was long deemed impossible – until now. A recent publication by Mok et al. describes a gene editing tool capable of installing point mutations in mtDNA, and it does not involve CRISPR.

  • Virus-Based CRISPR/Cas9 Genome Editing in Plants.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-19
    Huawei Liu,Baohong Zhang

    CRISPR/Cas9 is a versatile tool for plant gene function studies and crop improvement. However, traditional CRISPR/Cas9-mediated genome editing requires plant tissue culture that is both time-consuming and genotype-dependent. Ma et al. recently reported a novel virus-based method for delivering CRISPR/Cas9 into plant cells, and this should further expand the application of CRISPR/Cas9-mediated genome

  • Host Polymorphisms May Impact SARS-CoV-2 Infectivity.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-10
    Patrick Brest,Sadal Refae,Baharia Mograbi,Paul Hofman,Gerard Milano

    Based on a broad public database compilation, we support the hypothesis that germinal polymorphisms may regulate the expression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular target itself and proteases controlling the process of its shedding or, conversely, its internalization. Consequently, a genetic influence on individual susceptibility to coronavirus disease 2019

  • Emerging Insights into the Distinctive Neuronal Methylome.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-21
    Adam W Clemens,Harrison W Gabel

    The genomes of mammalian neurons are enriched for unique forms of DNA methylation, including exceptionally high levels of non-CG methylation. Here, we review recent studies defining how non-CG methylation accumulates in neurons and is read out by the critical regulator of neuronal transcription, MeCP2. We discuss the role of gene expression and genome architecture in establishing non-CG methylation

  • Alternative Synaptonemal Complex Structures: Too Much of a Good Thing?
    Trends Genet. (IF 11.333) Pub Date : 2020-08-13
    Stacie E Hughes,R Scott Hawley

    The synaptonemal complex (SC), a highly conserved structure built between homologous meiotic chromosomes, is required for crossover formation and ensuring proper chromosome segregation. In many organisms, SC components can also form alternative structures, including repeating SC structures that are known as polycomplexes (PCs), and extensively modified SC structures that are maintained late in meiosis

  • Alternative Applications of Genotyping Array Data Using Multivariant Methods.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-06
    David C Samuels,Jennifer E Below,Scott Ness,Hui Yu,Shuguang Leng,Yan Guo

    One of the forerunners that pioneered the revolution of high-throughput genomic technologies is the genotyping microarray technology, which can genotype millions of single-nucleotide variants simultaneously. Owing to apparent benefits, such as high speed, low cost, and high throughput, the genotyping array has gained lasting applications in genome-wide association studies (GWAS) and thus accumulated

  • Noncoding RNAs Set the Stage for RNA Polymerase II Transcription
    Trends Genet. (IF 11.333) Pub Date : 2020-10-09
    Cécilia Studniarek; Sylvain Egloff; Shona Murphy

    Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional

  • Spotlight on the Replisome: Aetiology of DNA Replication-Associated Genetic Diseases
    Trends Genet. (IF 11.333) Pub Date : 2020-10-08
    Roberto Bellelli; Simon J. Boulton

    Human development and tissue homeostasis depend on the regulated control of cellular proliferation and differentiation. DNA replication is essential to couple genome duplication and cell division with the establishment and maintenance of cellular differentiation programs. In eukaryotes, DNA replication is performed by a large machine known as the ‘replisome,’ which is strictly regulated in a cell cycle-dependent

  • Plant Genetic Networks Shaping Phyllosphere Microbial Community
    Trends Genet. (IF 11.333) Pub Date : 2020-10-06
    Sara Shakir; Syed Shan-e-Ali Zaidi; Franciska T. de Vries; Shahid Mansoor

    Phyllosphere microbial communities inhabit the aerial plant parts, such as leaves and flowers, where they form complex molecular interactions with the host plant. Contrary to the relatively well-studied rhizosphere microbiome, scientists are just starting to understand, and potentially utilize, the phyllosphere microbiome. In this article, we summarize the recent studies that have provided novel insights

  • Epigenetic Regulation of Tick Biology and Vectorial Capacity
    Trends Genet. (IF 11.333) Pub Date : 2020-10-02
    Sandip De; Chrysoula Kitsou; Daniel E. Sonenshine; Joao H.F. Pedra; Erol Fikrig; Judith A. Kassis; Utpal Pal

    Ticks exist across diverse environments and transmit numerous pathogens. Due to their long and unique life cycles, these arthropods likely evolved robust epigenetic mechanisms that provide sustainable responses and buffers against extreme environmental conditions. Herein, we highlight how the study of the epigenetic basis of tick biology and vectorial capacity will enrich our knowledge of tick-borne

  • DNA Damage Triggers a New Phase in Neurodegeneration
    Trends Genet. (IF 11.333) Pub Date : 2020-10-02
    Fabio Pessina; Ubaldo Gioia; Ornella Brandi; Stefania Farina; Marta Ceccon; Sofia Francia; Fabrizio d’Adda di Fagagna

    Subcellular compartmentalization contributes to the organization of a plethora of molecular events occurring within cells. This can be achieved in membraneless organelles generated through liquid–liquid phase separation (LLPS), a demixing process that separates and concentrates cellular reactions. RNA is often a critical factor in mediating LLPS. Recent evidence indicates that DNA damage response foci

  • Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics
    Trends Genet. (IF 11.333) Pub Date : 2020-09-30
    Emily Swanzey; Callan O’Connor; Laura G. Reinholdt

    Interrogation of disease-relevant cellular and molecular traits exhibited by genetically diverse cell populations enables in vitro systems genetics approaches for uncovering the basic properties of cellular function and identity. Primary cells, stem cells, and organoids derived from genetically diverse mouse strains, such as Collaborative Cross and Diversity Outbred populations, offer the opportunity

  • Site-Specific Recombination – How Simple DNA Inversions Produce Complex Phenotypic Heterogeneity in Bacterial Populations
    Trends Genet. (IF 11.333) Pub Date : 2020-09-29
    Dominika Trzilova; Rita Tamayo

    Many bacterial species generate phenotypically heterogeneous subpopulations as a strategy for ensuring the survival of the population as a whole – an environmental stress that eradicates one subpopulation may leave other phenotypic groups unharmed, allowing the lineage to continue. Phase variation, a process that functions as an ON/OFF switch for gene expression, is one way that bacteria achieve phenotypic

  • The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway
    Trends Genet. (IF 11.333) Pub Date : 2020-09-29
    Zhongxia Yi; Manu Sanjeev; Guramrit Singh

    Nonsense-mediated mRNA decay (NMD) is a conserved translation-coupled quality control mechanism in all eukaryotes that regulates the expression of a significant fraction of both the aberrant and normal transcriptomes. In vertebrates, NMD has become an essential process owing to expansion of the diversity of NMD-regulated transcripts, particularly during various developmental processes. Surprisingly

  • Read, Write, Adapt: Challenges and Opportunities during Kinetoplastid Genome Replication
    Trends Genet. (IF 11.333) Pub Date : 2020-09-28
    Jeziel D. Damasceno; Catarina A. Marques; Jennifer Black; Emma Briggs; Richard McCulloch

    The genomes of all organisms are read throughout their growth and development, generating new copies during cell division and encoding the cellular activities dictated by the genome’s content. However, genomes are not invariant information stores but are purposefully altered in minor and major ways, adapting cellular behaviour and driving evolution. Kinetoplastids are eukaryotic microbes that display

  • Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites
    Trends Genet. (IF 11.333) Pub Date : 2020-09-25
    Thomas Hollin; Mohit Gupta; Todd Lenz; Karine G. Le Roch

    Multiple hosts and various life cycle stages prompt the human malaria parasite, Plasmodium falciparum, to acquire sophisticated molecular mechanisms to ensure its survival, spread, and transmission to its next host. To face these environmental challenges, increasing evidence suggests that the parasite has developed complex and complementary layers of regulatory mechanisms controlling gene expression

  • Trash Talk: Mammalian Proteasome Regulation at the Transcriptional Level
    Trends Genet. (IF 11.333) Pub Date : 2020-09-25
    Hatem Elif Kamber Kaya; Senthil K. Radhakrishnan

    The key to a healthy mammalian cell lies in properly functioning proteolytic machineries called proteasomes. The proteasomes are multisubunit complexes that catalyze the degradation of unwanted proteins and also control half-lives of key cellular regulatory factors. Aberrant proteasome activity is often associated with human diseases such as cancer and neurodegeneration, and so an in-depth understanding

  • Tightening the Screws on PsbA in Cyanobacteria.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-22
    Amit Srivastava,Pratyoosh Shukla

    Cyanobacterial genomes encode several isoforms of the D1 (PsbA) subunit of Photosystem II (PSII). The distinct regulation of each isoform ensures adaptation under changing environmental conditions. Uncovering the missing elements of signal transduction pathways and psbA gene expression could open new avenues in engineering programs of cyanobacterial strains.

  • Genetic Lesions of Type I Interferon Signalling in Human Antiviral Immunity
    Trends Genet. (IF 11.333) Pub Date : 2020-09-22
    Christopher J.A. Duncan; Richard E. Randall; Sophie Hambleton

    The concept that type I interferons (IFN-I) are essential to antiviral immunity derives from studies on animal models and cell lines. Virtually all pathogenic viruses have evolved countermeasures to IFN-I restriction, and genetic loss of viral IFN-I antagonists leads to virus attenuation. But just how important is IFN-I to antiviral defence in humans? The recent discovery of genetic defects of IFN-I

  • Functions of PIWI Proteins in Gene Regulation: New Arrows Added to the piRNA Quiver.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-17
    Anne Ramat,Martine Simonelig

    Piwi-interacting RNAs (piRNAs) and PIWI proteins play key functions in a wide range of biological and developmental processes through the regulation of cellular mRNAs, in addition to their role in transposable element (TE) repression. Evolutionary studies indicate that these PIWI functions in mRNA regulatory programs, occurring in both germ and somatic cells, are ancestral. Recent advances have widely

  • Networks of Resistance: Small RNA Control of Antibiotic Resistance.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-17
    Daniel G Mediati,Sylvania Wu,Winton Wu,Jai J Tree

    The golden age of antibiotics has passed, and the threat of untreatable antimicrobial resistant infections is now a reality for many individuals. Understanding how bacteria resist antimicrobial treatment and regulate gene expression in response to antibiotics is an important step towards combating resistance. In this review we focus on a ubiquitous class of bacterial gene regulators termed regulatory

  • A New Protrait of Contitutive Heterochromatin: Lessons from Drosophila melanogaster: (Trends in Genetics, 35, 615-631, 2019).
    Trends Genet. (IF 11.333) Pub Date : 2020-09-18
    René M Marsano,Ennio Giordano,Giovanni Messina,Patrizio Dimitri

  • Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-16
    Mayra Petasny,Mercedes Bentata,Andrea Pawellek,Mai Baker,Gillian Kay,Maayan Salton

    Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the

  • Search and Capture: Disorder Rules Gene Promoter Selection.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-29
    U S Sandra,Arushi Shukla,Ullas Kolthur-Seetharam

    Intrinsically disordered regions (IDRs) are preponderant in transcription factors (TFs) and are evolutionarily less conserved vis-à-vis DNA-binding domains (DBDs). Unexpected findings from Barkai and colleagues, which demonstrate that promoter selectivity is determined by IDRs, should significantly enhance our understanding of gene expression regulation.

  • A Worldwide Map of Human Structural Variants.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-18
    Francesco Montinaro,Cristian Capelli

    Genomic variation extends from single nucleotide variants to large chromosomal rearrangements, but the extent of structural variation in Homo sapiens is still unclear. Almarri et al. provide a worldwide catalogue of structural variants present in human populations. Most of the reported variation is novel, with some variants being inherited from Neanderthals and Denisovans. Drift and selection shaped

  • Meiotic Executioner Genes Protect the Y from Extinction.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-06
    Paul D Waters,Aurora Ruiz-Herrera

    The Y has been described as a wimpy degraded relic of the X, with imminent demise should it lose sex-determining function. Why then has it persisted in almost all mammals? Here we present a novel mechanistic explanation for its evolutionary perseverance: the persistent Y hypothesis. The Y chromosome bears genes that act as their own judge, jury, and executioner in the tightly regulated meiotic surveillance

  • Simple Repeats as Building Blocks for Genetic Computers.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-18
    Alan Herbert

    Processing of RNA involves heterogeneous nuclear ribonucleoproteins. The simple sequence repeats (SSRs) they bind can also adopt alternative DNA structures, like Z DNA, triplexes, G quadruplexes, and I motifs. Those SSRs capable of switching conformation under physiological conditions (called flipons) are genetic elements that can encode alternative RNA processing by their effects on RNA processivity

  • Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-23
    Ben P Williams,Mary Gehring

    In diverse eukaryotes, epigenetic information such as DNA methylation is stably propagated over many cell divisions and generations, and can remain the same over thousands or millions of years. However, this stability is the product of dynamic processes that add and remove DNA methylation by specialized enzymatic pathways. The activities of these dynamic pathways must therefore be finely orchestrated

  • The Consequences of Abnormal Gene Dosage: Lessons from Chromosome 18.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-10
    Jannine DeMars Cody

    Accurate interpretation of genomic copy number variation (CNV) remains a challenge and has important consequences for both congenital and late-onset disease. Hemizygosity dosage characterization of the genes on chromosome 18 reveals a spectrum of outcomes ranging from no clinical effect, to risk factors for disease, to both low- and high-penetrance disease. These data are important for accurate and

  • DNA Damage Response and Metabolic Reprogramming in Health and Disease.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-17
    Ourania Chatzidoukaki,Evi Goulielmaki,Björn Schumacher,George A Garinis

    Nuclear DNA damage contributes to cellular malfunction and the premature onset of age-related diseases, including cancer. Until recently, the canonical DNA damage response (DDR) was thought to represent a collection of nuclear processes that detect, signal and repair damaged DNA. However, recent evidence suggests that beyond nuclear events, the DDR rewires an intricate network of metabolic circuits

  • Studying Natural Selection in the Era of Ubiquitous Genomes.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-13
    Timothy B Sackton

    A major goal of comparative genomics research is modeling changes in DNA sequences between species to understand the evolutionary forces acting on species differences. Application of these models to a number of species over the past decade has revealed some commonalities across organisms, most notably a consistent role of positive selection in shaping the molecular evolution of the immune system. However

  • New Approaches for Inferring Phylogenies in the Presence of Paralogs.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-10
    Megan L Smith,Matthew W Hahn

    The availability of whole genome sequences was expected to supply essentially unlimited data for phylogenetics. However, strict reliance on single-copy genes for this purpose has drastically limited the amount of data that can be used. Here, we review several approaches for increasing the amount of data used for phylogenetic inference, focusing on methods that allow for the inclusion of duplicated

  • Mediator Roles Going Beyond Transcription.
    Trends Genet. (IF 11.333) Pub Date : 2020-09-10
    Kévin M André,Eliet H Sipos,Julie Soutourina

    Dysfunctions of nuclear processes including transcription and DNA repair lead to severe human diseases. Gaining an understanding of how these processes operate in the crowded context of chromatin can be particularly challenging. Mediator is a large multiprotein complex conserved in eukaryotes with a key coactivator role in the regulation of RNA polymerase (Pol) II transcription. Despite intensive studies

  • Where Are the Disease-Associated eQTLs?
    Trends Genet. (IF 11.333) Pub Date : 2020-09-07
    Benjamin D Umans,Alexis Battle,Yoav Gilad

    Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem

  • Genetics and COVID-19: How to Protect the Susceptible.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-29
    Robert I Field,Anthony W Orlando,Arnold J Rosoff

    Along with the potential for breakthroughs in care and prevention, the search for genetic mechanisms underlying the spread and severity of COVID-19 introduces the risk of discrimination against those found to have markers for susceptibility. We propose new legal protections to mitigate gaps in protections under existing laws.

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Springer 纳米技术权威期刊征稿