Advances in the Evolutionary Understanding of MHC Polymorphism.
Abstract 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 features may arise due to pathogens evolving ways to evade immune response guided by the locally common MHC alleles. However, complexities of selection on MHC genes are simultaneously being revealed that need t...
Source: Trends in Genetics : TIG - February 7, 2020 Category: Genetics & Stem Cells Authors: Radwan J, Babik W, Kaufman J, Lenz TL, Winternitz J Tags: Trends Genet Source Type: research

Genetic Variation across Phenotypic Severity of Autism.
Abstract 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. PMID: 32037010 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 6, 2020 Category: Genetics & Stem Cells Authors: Toma C Tags: Trends Genet Source Type: research

Mouse Systems Genetics as a Prelude to Precision Medicine.
Abstract 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 emulate human populations. Systems genetics is one promising paradigm that may promote the transition to novel precision medicine strategies. Here, we review the state-of-the-art resources and discuss...
Source: Trends in Genetics : TIG - February 6, 2020 Category: Genetics & Stem Cells Authors: Li H, Auwerx J Tags: Trends Genet Source Type: research

What Is a Transcriptional Burst?
Abstract 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 of basic transcriptional mechanisms and their regulation and provides a real-time readout of gene activity during the life of a cell. In this review, we try to reconcile the different views of the transcrip...
Source: Trends in Genetics : TIG - February 5, 2020 Category: Genetics & Stem Cells Authors: Tunnacliffe E, Chubb JR Tags: Trends Genet Source Type: research

Marmota marmota.
PMID: 32029288 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 3, 2020 Category: Genetics & Stem Cells Authors: Gossmann TI, Ralser M Tags: Trends Genet Source Type: research

A Molecular Investigation of Human Self-Domestication.
Abstract 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'. PMID: 32008870 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - January 30, 2020 Category: Genetics & Stem Cells Authors: Wilkins AS Tags: Trends Genet Source Type: research

Hansel, Gretel, and the Consequences of Failing to Remove Histone Methylation Breadcrumbs.
Abstract 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 discuss the consequences of failure to reprogram histone methylation during three crucial epigenetic reprogramming windows: maternal reprogramming at fertilization, embryonic stem cell (ESC) differentiation, an...
Source: Trends in Genetics : TIG - January 29, 2020 Category: Genetics & Stem Cells Authors: Lee TW, Katz DJ Tags: Trends Genet Source Type: research

Advances in Chromatin Imaging at Kilobase-Scale Resolution.
Abstract 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 regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an indi...
Source: Trends in Genetics : TIG - January 29, 2020 Category: Genetics & Stem Cells Authors: Boettiger A, Murphy S Tags: Trends Genet Source Type: research

Transcriptional Regulation at DSBs: Mechanisms and Consequences.
Abstract 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 that ensure DSB-induced silencing via two distinct pathways: direct inhibition of RNA Polymerase II (Pol II) mediated by negative elongation factor (NELF), and histone code editing by CDYL1 and histone deac...
Source: Trends in Genetics : TIG - January 27, 2020 Category: Genetics & Stem Cells Authors: Machour FE, Ayoub N Tags: Trends Genet Source Type: research

Therapeutic Germline Editing: Sense and Sensibility.
Abstract 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. PMID: 31982142 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - January 22, 2020 Category: Genetics & Stem Cells Authors: Adashi EY, Cohen IG Tags: Trends Genet Source Type: research

Clonal Reproduction through Seeds in Sight for Crops.
Abstract 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 reproduction would reveal deleterious alleles in less fit genotypes. Apomixis, widespread across flowering plant orders, does not occur in major crop species, yet its introduction could add a valuable tool to th...
Source: Trends in Genetics : TIG - January 20, 2020 Category: Genetics & Stem Cells Authors: Ozias-Akins P, Conner JA Tags: Trends Genet Source Type: research

Molecular Mechanisms Driving mRNA Degradation by m6A Modification.
Abstract 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 2 (YTHDF2; an m6A reader protein)-CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2-HRSP12-ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m...
Source: Trends in Genetics : TIG - January 18, 2020 Category: Genetics & Stem Cells Authors: Lee Y, Choe J, Park OH, Kim YK Tags: Trends Genet Source Type: research

Pisum sativum (Pea).
PMID: 31959367 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - January 17, 2020 Category: Genetics & Stem Cells Authors: Burstin J, Kreplak J, Macas J, Lichtenzveig J Tags: Trends Genet Source Type: research

From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection.
Abstract 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 simulation and ARG reconstruction. Finally, we describe opportunities for future work on a variety of related topics, including the genetics of speciation, estimation of selection coefficients, and inference o...
Source: Trends in Genetics : TIG - January 15, 2020 Category: Genetics & Stem Cells Authors: Hejase HA, Dukler N, Siepel A Tags: Trends Genet Source Type: research

Flipping Shells! Unwinding LR Asymmetry in Mirror-Image Molluscs.
Abstract 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 pathology. Here, I describe recent progress in understanding the evolution, development, and genetics of chiral variation in snails, and place it in context with other animals. I argue that the natural vari...
Source: Trends in Genetics : TIG - January 14, 2020 Category: Genetics & Stem Cells Authors: Davison A Tags: Trends Genet Source Type: research

Small RNAs in the Transgenerational Inheritance of Epigenetic Information.
r M Abstract 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 relevance of such regulation. In this review, we highlight mechanistic studies in model organisms that advance our understanding of how small RNAs trigger long-lasting epigenetic changes in gene expression ...
Source: Trends in Genetics : TIG - January 14, 2020 Category: Genetics & Stem Cells Authors: Duempelmann L, Skribbe M, Bühler M Tags: Trends Genet Source Type: research

Omics in Neurodegenerative Disease: Hope or Hype?
Abstract 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), frontotemporal lobar degeneration (FTLD), and amyotrophic lateral sclerosis (ALS). We next discuss how these studies can advance human health in the form of generating leads for downstream mechanistic investigat...
Source: Trends in Genetics : TIG - January 10, 2020 Category: Genetics & Stem Cells Authors: Diaz-Ortiz ME, Chen-Plotkin AS Tags: Trends Genet Source Type: research

Silencers, Enhancers, and the Multifunctional Regulatory Genome.
Abstract 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. PMID: 31918861 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - January 7, 2020 Category: Genetics & Stem Cells Authors: Halfon MS Tags: Trends Genet Source Type: research

Unknown to Known: Advancing Knowledge of Coral Gene Function.
Abstract 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. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown gene...
Source: Trends in Genetics : TIG - December 24, 2019 Category: Genetics & Stem Cells Authors: Cleves PA, Shumaker A, Lee J, Putnam HM, Bhattacharya D Tags: Trends Genet Source Type: research

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications.
Abstract 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 construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely ...
Source: Trends in Genetics : TIG - December 24, 2019 Category: Genetics & Stem Cells Authors: Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D Tags: Trends Genet Source Type: research

Ubiquitously Expressed Proteins and Restricted Phenotypes: Exploring Cell-Specific Sensitivities to Impaired tRNA Charging.
Abstract 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 which ARS is mutated. A preponderance of evidence has shown that both phenotypic classes are associated with loss-of-function alleles, suggesting that tRNA charging plays a central role in disease pathogenesis. ...
Source: Trends in Genetics : TIG - December 12, 2019 Category: Genetics & Stem Cells Authors: Kuo ME, Antonellis A Tags: Trends Genet Source Type: research

New Roles for Canonical Transcription Factors in Repeat Expansion Diseases.
Abstract 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 focusing on GGGGCC-transcription have identified specific, canonical complexes that may promote RNAPII-transcription at these GC-rich microsatellites: the DSIF complex and PAF1C. These complexes may ...
Source: Trends in Genetics : TIG - December 11, 2019 Category: Genetics & Stem Cells Authors: Goodman LD, Bonini NM Tags: Trends Genet Source Type: research

Rosa spp.
PMID: 31836193 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - December 10, 2019 Category: Genetics & Stem Cells Authors: Just J, Bendahmane M Tags: Trends Genet Source Type: research

Emerging Role of C/EBP β and Epigenetic DNA Methylation in Ageing.
Emerging Role of C/EBPβ and Epigenetic DNA Methylation in Ageing. Trends Genet. 2019 Dec 07;: Authors: Niehrs C, Calkhoven CF Abstract Changes in epigenetic DNA methylation are the most promising predictor of biological age and lifespan in humans, but whether methylation changes affect ageing is unresolved. Here, we discuss converging data, which indicate that one mode by which aberrant DNA methylation can affect ageing is via CCAAT/enhancer binding protein beta (C/EBPβ). This basic leucine-zipper (bZIP) transcription factor is controlled by the lifespan regulator mechanistic/mammalian targe...
Source: Trends in Genetics : TIG - December 7, 2019 Category: Genetics & Stem Cells Authors: Niehrs C, Calkhoven CF Tags: Trends Genet Source Type: research

The Bivalent Genome: Characterization, Structure, and Regulation.
Di Croce L Abstract An intricate molecular machinery is at the core of gene expression regulation in every cell. During the initial stages of organismal development, the coordinated activation of diverse transcriptional programs is crucial and must be carefully executed to shape every organ and tissue. Bivalent promoters and poised enhancers are regulatory regions decorated with histone marks that are associated with both positive and negative transcriptional outcomes. These apparently contradictory signals are important for setting bivalent genes in a poised state, which is subsequently resolved during different...
Source: Trends in Genetics : TIG - December 6, 2019 Category: Genetics & Stem Cells Authors: Blanco E, González-Ramírez M, Alcaine-Colet A, Aranda S, Di Croce L Tags: Trends Genet Source Type: research

The Biogenesis and Precise Control of RNA m6A Methylation.
Abstract N6-Methyladenosine (m6A) is the most prevalent internal RNA modification in mRNA, and has been found to be highly conserved and hard-coded in mammals and other eukaryotic species. The importance of m6A for gene expression regulation and cell fate decisions has been well acknowledged in the past few years. However, it was only until recently that the mechanisms underlying the biogenesis and specificity of m6A modification in cells were uncovered. We review up-to-date knowledge on the biogenesis of the RNA m6A modification, including the cis-regulatory elements and trans-acting factors that determine genera...
Source: Trends in Genetics : TIG - December 3, 2019 Category: Genetics & Stem Cells Authors: Huang H, Weng H, Chen J Tags: Trends Genet Source Type: research

Population Genetics in the Human Microbiome.
Abstract While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population geneti...
Source: Trends in Genetics : TIG - November 25, 2019 Category: Genetics & Stem Cells Authors: Garud NR, Pollard KS Tags: Trends Genet Source Type: research

Asymmetric Histone Inheritance in Asymmetrically Dividing Stem Cells.
Abstract Epigenetic mechanisms play essential roles in determining distinct cell fates during the development of multicellular organisms. Histone proteins represent crucial epigenetic components that help specify cell identities. Previous work has demonstrated that during the asymmetric cell division of Drosophila male germline stem cells (GSCs), histones H3 and H4 are asymmetrically inherited, such that pre-existing (old) histones are segregated towards the self-renewing GSC whereas newly synthesized (new) histones are enriched towards the differentiating daughter cell. In order to further understand the mol...
Source: Trends in Genetics : TIG - November 18, 2019 Category: Genetics & Stem Cells Authors: Wooten M, Ranjan R, Chen X Tags: Trends Genet Source Type: research

Endogenous Retroviruses and the Pregnancy Compensation Hypothesis: A Reply to David.
PMID: 31753529 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - November 18, 2019 Category: Genetics & Stem Cells Authors: Natri H, Garcia AR, Buetow KH, Trumble BC, Wilson MA Tags: Trends Genet Source Type: research

Evolution of Immune Sexual Dimorphism in Response to Placental Invasiveness: A  Response to Natri et al.
Evolution of Immune Sexual Dimorphism in Response to Placental Invasiveness: A Response to Natri et al. Trends Genet. 2019 Nov 18;: Authors: Greenbaum S, Greenbaum G PMID: 31753530 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - November 18, 2019 Category: Genetics & Stem Cells Authors: Greenbaum S, Greenbaum G Tags: Trends Genet Source Type: research

Ailuropoda melanoleuca (Giant Panda).
PMID: 31727389 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - November 11, 2019 Category: Genetics & Stem Cells Authors: Wei F, Fan H, Hu Y Tags: Trends Genet Source Type: research

Evolution of Immune Sexual Dimorphism in Response to Placental Invasiveness: A Reply to Greenbaum and Greenbaum.
PMID: 31718808 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - November 9, 2019 Category: Genetics & Stem Cells Authors: Garcia AR, Natri H, Buetow KH, Trumble BC, Wilson MA Tags: Trends Genet Source Type: research

Evolution of Epistatic Networks and the Genetic Basis of Innate Behaviors.
Abstract Instinctive behaviors are genetically programmed behaviors that occur independent of experience. How genetic programs that give rise to the manifestation of such behaviors evolve remains an unresolved question. I propose that evolution of species-specific innate behaviors is accomplished through progressive modifications of pre-existing genetic networks composed of allelic variants. I hypothesize that changes in frequencies of one or more constituent allelic variants within the network leads to changes in gene network connectivity and the emergence of a reorganized network that can support the emergence o...
Source: Trends in Genetics : TIG - November 7, 2019 Category: Genetics & Stem Cells Authors: Anholt RRH Tags: Trends Genet Source Type: research

Endogenous Retroviruses and the Pregnancy Compensation Hypothesis: A Response to Natri et  al.
Endogenous Retroviruses and the Pregnancy Compensation Hypothesis: A Response to Natri et al. Trends Genet. 2019 Nov 06;: Authors: David MD PMID: 31706689 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - November 6, 2019 Category: Genetics & Stem Cells Authors: David MD Tags: Trends Genet Source Type: research

Evolvability Costs of Niche Expansion.
Abstract What prevents generalists from displacing specialists, despite obvious competitive advantages of utilizing a broad niche? The classic genetic explanation is antagonistic pleiotropy: genes underlying the generalism produce 'jacks-of-all-trades' that are masters of none. However, experiments challenge this assumption that mutations enabling niche expansion must reduce fitness in other environments. Theory suggests an alternative cost of generalism: decreased evolvability, or the reduced capacity to adapt. Generalists using multiple environments experience relaxed selection in any one environment, producing ...
Source: Trends in Genetics : TIG - November 4, 2019 Category: Genetics & Stem Cells Authors: Bono LM, Draghi JA, Turner PE Tags: Trends Genet Source Type: research

Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?
Abstract Our recent ability to sequence entire genomes, along with all of their transcribed RNAs, has led to the surprising finding that only ∼1% of the human genome is used to encode proteins. This finding has led to vigorous debate over the functional importance of the transcribed but untranslated portions of the genome. Currently, scientists tend to assume coding genes are functional until proven not to be, while the opposite is true for noncoding genes. This review takes a new look at the evidence for and against widespread noncoding gene functionality. We focus in particular on long noncoding RNA (no...
Source: Trends in Genetics : TIG - October 26, 2019 Category: Genetics & Stem Cells Authors: Lee H, Zhang Z, Krause HM Tags: Trends Genet Source Type: research

The Selfishness of Law-Abiding Genes.
Abstract Selfish genes were once controversial, but it is now accepted that the genome contains parasitic elements in addition to a complement of conventional genes. This opinion article argues that 'law-abiding' genes also indulge in game playing to ensure their propagation, so that initially nonessential processes secure a genetic heritage. A gene-centered view of this kind can help to explain otherwise puzzling aspects of biology, including the complexity and stability of living systems. PMID: 31662191 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 26, 2019 Category: Genetics & Stem Cells Authors: Bird A Tags: Trends Genet Source Type: research

The Editor's I on Disease Development.
Abstract Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventin...
Source: Trends in Genetics : TIG - October 22, 2019 Category: Genetics & Stem Cells Authors: Jain M, Jantsch MF, Licht K Tags: Trends Genet Source Type: research

Compensatory Evolution of Gene Expression.
PMID: 31645272 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 20, 2019 Category: Genetics & Stem Cells Authors: Signor SA, Nuzhdin SV Tags: Trends Genet Source Type: research

Saccharomyces cerevisiae.
PMID: 31630852 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 17, 2019 Category: Genetics & Stem Cells Authors: Belda I, Ruiz J, Santos A, Van Wyk N, Pretorius IS Tags: Trends Genet Source Type: research

Many Ways to Build a Polyp.
Abstract The freshwater cnidarian Hydra has been studied for centuries for its unique regenerative capacities. Whole-body single-cell transcriptomics now reveal cellular lineages and gene regulatory networks that build the Hydra polyp. For the first time, transcription factor signatures allow direct comparison of the polyp body plan between Hydra and sea anemone. PMID: 31629552 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 16, 2019 Category: Genetics & Stem Cells Authors: Arendt D Tags: Trends Genet Source Type: research

Gene Regulation Knows Its Boundaries.
Abstract The genome is folded nonrandomly inside the cell nucleus. How this contributes to gene regulation is an important subject of investigation. A new study by Despang et al. shows how the spatial segregation of genes and regulatory regions can influence developmental expression in subtle, but critical ways. PMID: 31623870 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 14, 2019 Category: Genetics & Stem Cells Authors: de Wit E Tags: Trends Genet Source Type: research

Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?
Abstract Next-generation sequencing (NGS) technologies have changed the landscape of genetic testing in rare diseases. However, the rapid evolution of NGS technologies has outpaced its clinical adoption. Here, we re-evaluate the critical steps in the clinical application of NGS-based genetic testing from an informatics perspective. We suggest a 'fit-for-purpose' triage of current NGS technologies. We also point out potential shortcomings in the clinical management of genetic variants and offer ideas for potential improvement. We specifically emphasize the importance of ensuring the accuracy and reproducibility of ...
Source: Trends in Genetics : TIG - October 14, 2019 Category: Genetics & Stem Cells Authors: Liu Z, Zhu L, Roberts R, Tong W Tags: Trends Genet Source Type: research

Landscape of Noncoding RNA in Prostate Cancer.
Abstract The transcriptome of prostate cancer is highly heterogeneous, with noncoding transcripts being essential players. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are two unique classes of noncoding RNA drawing increasing attention. Biologically, they have intriguing properties with important regulatory functions. Clinically, they present as promising biomarkers and therapeutic targets. Recent advancements in technologies have opened up new directions for noncoding RNA research, which include RNA-protein interaction, RNA secondary structure, and spatial transcriptomics. Furthermore, recent work ...
Source: Trends in Genetics : TIG - October 14, 2019 Category: Genetics & Stem Cells Authors: Hua JT, Chen S, He HH Tags: Trends Genet Source Type: research

New Gene Origin and Deep Taxon Phylogenomics: Opportunities and Challenges.
RJ Abstract The immense morphological and phenotypic diversity within eukaryotes coincides with large-scale differences in genic repertoires, including the presence of thousands of new genes in every genome. New genes arise through duplication and divergence of existing coding sequences or de novo from noncoding sequences. These processes together cause individual genomes to contain up to one-third of orphan genes without any detectable homology in other lineages. Recently, deep taxon phylogenomics, the genome comparisons of extremely closely related species, provided novel insight into the evolutionary dynamics ...
Source: Trends in Genetics : TIG - October 11, 2019 Category: Genetics & Stem Cells Authors: Rödelsperger C, Prabh N, Sommer RJ Tags: Trends Genet Source Type: research

De Novo Mutations Reflect Development and Aging of the Human Germline.
Abstract Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life. PMID: 31610893 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 11, 2019 Category: Genetics & Stem Cells Authors: Goldmann JM, Veltman JA, Gilissen C Tags: Trends Genet Source Type: research

Apis mellifera.
PMID: 31606268 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 9, 2019 Category: Genetics & Stem Cells Authors: Webster MT Tags: Trends Genet Source Type: research

De novo DNA Methylation: Who's Your DADdy?
Abstract DNA methylation regulates the organization and function of the genome. Yamanaka et al. now report that de novo methylation of male germ cells of mice involves the transient opening of heterochromatin at megabase-size differentially accessible domains (DADs). This chromatin remodeling likely facilitates de novo methylation of the germ cell genome. PMID: 31597610 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 6, 2019 Category: Genetics & Stem Cells Authors: Tharp ME, Bortvin A Tags: Trends Genet Source Type: research

Subcellular Heterogeneity of the microRNA Machinery.
PMID: 31597611 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - October 6, 2019 Category: Genetics & Stem Cells Authors: Trabucchi M, Mategot R Tags: Trends Genet Source Type: research

Surviving Telomere Attrition with the MiDAS Touch.
Abstract Cancer cells maintain telomere lengths through telomerase activity or by alternative lengthening of telomeres (ALT). Using an engineered model system, a recent study by Min et al. reveals that the combination of BLM-mediated DNA resection and telomere clustering, a characteristic of ALT telomeres, catalyzes RAD52-dependent mitotic DNA synthesis (MiDAS) specifically at telomeres to drive ALT activity. PMID: 31526614 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - September 13, 2019 Category: Genetics & Stem Cells Authors: Flynn RL, Heaphy CM Tags: Trends Genet Source Type: research