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  • 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

  • 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

  • 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

  • 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

  • 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.

  • Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-29
    Yang Li,Anjun Ma,Ewy A Mathé,Lang Li,Bingqiang Liu,Qin Ma

    Single-cell multimodal omics (scMulti-omics) technologies have made it possible to trace cellular lineages during differentiation and to identify new cell types in heterogeneous cell populations. The derived information is especially promising for computing cell-type-specific biological networks encoded in complex diseases and improving our understanding of the underlying gene regulatory mechanisms

  • 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.

  • Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-29
    Richard C Centore,Gabriel J Sandoval,Luis Miguel Mendes Soares,Cigall Kadoch,Ho Man Chan

    Small molecule-based targeting of chromatin regulatory factors has emerged as a promising therapeutic strategy in recent years. The development and ongoing clinical evaluation of novel agents targeting a range of chromatin regulatory processes, including DNA or histone modifiers, histone readers, and chromatin regulatory protein complexes, has inspired the field to identify and act upon the full compendium

  • 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

  • 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

  • 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.

  • Challenges of Genetic Data Sharing in African Studies.
    Trends Genet. (IF 11.333) Pub Date : 2020-08-14
    Catherine M Stein

    Data sharing is a valuable aspect of science and required by most funding bodies and journals. However, the national regulatory guidelines of many African nations do not explicitly allow for broad genetic data sharing. Given these restrictions, there is a need to reconsider these policies and propose creative solutions.

  • 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

  • Genetics Needs Non-geneticists.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-24
    Chris P Ponting

    Answering genetics’ big data questions often needs an interdisciplinary team whose members freely share their diverse expertise in analysis, statistics, and computation. Sharing requires mutual trust and open acknowledgement of strengths and weaknesses, including those of established geneticists. Only then will newcomers to genetics contribute far beyond their entry-level expectations.

  • The Claims of Biospecimen Donors to Credit and Compensation.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-10
    David S Wendler

    The biorights movement argues that current treatment of biospecimen donors is unfair. To evaluate this claim, the present Science & Society article identifies the standards used to determine credit and compensation in research, and applies them to donors. This analysis suggests most donors deserve credit and, contrary to current practice, some deserve compensation.

  • MOF Histone Acetyltransferase in Blood Cell Development.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-03
    Yasmin Serina Secanechia,Christophe Lancrin

    Gene expression is regulated by transcription factors (TFs) and chromatin modifiers such as histone acetyltransferases (HATs). Pessoa Rodrigues et al. revealed the role of the Males absent on the first (MOF) HAT in hematopoietic stem cell (HSC) differentiation into red blood cells. This work raises interesting questions about how MOF controls other hematopoietic differentiation processes.

  • 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.

  • Relaxed Selection and the Rapid Evolution of Reproductive Genes.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-23
    Amy L Dapper,Michael J Wade

    Evolutionary genomic studies find that reproductive protein genes, those directly involved in reproductive processes, diversify more rapidly than most other gene categories. Strong postcopulatory sexual selection acting within species is the predominant hypothesis proposed to account for the observed pattern. Recently, relaxed selection due to sex-specific gene expression has also been put forward

  • Genetics and Epigenetics of Sex Bias: Insights from Human Cancer and Autoimmunity.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-28
    Sara Carmela Credendino,Christoph Neumayer,Irene Cantone

    High-throughput sequencing and genome-wide association studies have revealed a sex bias in human diseases. The underlying molecular mechanisms remain, however, unknown. Here, we cover recent advances in cancer and autoimmunity focusing on intrinsic genetic and epigenetic differences underlying sex biases in human disease. These studies reveal a central role of genome regulatory mechanisms including

  • 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

  • Transcriptional and Epigenetic Regulation of Autophagy in Plants.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-13
    Chao Yang,Ming Luo,Xiaohong Zhuang,Faqiang Li,Caiji Gao

    Autophagy, a highly conserved quality control mechanism, is essential for maintaining cellular homeostasis and healthy growth of plants. Compared with extensive research in the cytoplasmic control of autophagy, studies regarding the nuclear events involved in the regulation of plant autophagy are just beginning to emerge. Accumulating evidence reveals a coordinated expression of plant autophagy genes

  • Monarch Butterfly Migration Moving into the Genetic Era.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-24
    Christine Merlin,Samantha E Iiams,Aldrin B Lugena

    The genetic architecture and neurogenetics of animal migration remain poorly understood. With a sequenced genome and the establishment of reverse genetic tools, the monarch butterfly has emerged as a promising model to uncover the genetic basis of migratory behavior and associated traits. Here, we synthesize major advances made in the genetics of monarch migration, which includes the discovery of genomic

  • Mitochondrial Diseases: A Diagnostic Revolution.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-13
    Katherine R Schon,Thiloka Ratnaike,Jelle van den Ameele,Rita Horvath,Patrick F Chinnery

    Mitochondrial disorders have emerged as a common cause of inherited disease, but are traditionally viewed as being difficult to diagnose clinically, and even more difficult to comprehensively characterize at the molecular level. However, new sequencing approaches, particularly whole-genome sequencing (WGS), have dramatically changed the landscape. The combined analysis of nuclear and mitochondrial

  • 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 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 COVID-19 infection is strongly suspected.

  • 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

  • Naja naja (Indian Cobra).
    Trends Genet. (IF 11.333) Pub Date : 2020-08-04
    Kushal Suryamohan,Somasekar Seshagiri

  • The Role of Noncoding Variants in Heritable Disease.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-31
    J D French,S L Edwards

    The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common

  • Positive and Negative Regulation of DNA Replication Initiation.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-29
    Qiliang Ding,Amnon Koren

    Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation

  • Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-23
    Patroula Nathanailidou,Stavros Taraviras,Zoi Lygerou

    In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication

  • Molecular Clocks without Rocks: New Solutions for Old Problems.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-22
    George P Tiley,Jelmer W Poelstra,Mario Dos Reis,Ziheng Yang,Anne D Yoder

    Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies

  • Equity in Health: Consideration of Race and Ethnicity in Precision Medicine.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-22
    Todd L Edwards,Joseph Breeyear,Jacqueline A Piekos,Digna R Velez Edwards

    The causes for disparities in implementation of precision medicine are complex, due in part to differences in clinical care and a lack of engagement and recruitment of under-represented populations in studies. New tools and large genetic cohorts can change these circumstances and build access to personalized medicine for disadvantaged populations.

  • Be the Change You Wish to See.
    Trends Genet. (IF 11.333) Pub Date : 2020-07-14
    Sonia Muliyil

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

    Within the ivory tower of academia, the coronavirus disease 2019 (COVID-19) pandemic stands to disproportionately impact the invisible workforce of postdoctoral researchers (postdocs). Faced with university closures, hiring freezes, and a general lack of support and benefits, an entire generation of postdocs and their knowledge and skills may be lost to academia without intervention.

  • 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 in the origin, spread, and evolution of SARS-CoV-2. Lu et al. recently 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.

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Nymphaea colorata (Blue-Petal Water Lily).
    Trends Genet. (IF 11.333) Pub Date : 2020-07-03
    Haibao Tang,Liangsheng Zhang,Fei Chen,Xingtan Zhang,Feng Chen,Hong Ma,Yves Van de Peer

  • Is CpG Density the Link between Epigenetic Aging and Lifespan?
    Trends Genet. (IF 11.333) Pub Date : 2020-07-02
    Emily M Bertucci,Benjamin B Parrott

    The genetic mechanisms contributing to lifespan variation remain unresolved. Based on recent conceptual advances in our understanding of epigenetic potential and the relocalization of chromatin modifiers (RCM), we hypothesize that increased CpG density is protective against age-related erosion of the epigenetic landscape and may explain interspecific variation in lifespan.

  • 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

  • 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

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