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  • Demystifying Cancer Etiology via 3D Genome Mapping.
    Trends Genet. (IF 11.333) Pub Date : 2020-06-16
    Yuliang Feng,Siim Pauklin

    Ramanand et al. perform the first high-resolution 3D genome mapping via ChIA-PET to capture RNAPII-associated chromatin interactions in normal prostate epithelial and prostate cancer cells. They describe how genetics, epigenetics, and the 3D genome architecture are coordinated in the aberrant gene expression that drives prostate cancer development.

  • Extended ncRNAs Interfere with Promoter Nucleosome Dynamics.
    Trends Genet. (IF 11.333) Pub Date : 2020-06-13
    Tomasz W Turowski,David Tollervey

    Eukaryotic genomes generate vast numbers of non-protein-coding RNAs (ncRNAs) that can inhibit mRNA synthesis through transcription interference, but the mechanisms are unclear. Gill et al. show that transcription of antisense ncRNAs induces ‘elongation marks’ on histones in promoter regions. These inhibit active nucleosome positioning required to maintain open transcription-initiation sites.

  • In The Blood: Connecting Variant to Function In Human Hematopoiesis.
    Trends Genet. (IF 11.333) Pub Date : 2020-06-10
    Satish K Nandakumar,Xiaotian Liao,Vijay G Sankaran

    Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with a range of human diseases and traits. However, understanding the mechanisms by which these genetic variants have an impact on associated diseases and traits, often referred to as the variant-to-function (V2F) problem, remains a significant hurdle. Solving the V2F challenge requires us to identify causative

  • Chemical Embryology Redux: Metabolic Control of Development.
    Trends Genet. (IF 11.333) Pub Date : 2020-06-09
    Yonghyun Song,Stanislav Y Shvartsman

    New studies of metabolic reactions and networks in embryos are making important additions to regulatory models of development, so far dominated by genes and signals. Metabolic control of development is not a new idea and can be traced back to Joseph Needham's 'Chemical Embryology', published in the 1930s. Even though Needham's ideas fell by the wayside with the advent of genetic studies of embryogenesis

  • Termination of Transcription by RNA Polymerase II: BOOM!
    Trends Genet. (IF 11.333) Pub Date : 2020-06-08
    Joshua D Eaton,Steven West

    RNA polymerase II (Pol II) transcribes hundreds of thousands of transcription units – a reaction always brought to a close by its termination. Because Pol II transcribes multiple gene types, its termination occurs in a variety of ways, with the polymerase being responsive to different inputs. Moreover, it is not just a default process occurring at the end of genes. Promoter-proximal and premature termination

  • Transposable Elements: A Common Feature of Neurodevelopmental and Neurodegenerative Disorders.
    Trends Genet. (IF 11.333) Pub Date : 2020-06-01
    Marie E Jönsson,Raquel Garza,Pia A Johansson,Johan Jakobsson

    The etiology of most neurological disorders is poorly understood and current treatments are largely ineffective. New ideas and concepts are therefore vitally important for future research in this area. This review explores the concept that dysregulation of transposable elements (TEs) contributes to the appearance and pathology of neurodevelopmental and neurodegenerative disorders. Despite TEs making

  • Genetic Variants Affecting Skeletal Morphology in Domestic Dogs.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-30
    Danika L Bannasch,Christine F Baes,Tosso Leeb

    Purebred dog breeds provide a powerful resource for the discovery of genetic variants affecting skeletal morphology. Domesticated and subsequently purebred dogs have undergone strong artificial selection for a broad range of skeletal variation, which include both the size and shapes of their bones. While the phenotypic variation between breeds is high, within-breed morphological variation is typically

  • Unraveling the Epigenetic Basis of Liver Development, Regeneration and Disease.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-30
    Filippo Macchi,Kirsten C Sadler

    A wealth of studies over several decades has revealed an epigenetic prepattern that determines the competence of cellular differentiation in the developing liver. More recently, studies focused on the impact of epigenetic factors during liver regeneration suggest that an epigenetic code in the quiescent liver may establish its regenerative potential. We review work on the pioneer factors and other

  • Facilitating Complex Trait Analysis via Reduced Complexity Crosses.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-29
    Camron D Bryant,Desmond J Smith,Kathleen M Kantak,Thaddeus S Nowak,Robert W Williams,M Imad Damaj,Eva E Redei,Hao Chen,Megan K Mulligan

    Genetically diverse inbred strains are frequently used in quantitative trait mapping to identify sequence variants underlying trait variation. Poor locus resolution and high genetic complexity impede variant discovery. As a solution, we explore reduced complexity crosses (RCCs) between phenotypically divergent, yet genetically similar, rodent substrains. RCCs accelerate functional variant discovery

  • Tracking the Genomic Footprints of SARS-CoV-2 Transmission.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-28
    Tommy Tsan-Yuk Lam

    There is considerable public and scientific interest on the origin, spread and evolution of SARS-CoV-2. A recent study by Lu et al. [1], conducted genomic sequencing and analysis of SARS-CoV-2 in Guangdong, revealing its early transmission out of Hubei and shedding light on the effectiveness of controlling local transmission chains.

  • The Invisible University Is COVID-19 Positive.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-28
    Daniel S Park

    Within the ivory tower, the COVID-19 pandemic stands to disproportionately impact the invisible workforce of postdoctoral researchers. Faced with university closures, hiring freezes and a general lack of support and benefits, an entire generation of Ph.Ds. and their knowledge and skills may be lost to academia without intervention.

  • Taming the Turmoil Within: New Insights on the Containment of Transposable Elements.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-27
    Erin S Kelleher,Daniel A Barbash,Justin P Blumenstiel

    Transposable elements (TEs) are mobile genetic parasites that can exponentially increase their genomic abundance through self-propagation. Classic theoretical papers highlighted the importance of two potentially escalating forces that oppose TE spread: regulated transposition and purifying selection. Here, we review new insights into mechanisms of TE regulation and purifying selection, which reveal

  • Ancient Memories of Seeds: ABA-Dependent Growth Arrest and Reserve Accumulation.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-25
    Hiroyuki Nonogaki,Eri Nishiyama,Kazuhiko Ohshima,Mariko Nonogaki

    Genetic studies of seed maturation regulators, combining transcriptomics and network analysis, suggest the significance of genetic diversification for maturation programs, particularly in seed plants. By contrast, analogs of the maturation programs, such as dormancy and desiccation tolerance, are also found in non-seed plants. It is thus conceivable that seeds recalled or renovated ancient programs

  • SpRY: Engineered CRISPR/Cas9 Harnesses New Genome-Editing Power.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-23
    Dangquan Zhang,Baohong Zhang

    Due to protospacer adjacent motif (PAM) requirements, CRISPR/Cas9 cannot access many genetic loci. A recent study by Walton et al. structurally engineered Streptococcus pyogenes Cas9 (SpCas9) to near-PAMless SpRY that can target most DNA sequences with high editing efficiency and flexibility. This newly engineered SpRY will potentially expand genome-editing capabilities for basic and applied research

  • Deregulated Regulators: Disease-Causing cis Variants in Transcription Factor Genes.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-22
    Robin van der Lee,Solenne Correard,Wyeth W Wasserman

    Whole-genome sequencing is accelerating identification of noncoding variants that disrupt gene expression, although reports of such regulatory variants implicated in disease remain rare. A notable subset of described variants affect transcription factor (TF) genes and other master regulators in cis through dosage effects. From the literature, we compiled 46 regulatory variants linked to 40 TF genes

  • The Y Chromosome as a Battleground for Intragenomic Conflict.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-21
    Doris Bachtrog

    Y chromosomes are typically viewed as genetic wastelands with few intact genes. Recent genomic analyses in Drosophila, however, show that gene gain is prominent on young Y chromosomes. Meiosis- and RNAi-related genes often coamplify on recently formed X and Y chromosomes, are testis-expressed, and produce antisense transcripts and short RNAs. RNAi pathways are also involved in suppressing sex ratio

  • Picking Winners and Losers: Cell Competition in Tissue Development and Homeostasis.
    Trends Genet. (IF 11.333) Pub Date : 2020-05-14
    Wonho Kim,Rajan Jain

    Viable cells with reduced fitness are often eliminated by neighboring cells with greater fitness. This phenomenon, called cell competition, is an important mechanism for maintaining a high-quality population of cells in tissues. Foundational studies characterizing cellular competition and its molecular underpinnings were first carried out utilizing Drosophila as a model system. More recently, competitive

  • Ailurus fulgens (Himalayan Red Panda) and Ailurus styani (Chinese Red Panda).
    Trends Genet. (IF 11.333) Pub Date : 2020-05-07
    Yibo Hu,Arjun Thapa,Fuwen Wei

  • Compensatory Evolution of Gene Expression: (Trends in Genetics, 35, 890-891, 2019).
    Trends Genet. (IF 11.333) Pub Date : 2020-05-05
    Sarah A Signor,Sergey V Nuzhdin

  • Using Genetic and Species Diversity to Tackle Kidney Disease.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-30
    Michael R Garrett,Ron Korstanje

    Progress in the identification of causal genes and understanding of the mechanism underlying kidney disease is hindered by the almost exclusive use of a few animal models with restrictive monogenic backgrounds that may be more resistant to kidney disease compared with humans and, therefore, poor models. Exploring the large genetic diversity in classical animal models, such as mice and rats, and leveraging

  • Enhancer-Promoter Communication: Thinking Outside the TAD.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-23
    Rafael Galupa,Justin Crocker

    How does the folding of the genome relate to the regulation of gene expression? Using fly embryos and quantitative live imaging, a recent study by Yokoshi et al. reveals that the answer might depend on whether enhancer–promoter communication occurs inside or in-between topological domains.

  • Opening the Black Box: Interpretable Machine Learning for Geneticists.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-17
    Christina B Azodi,Jiliang Tang,Shin-Han Shiu

    Because of its ability to find complex patterns in high dimensional and heterogeneous data, machine learning (ML) has emerged as a critical tool for making sense of the growing amount of genetic and genomic data available. While the complexity of ML models is what makes them powerful, it also makes them difficult to interpret. Fortunately, efforts to develop approaches that make the inner workings

  • Quo vadis microRNAs?
    Trends Genet. (IF 11.333) Pub Date : 2020-04-16
    Bastian Fromm,Andreas Keller,Xiaozeng Yang,Marc R Friedlander,Kevin J Peterson,Sam Griffiths-Jones

    Since 2002, published miRNAs have been collected and named by the online repository miRBase. However, with 11 000 annual publications this has become challenging. Recently, four specialized miRNA databases were published, addressing particular needs for diverse scientific communities. This development provides major opportunities for the future of miRNA annotation and nomenclature.

  • The Genomics of Human Local Adaptation.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-15
    Jasmin S Rees,Sergi Castellano,Aida M Andrés

    Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the

  • Are Public Repository Requirements Exacerbating Lack of Diversity?
    Trends Genet. (IF 11.333) Pub Date : 2020-04-14
    Thomas May

    Although public repository requirements are aimed at researchers and designed to ensure that the utility of the limited data we have is optimized, these policies also have ramifications for research participants. In this opinion article, I discuss how the nature of such repositories can subject participants whose data are 'banked' to unwitting participation in scientific projects they might find objectionable

  • Mitonuclear Compensatory Coevolution.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-11
    Geoffrey E Hill

    In bilaterian animals, the mitochondrial genome is small, haploid, does not typically recombine, and is subject to accumulation of deleterious alleles via Muller's ratchet. These basic features of the genomic architecture present a paradox: mutational erosion of these genomes should lead to decline in mitochondrial function over time, yet no such decline is observed. Compensatory coevolution, whereby

  • Repetitive Elements: Different Subtypes Hint at Distinct Functions.
    Trends Genet. (IF 11.333) Pub Date : 2020-04-06
    Zhenyu Zuo,Pedro P Rocha

    Lu et al. report that the association of different repeat types with distinct gene classes goes far beyond what has previously been shown and suggest that such relationship might be essential for gene function and regulation. As an example, they describe how long interspersed nuclear repeat (LINE1) transcripts are recruited together with associated genes to silent nuclear regions.

  • Cohesin Biology: From Passive Rings to Molecular Motors.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-31
    Nina Mayerova,Lubos Cipak,Juraj Gregan

    The loop extrusion hypothesis postulated that extrusion of DNA loops through cohesin rings organizes genomes. Recent findings suggest that cohesin itself is a molecular motor that extrudes DNA. This has important implications not only for the organization of interphase chromatin but also for other processes where cohesin plays vital roles.

  • The Epigenetic Drug Discovery Landscape for Metabolic-associated Fatty Liver Disease.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-28
    Ali Bayoumi,Henning Grønbæk,Jacob George,Mohammed Eslam

    Despite decades of research, effective therapies for metabolic (dysfunction)-associated fatty liver disease (MAFLD) are lacking. An increasing body of evidence suggests that epigenetic dysregulation is frequent in MAFLD, and orchestrates many aspects of its development and progression. Furthermore, the high plasticity of epigenetic modifications in response to environmental cues renders epigenetics

  • New Solutions to Old Problems: Molecular Mechanisms of Meiotic Crossover Control.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-21
    Gerald R Smith,Mridula Nambiar

    During scientific investigations, the explanation of remarkably interesting phenomena must often await development of new methods or accrual of new observations that in retrospect can lead to lucid answers to the initial problem. A case in point is the control of genetic recombination during meiosis, which leads to crossovers between chromosomes critical for production of healthy offspring. Crossovers

  • The Muller's Ratchet and Aging.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-18
    Diddahally R Govindaraju,Hideki Innan,Reiner A Veitia

    Aging entails an irreversible deceleration of physiological processes, altered metabolic activities, and a decline of the integrity of tissues, organs, and organ systems. The accumulation of alterations in the genetic and epigenetic spaces has been proposed as an explanation for aging. They result, at least in part, from DNA replication and chromosome segregation errors due to cell division during

  • Evolutionary Conservation of Transcription Factors Affecting Longevity.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-17
    Guillermo Martínez Corrales,Nazif Alic

    The increasing number of older people is resulting in an increased prevalence of age-related diseases. Research has shown that the ageing process itself is a potential point of intervention. Indeed, gene expression can be optimised for health in older ages through manipulation of transcription factor (TF) activity. This review is focused on the ever-growing number of TFs whose effects on ageing are

  • Catastrophic Endgames: Emerging Mechanisms of Telomere-Driven Genomic Instability.
    Trends Genet. (IF 11.333) Pub Date : 2020-03-13
    Kez Cleal,Duncan M Baird

    When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, hyperactivation of autophagy, and cell death. Recently, it has become apparent that that the resolution of dicentric chromosomes, which arise from telomere

  • Nothobranchius furzeri (African Turquoise Killifish).
    Trends Genet. (IF 11.333) Pub Date : 2020-02-28
    Rongfeng Cui,David Willemsen,Dario Riccardo Valenzano

  • A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-24
    Youqiong Ye,Zhao Zhang,Yaoming Liu,Lixia Diao,Leng Han

    Quantitative trait loci (QTL) analysis is an important approach to investigate the effects of genetic variants identified through an increasing number of large-scale, multidimensional 'omics data sets. In this 'big data' era, the research community has identified a significant number of molecular QTLs (molQTLs) and increased our understanding of their effects. Herein, we review multiple categories

  • The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins
    Trends Genet. (IF 11.333) Pub Date : 2020-02-12
    Bastien Saint-Leandre; Mia T. Levine

    Telomeres ensure chromosome length homeostasis and protection from catastrophic end-to-end chromosome fusions. All eukaryotes require this essential, strictly conserved telomere-dependent genome preservation. However, recent evolutionary analyses of mammals, plants, and flies report pervasive rapid evolution of telomere proteins. The causes of this paradoxical observation – that unconserved machinery

  • On the Molecular Mechanisms Regulating Animal Cell Size Homeostasis.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-20
    Evgeny Zatulovskiy,Jan M Skotheim

    Cell size is fundamental to cell physiology because it sets the scale of intracellular geometry, organelles, and biosynthetic processes. In animal cells, size homeostasis is controlled through two phenomenologically distinct mechanisms. First, size-dependent cell cycle progression ensures that smaller cells delay cell cycle progression to accumulate more biomass than larger cells prior to cell division

  • Citrullus lanatus.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-17
    Shaogui Guo,Honghe Sun,Yong Xu,Zhangjun Fei

  • Advances in the Evolutionary Understanding of MHC Polymorphism.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-07
    Jacek Radwan,Wiesław Babik,Jim Kaufman,Tobias L Lenz,Jamie Winternitz

    Proteins encoded by the classical major histocompatibility complex (MHC) genes incite the vertebrate adaptive immune response by presenting peptide antigens on the cell surface. Here, we review mechanisms explaining landmark features of these genes: extreme polymorphism, excess of nonsynonymous changes in peptide-binding domains, and long gene genealogies. Recent studies provide evidence that these

  • Genetic Variation across Phenotypic Severity of Autism.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-06
    Claudio Toma

    It is still unclear how genetic factors of autism spectrum disorder (ASD) are implicated in the significant clinical heterogeneity ranging from intellectual disability (ID) to high-functioning profiles. Here, evidence from recent genetic studies encompassing common and rare variants are combined to suggest a genetic model that may explain the broad gradient of phenotypic severity observed in ASD.

  • Mouse Systems Genetics as a Prelude to Precision Medicine.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-06
    Hao Li,Johan Auwerx

    Mouse models have been instrumental in understanding human disease biology and proposing possible new treatments. The precise control of the environment and genetic composition of mice allows more rigorous observations, but limits the generalizability and translatability of the results into human applications. In the era of precision medicine, strategies using mouse models have to be revisited to effectively

  • What Is a Transcriptional Burst?
    Trends Genet. (IF 11.333) Pub Date : 2020-02-05
    Edward Tunnacliffe,Jonathan R Chubb

    The idea that gene activity can be discontinuous will not surprise many biologists - many genes are restricted in when and where they can be expressed. Yet during the past 15 years, a collection of observations compiled under the umbrella term 'transcriptional bursting' has received considerable interest. Direct visualization of the dynamics of discontinuous transcription has expanded our understanding

  • Marmota marmota.
    Trends Genet. (IF 11.333) Pub Date : 2020-02-03
    Toni I Gossmann,Markus Ralser

  • A Molecular Investigation of Human Self-Domestication.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-30
    Adam S Wilkins

    The question of whether human beings are like domesticated animals in their behavior has been simultaneously intriguing, hard to define precisely, and seemingly resistant to any kind of scientific test. A recent paper by Zanella et al. reports a molecular-genetic approach to it and provides a provisional 'yes'.

  • Hansel, Gretel, and the Consequences of Failing to Remove Histone Methylation Breadcrumbs.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-29
    Teresa W Lee,David J Katz

    Like breadcrumbs in the forest, cotranscriptionally acquired histone methylation acts as a memory of prior transcription. Because it can be retained through cell divisions, transcriptional memory allows cells to coordinate complex transcriptional programs during development. However, if not reprogrammed properly during cell fate transitions, it can also disrupt cellular identity. In this review, we

  • Advances in Chromatin Imaging at Kilobase-Scale Resolution.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-29
    Alistair Boettiger,Sedona Murphy

    It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that

  • Transcriptional Regulation at DSBs: Mechanisms and Consequences.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-28
    Feras E Machour,Nabieh Ayoub

    Defective double-strand break (DSB) repair leads to genomic instabilities that may augment carcinogenesis. DSBs trigger transient transcriptional silencing in the vicinity of transcriptionally active genes through multilayered processes instigated by Ataxia telangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK), and poly-(ADP-ribose) polymerase 1 (PARP1). Novel factors have been identified

  • Therapeutic Germline Editing: Sense and Sensibility.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-22
    Eli Y Adashi,I Glenn Cohen

    Safe and effective heritable editing of the human genome is years away from the clinic because of formidable technical, statutory, regulatory, and societal challenges. In particular, we note the fledgling state of the science, the imperatives of editing efficiency, specificity, and uniformity, and the extant legal roadblock.

  • Clonal Reproduction through Seeds in Sight for Crops.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-20
    Peggy Ozias-Akins,Joann A Conner

    Apomixis or asexual reproduction through seeds, enables the preservation of hybrid vigor. Hybrids are heterozygous and segregate for genotype and phenotype upon sexual reproduction. While apomixis, that is, clonal reproduction, is intuitively antithetical to diversity, it is rarely obligate and actually provides a mechanism to recover and maintain superior hybrid gene combinations for which sexual

  • Molecular Mechanisms Driving mRNA Degradation by m6A Modification.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-18
    Yujin Lee,Junho Choe,Ok Hyun Park,Yoon Ki Kim

    N6-Methyladenosine (m6A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m6A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein

  • Pisum sativum (Pea).
    Trends Genet. (IF 11.333) Pub Date : 2020-01-17
    Judith Burstin,Jonathan Kreplak,Jiří Macas,Judith Lichtenzveig

  • From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-15
    Hussein A Hejase,Noah Dukler,Adam Siepel

    Methods to detect signals of natural selection from genomic data have traditionally emphasized the use of simple summary statistics. Here, we review a new generation of methods that consider combinations of conventional summary statistics and/or richer features derived from inferred gene trees and ancestral recombination graphs (ARGs). We also review recent advances in methods for population genetic

  • Flipping Shells! Unwinding LR Asymmetry in Mirror-Image Molluscs.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-14
    Angus Davison

    In seeking to understand the establishment of left-right (LR) asymmetry, a limiting factor is that most animals are ordinarily invariant in their asymmetry, except when manipulated or mutated. It is therefore surprising that the wider scientific field does not appear to fully appreciate the remarkable fact that normal development in molluscs, especially snails, can flip between two chiral types without

  • Small RNAs in the Transgenerational Inheritance of Epigenetic Information.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-14
    Lea Duempelmann,Merle Skribbe,Marc Bühler

    In recent years it has become evident that RNA interference-related mechanisms can mediate the deposition and transgenerational inheritance of specific chromatin modifications in a truly epigenetic fashion. Rapid progress has been made in identifying the RNAi effector proteins and how they work together to confer long-lasting epigenetic responses, and initial studies hint at potential physiological

  • Omics in Neurodegenerative Disease: Hope or Hype?
    Trends Genet. (IF 11.333) Pub Date : 2020-01-10
    Maria E Diaz-Ortiz,Alice S Chen-Plotkin

    The past 15 years have seen a boom in the use and integration of 'omic' approaches (limited here to genomic, transcriptomic, and epigenomic techniques) to study neurodegenerative disease in an unprecedented way. We first highlight advances in and the limitations of using such approaches in the neurodegenerative disease literature, with a focus on Alzheimer's disease (AD), Parkinson's disease (PD),

  • Silencers, Enhancers, and the Multifunctional Regulatory Genome.
    Trends Genet. (IF 11.333) Pub Date : 2020-01-07
    Marc S Halfon

    Negative regulation of gene expression by transcriptional silencers has been difficult to study due to limited defined examples. A new study by Gisselbrecht et al. has dramatically increased the number of identified silencers and reveals that they are bifunctional regulatory sequences that also act as gene expression-promoting enhancers.

  • Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications.
    Trends Genet. (IF 11.333) Pub Date : 2019-12-24
    Agnieszka A Golicz,Philipp E Bayer,Prem L Bhalla,Jacqueline Batley,David Edwards

    The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed

  • Unknown to Known: Advancing Knowledge of Coral Gene Function.
    Trends Genet. (IF 11.333) Pub Date : 2019-12-24
    Phillip A Cleves,Alexander Shumaker,JunMo Lee,Hollie M Putnam,Debashish Bhattacharya

    Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation

  • Ubiquitously Expressed Proteins and Restricted Phenotypes: Exploring Cell-Specific Sensitivities to Impaired tRNA Charging.
    Trends Genet. (IF 11.333) Pub Date : 2019-12-12
    Molly E Kuo,Anthony Antonellis

    Aminoacyl-tRNA synthetases (ARS) are ubiquitously expressed, essential enzymes that charge tRNA with cognate amino acids. Variants in genes encoding ARS enzymes lead to myriad human inherited diseases. First, missense alleles cause dominant peripheral neuropathy. Second, missense, nonsense, and frameshift alleles cause recessive multisystem disorders that differentially affect tissues depending on

  • New Roles for Canonical Transcription Factors in Repeat Expansion Diseases.
    Trends Genet. (IF 11.333) Pub Date : 2019-12-11
    Lindsey D Goodman,Nancy M Bonini

    The presence of microsatellite repeat expansions within genes is associated with >30 neurological diseases. Of interest, (GGGGCC)>30-repeats within C9orf72 are associated with amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These expansions can be 100s to 1000s of units long. Thus, it is perplexing how RNA-polymerase II (RNAPII) can successfully transcribe them. Recent investigations

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