Insights into the Relationship between Nucleolar Stress and the NF-κB Pathway
Publication date: Available online 19 August 2019Source: Trends in GeneticsAuthor(s): Jingyu Chen, Lesley A. StarkThe nuclear organelle the nucleolus and the transcription factor nuclear factor of κ-light-chain-enhancer of activated B cells (NF-κB) are both central to the control of cellular homeostasis, dysregulated in common diseases and implicated in the ageing process. Until recently, it was believed that they acted independently to regulate homeostasis in health and disease. However, there is an emerging body of evidence suggesting that nucleoli and NF-κB signalling converge at multiple levels. Here ...
Source: Trends in Genetics - August 19, 2019 Category: Genetics & Stem Cells Source Type: research

Haploid Induction and Genome Instability
Publication date: Available online 14 August 2019Source: Trends in GeneticsAuthor(s): Luca Comai, Ek Han TanThe advent of affordable, large-scale DNA sequencing methods, coupled with advanced computing power, is empowering a detailed analysis of the structure and function of chromosomes. Genomic instability, involving chromosome number and structure changes, has been documented in multiple systems. In plants, haploid induction through genome elimination has recently been connected mechanistically to the formation of complex chromosome reorganizations, known collectively as chromoanagenesis. These abnormalities can be trigg...
Source: Trends in Genetics - August 16, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: September 2019Source: Trends in Genetics, Volume 35, Issue 9Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - August 13, 2019 Category: Genetics & Stem Cells Source Type: research

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Publication date: September 2019Source: Trends in Genetics, Volume 35, Issue 9Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - August 13, 2019 Category: Genetics & Stem Cells Source Type: research

DNA Methylation: Shared and Divergent Features across Eukaryotes
Publication date: Available online 6 August 2019Source: Trends in GeneticsAuthor(s): Robert J. Schmitz, Zachary A. Lewis, Mary G. GollChemical modification of nucleotide bases in DNA provides one mechanism for conveying information in addition to the genetic code. 5-methylcytosine (5mC) represents the most common chemically modified base in eukaryotic genomes. Sometimes referred to simply as DNA methylation, in eukaryotes 5mC is most prevalent at CpG dinucleotides and is frequently associated with transcriptional repression of transposable elements. However, 5mC levels and distributions are variable across phylogenies, and...
Source: Trends in Genetics - August 7, 2019 Category: Genetics & Stem Cells Source Type: research

Mechanisms of rDNA Copy Number Maintenance
Publication date: Available online 5 August 2019Source: Trends in GeneticsAuthor(s): Jonathan O. Nelson, George J. Watase, Natalie Warsinger-Pepe, Yukiko M. YamashitarDNA, the genes encoding the RNA components of ribosomes (rRNA), are highly repetitive in all eukaryotic genomes, containing 100s to 1000s of copies, to meet the demand for ribosome biogenesis. rDNA genes are arranged in large stretches of tandem repeats, forming loci that are highly susceptible to copy loss due to their repetitiveness and active transcription throughout the cell cycle. Despite this inherent instability, rDNA copy number is generally maintaine...
Source: Trends in Genetics - August 6, 2019 Category: Genetics & Stem Cells Source Type: research

Ribosomopathies: Old Concepts, New Controversies
Publication date: Available online 31 July 2019Source: Trends in GeneticsAuthor(s): Katherine I. Farley-Barnes, Lisa M. Ogawa, Susan J. BasergaRibosomopathies are a diverse subset of diseases caused by reduced expression of, or mutations in, factors necessary for making ribosomes, the protein translation machinery in the cell. Despite the ubiquitous need for ribosomes in all cell types, ribosomopathies manifest with tissue-specific defects and sometimes increased cancer susceptibility, but few treatments target the underlying cause. By highlighting new research in the field, we review current hypotheses for the basis of th...
Source: Trends in Genetics - August 1, 2019 Category: Genetics & Stem Cells Source Type: research

Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics
Publication date: Available online 29 July 2019Source: Trends in GeneticsAuthor(s): O. Shukron, A. Seeber, A. Amitai, D. HolcmanChromatin organization remains complex and far from understood. In this article, we review recent statistical methods of extracting biophysical parameters from in vivo single-particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damage. We look at methods for analyzing both single locus and multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters. These par...
Source: Trends in Genetics - July 31, 2019 Category: Genetics & Stem Cells Source Type: research

Nucleolar DNA Double-Strand Break Responses Underpinning rDNA Genomic Stability
Publication date: Available online 25 July 2019Source: Trends in GeneticsAuthor(s): Marjolein van Sluis, Brian McStayNucleoli, the sites of ribosome biogenesis, form around ribosomal gene (rDNA) arrays termed nucleolar organiser regions (NORs). These are the most transcriptionally active regions of the human genome and specialised responses have evolved to ensure their genomic stability. This review focuses on nucleolar responses to DNA double-strand breaks (DSBs) introduced into rDNA arrays using sequence-specific endonucleases, including CRISPR/Cas9. Repair of rDNA DSBs is predominantly carried out by the homology-direct...
Source: Trends in Genetics - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

Coordinated Control of rRNA Processing by RNA Polymerase I
Publication date: Available online 26 July 2019Source: Trends in GeneticsAuthor(s): Catherine E. Scull, David A. SchneiderRibosomal RNA (rRNA) is co- and post-transcriptionally processed into active ribosomes. This process is dynamically regulated by direct covalent modifications of the polymerase that synthesizes the rRNA, RNA polymerase I (Pol I), and by interactions with cofactors that influence initiation, elongation, and termination activities of Pol I. The rate of transcription elongation by Pol I directly influences processing of nascent rRNA, and changes in Pol I transcription rate result in alternative rRNA proces...
Source: Trends in Genetics - July 27, 2019 Category: Genetics & Stem Cells Source Type: research

Acyrthosiphon pisum
Publication date: Available online 24 July 2019Source: Trends in GeneticsAuthor(s): Federica Calevro, Denis Tagu, Patrick Callaerts (Source: Trends in Genetics)
Source: Trends in Genetics - July 25, 2019 Category: Genetics & Stem Cells Source Type: research

Potential of Genome Editing to Improve Aquaculture Breeding and Production
Publication date: Available online 19 July 2019Source: Trends in GeneticsAuthor(s): Remi L. Gratacap, Anna Wargelius, Rolf Brudvik Edvardsen, Ross D. HoustonAquaculture is the fastest growing food production sector and is rapidly becoming the primary source of seafood for human diets. Selective breeding programs are enabling genetic improvement of production traits, such as disease resistance, but progress is limited by the heritability of the trait and generation interval of the species. New breeding technologies, such as genome editing using CRISPR/Cas9 have the potential to expedite sustainable genetic improvement in aq...
Source: Trends in Genetics - July 21, 2019 Category: Genetics & Stem Cells Source Type: research

Nucleolus and rRNA Gene Chromatin in Early Embryo Development
Publication date: Available online 18 July 2019Source: Trends in GeneticsAuthor(s): Jelena Kresoja-Rakic, Raffaella SantoroThe nucleolus is the largest substructure in the nucleus and forms around the nucleolar organizer regions (NORs), which comprise hundreds of rRNA genes. Recent evidence highlights further functions of the nucleolus that go beyond ribosome biogenesis. Data indicate that the nucleolus acts as a compartment for the location and regulation of repressive genomic domains and, together with the nuclear lamina, represents the hub for the organization of the inactive heterochromatin. In this review, we discuss ...
Source: Trends in Genetics - July 19, 2019 Category: Genetics & Stem Cells Source Type: research

A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster
Publication date: Available online 15 July 2019Source: Trends in GeneticsAuthor(s): René M. Marsano, Ennio Giordano, Giovanni Messina, Patrizio DimitriConstitutive heterochromatin represents a significant portion of eukaryotic genomes, but its functions still need to be elucidated. Even in the most updated genetics and molecular biology textbooks, constitutive heterochromatin is portrayed mainly as the ‘silent’ component of eukaryotic genomes. However, there may be more complexity to the relationship between heterochromatin and gene expression. In the fruit fly Drosophila melanogaster, a model for hetero...
Source: Trends in Genetics - July 17, 2019 Category: Genetics & Stem Cells Source Type: research

Phaeodactylum tricornutum
Publication date: Available online 15 July 2019Source: Trends in GeneticsAuthor(s): Chris Bowler, Angela Falciatore (Source: Trends in Genetics)
Source: Trends in Genetics - July 17, 2019 Category: Genetics & Stem Cells Source Type: research

The Unexpected Noncatalytic Roles of Histone Modifiers in Development and Disease
Publication date: Available online 10 July 2019Source: Trends in GeneticsAuthor(s): Yann Aubert, Shaun Egolf, Brian C. CapellEpigenetic regulation is critical for the precise control of cellular fate and developmental programs. Disruption of epigenetic information is increasingly appreciated as a potential driving mechanism in both developmental disorders as well as ubiquitous diseases such as cancer. Consistent with this, mutations in histone modifying enzymes are amongst the most frequent events in all of human cancer. While early studies have focused on the canonical enzymatic functions involved in catalyzing modificati...
Source: Trends in Genetics - July 12, 2019 Category: Genetics & Stem Cells Source Type: research

Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining
Publication date: Available online 8 July 2019Source: Trends in GeneticsAuthor(s): Joost Schimmel, Robin van Schendel, Johan T. den Dunnen, Marcel TijstermanA recognized source of disease-causing genome alterations is erroneous repair of broken chromosomes, which can be executed by two distinct mechanisms: non-homologous end joining (NHEJ) and the recently discovered polymerase theta-mediated end joining (TMEJ) pathway. While TMEJ has previously been considered to act as an alternative mechanism backing up NHEJ, recent work points to a role for TMEJ in the repair of replication-associated DNA breaks that are excluded from ...
Source: Trends in Genetics - July 9, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: August 2019Source: Trends in Genetics, Volume 35, Issue 8Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - July 9, 2019 Category: Genetics & Stem Cells Source Type: research

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Publication date: August 2019Source: Trends in Genetics, Volume 35, Issue 8Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - July 9, 2019 Category: Genetics & Stem Cells Source Type: research

SOXopathies: Growing Family of Developmental Disorders Due to SOX Mutations
Publication date: Available online 6 July 2019Source: Trends in GeneticsAuthor(s): Marco Angelozzi, Véronique LefebvreThe SRY-related (SOX) transcription factor family pivotally contributes to determining cell fate and identity in many lineages. Since the original discovery that SRY deletions cause sex reversal, mutations in half of the 20 human SOX genes have been associated with rare congenital disorders, henceforward called SOXopathies. Mutations are generally de novo, heterozygous, and inactivating, revealing gene haploinsufficiency, but other types, including duplications, have been reported too. Missense varia...
Source: Trends in Genetics - July 7, 2019 Category: Genetics & Stem Cells Source Type: research

The Nuclear Pore Complex in Cell Type-Specific Chromatin Structure and Gene Regulation
Publication date: Available online 15 June 2019Source: Trends in GeneticsAuthor(s): Jiayu Sun, Yuming Shi, Eda YildirimNuclear pore complex (NPC)-mediated nucleocytoplasmic trafficking is essential for key cellular processes, such as cell growth, cell differentiation, and gene regulation. The NPC has also been viewed as a nuclear architectural platform that impacts genome function and gene expression by mediating spatial and temporal coordination between transcription factors, chromatin regulatory proteins, and transcription machinery. Recent findings have uncovered differential and cell type-specific expression and distin...
Source: Trends in Genetics - June 16, 2019 Category: Genetics & Stem Cells Source Type: research

Transcriptional Control by Premature Termination: A Forgotten Mechanism
Publication date: Available online 15 June 2019Source: Trends in GeneticsAuthor(s): Kinga Kamieniarz-Gdula, Nick J. ProudfootThe concept of early termination as an important means of transcriptional control has long been established. Even so, its role in metazoan gene expression is underappreciated. Recent technological advances provide novel insights into premature transcription termination (PTT). This process is frequent, widespread, and can occur close to the transcription start site (TSS), or within the gene body. Stable prematurely terminated transcripts contribute to the transcriptome as instances of alternative poly...
Source: Trends in Genetics - June 16, 2019 Category: Genetics & Stem Cells Source Type: research

The Impact of Centromeres on Spatial Genome Architecture
Publication date: Available online 11 June 2019Source: Trends in GeneticsAuthor(s): Héloïse Muller, José Gil, Ines Anna DrinnenbergThe development of new technologies and experimental techniques is enabling researchers to see what was once unable to be seen. For example, the centromere was first seen as the mediator between spindle fiber and chromosome during mitosis and meiosis. Although this continues to be its most prominent role, we now know that the centromere functions beyond cellular division with important roles in genome organization and chromatin regulation. Here we aim to share the structures ...
Source: Trends in Genetics - June 12, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: July 2019Source: Trends in Genetics, Volume 35, Issue 7Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - June 12, 2019 Category: Genetics & Stem Cells Source Type: research

The Pregnancy Pickle: Evolved Immune Compensation Due to Pregnancy Underlies Sex Differences in Human Diseases
Publication date: July 2019Source: Trends in Genetics, Volume 35, Issue 7Author(s): Heini Natri, Angela R. Garcia, Kenneth H. Buetow, Benjamin C. Trumble, Melissa A. WilsonWe hypothesize that, ancestrally, sex-specific immune modulation evolved to facilitate survival of the pregnant person in the presence of an invasive placenta and an immunologically challenging pregnancy – an idea we term the 'pregnancy compensation hypothesis' (PCH). Further, we propose that sex differences in immune function are mediated, at least in part, by the evolution of gene content and dosage on the sex chromosomes, and are regulated by re...
Source: Trends in Genetics - June 12, 2019 Category: Genetics & Stem Cells Source Type: research

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Publication date: July 2019Source: Trends in Genetics, Volume 35, Issue 7Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - June 12, 2019 Category: Genetics & Stem Cells Source Type: research

Poly(ADP-Ribosylation) in Age-Related Neurological Disease
Publication date: Available online 7 June 2019Source: Trends in GeneticsAuthor(s): Leeanne McGurk, Olivia M. Rifai, Nancy M. BoniniA central and causative feature of age-related neurodegenerative disease is the deposition of misfolded proteins in the brain. To devise novel approaches to treatment, regulatory pathways that modulate these aggregation-prone proteins must be defined. One such pathway is post-translational modification by the addition of poly(ADP-ribose) (PAR), which promotes protein recruitment and localization in several cellular contexts. Mounting evidence implicates PAR in seeding the abnormal localization ...
Source: Trends in Genetics - June 9, 2019 Category: Genetics & Stem Cells Source Type: research

Phase Separation as a Melting Pot for DNA Repeats
Publication date: Available online 31 May 2019Source: Trends in GeneticsAuthor(s): Amanda C. Hall, Lauren A. Ostrowski, Karim MekhailGenome expression and stability are dependent on biological processes that control repetitive DNA sequences and nuclear compartmentalization. The phase separation of macromolecules has recently emerged as a major player in the control of biological pathways. Here, we summarize recent studies that collectively reveal intersections between phase separation, repetitive DNA elements, and nuclear compartments. These intersections modulate fundamental processes, including gene expression, DNA repai...
Source: Trends in Genetics - May 31, 2019 Category: Genetics & Stem Cells Source Type: research

Beneficial Noncancerous Mutations in Liver Disease
Publication date: Available online 28 May 2019Source: Trends in GeneticsAuthor(s): Miryam Müller, Stuart J. Forbes, Thomas G. BirdChronic liver disease results in fibrosis and cancer. While injury is associated with mutational burden, a recent study (Zhu et al. Cell 2019;177:608–621) highlights that not all positively selected mutations in the liver are precancerous. Indeed, some may be beneficial to the ability of the liver to not only withstand injury , but also to regenerate. (Source: Trends in Genetics)
Source: Trends in Genetics - May 29, 2019 Category: Genetics & Stem Cells Source Type: research

High-Diversity Mouse Populations for Complex Traits
Publication date: Available online 24 May 2019Source: Trends in GeneticsAuthor(s): Michael C. Saul, Vivek M. Philip, Laura G. Reinholdt, Center for Systems Neurogenetics of Addiction, Elissa J. CheslerContemporary mouse genetic reference populations are a powerful platform to discover complex disease mechanisms. Advanced high-diversity mouse populations include the Collaborative Cross (CC) strains, Diversity Outbred (DO) stock, and their isogenic founder strains. When used in systems genetics and integrative genomics analyses, these populations efficiently harnesses known genetic variation for precise and contextualized id...
Source: Trends in Genetics - May 25, 2019 Category: Genetics & Stem Cells Source Type: research

The Many Roles of Cohesin in Drosophila Gene Transcription
Publication date: Available online 23 May 2019Source: Trends in GeneticsAuthor(s): Dale DorsettThe cohesin protein complex mediates sister chromatid cohesion to ensure accurate chromosome segregation, and also influences gene transcription in higher eukaryotes. Modest deficits in cohesin function that do not alter chromosome segregation cause significant birth defects. The mechanisms by which cohesin participates in gene regulation have been studied in Drosophila, revealing that it is involved in gene activation by transcriptional enhancers and epigenetic gene silencing mediated by Polycomb group proteins. Recent studies r...
Source: Trends in Genetics - May 25, 2019 Category: Genetics & Stem Cells Source Type: research

Off to a Bad Start: Cancer Initiation by Pluripotency Regulator PRDM14
Publication date: Available online 23 May 2019Source: Trends in GeneticsAuthor(s): Lauren J. Tracey, Monica J. JusticeDespite advances in chemotherapies that improve cancer survival, most patients who relapse succumb to the disease due to the presence of cancer stem cells (CSCs), which are highly chemoresistant. The pluripotency factor PR domain 14 (PRDM14) has a key role in initiating many types of cancer. Normally, PRDM14 uses epigenetic mechanisms to establish and maintain the pluripotency of embryonic cells, and its role in cancer is similar. This important link between cancer and induced pluripotency is a key revelati...
Source: Trends in Genetics - May 25, 2019 Category: Genetics & Stem Cells Source Type: research

Germline Variants Impact Somatic Events during Tumorigenesis
Publication date: Available online 22 May 2019Source: Trends in GeneticsAuthor(s): Johnny R. Ramroop, Madelyn M. Gerber, Amanda Ewart TolandCancer is characterized by diverse genetic alterations in both germline and somatic genomes that disrupt normal biology and provide a selective advantage to cells during tumorigenesis. Germline and somatic genomes have been extensively studied independently, leading to numerous biological insights. Analyses integrating data from both genomes have identified genetic variants impacting somatic events in tumors, including hotspot driver mutations. Interactions among specific germline vari...
Source: Trends in Genetics - May 24, 2019 Category: Genetics & Stem Cells Source Type: research

Live-Animal Epigenome Editing: Convergence of Novel Techniques
Publication date: Available online 22 May 2019Source: Trends in GeneticsAuthor(s): J. Antonio Gomez, Ulrika Beitnere, David J. SegalEpigenome editing refers to the generation of precise chromatin alterations and their effects on gene expression and cell biology. Until recently, much of the efforts in epigenome editing were limited to tissue culture models of disease. However, the convergence of techniques from different fields including mammalian genetics, virology, and CRISPR engineering is advancing epigenome editing into a new era. Researchers are increasingly embracing the use of multicellular model organisms to test t...
Source: Trends in Genetics - May 24, 2019 Category: Genetics & Stem Cells Source Type: research

Horse Paleogenomes and Human–Animal Interactions in Prehistory
Publication date: Available online 17 May 2019Source: Trends in GeneticsAuthor(s): George H. Perry, Cheryl A. MakarewiczA new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cell http://doi.org/10.1016/j.cell.2019.03.049) finds that this animal – crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more – was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotempo...
Source: Trends in Genetics - May 18, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board
Publication date: June 2019Source: Trends in Genetics, Volume 35, Issue 6Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - May 14, 2019 Category: Genetics & Stem Cells Source Type: research

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Publication date: June 2019Source: Trends in Genetics, Volume 35, Issue 6Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - May 14, 2019 Category: Genetics & Stem Cells Source Type: research

General Mechanisms Leading to Persister Formation and Awakening
Publication date: Available online 27 April 2019Source: Trends in GeneticsAuthor(s): Dorien Wilmaerts, Etthel M. Windels, Natalie Verstraeten, Jan MichielsAll bacterial populations harbor a small fraction of transiently antibiotic-tolerant cells called persisters. These phenotypic variants compromise successful antibiotic treatment because they are held responsible for the relapse of many chronic infections. In addition, studies employing experimental evolution have demonstrated that persistence contributes to the development of antibiotic resistance. Persisters are typically described as dormant cells. However, recent fin...
Source: Trends in Genetics - April 29, 2019 Category: Genetics & Stem Cells Source Type: research

Three New Cs for CRISPR: Collateral, Communicate, Cooperate
Publication date: Available online 27 April 2019Source: Trends in GeneticsAuthor(s): Andrew Varble, Luciano A. MarraffiniClustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated (cas) genes provide protection against invading phages and plasmids in prokaryotes. Typically, short sequences are captured from the genome of the invader, integrated into the CRISPR locus, and transcribed into short RNAs that direct RNA-guided Cas nucleases to the nucleic acids of the invader for their degradation. Recent work in the field has revealed unexpected features of the CRISPR-Cas mechanism: (i) collate...
Source: Trends in Genetics - April 29, 2019 Category: Genetics & Stem Cells Source Type: research

How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes
Publication date: Available online 27 April 2019Source: Trends in GeneticsAuthor(s): Oleksandr Dergai, Nouria HernandezNuclear eukaryotic genomes are transcribed by three related RNA polymerases (Pol), which transcribe distinct gene sets. Specific Pol recruitment is achieved through selective core promoter recognition by basal transcription factors (TFs). Transcription by an inappropriate Pol appears to be rare and to generate mostly unstable products. A collection of short noncoding RNA genes [for example, small nuclear RNA (snRNA) or 7SK RNA genes], which play essential roles in processes such as maturation of RNA molecu...
Source: Trends in Genetics - April 29, 2019 Category: Genetics & Stem Cells Source Type: research

Aedes aegypti
Publication date: Available online 27 April 2019Source: Trends in GeneticsAuthor(s): Benjamin J. Matthews (Source: Trends in Genetics)
Source: Trends in Genetics - April 29, 2019 Category: Genetics & Stem Cells Source Type: research

New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli
Publication date: Available online 26 April 2019Source: Trends in GeneticsAuthor(s): Bijoy K. Mohanty, Sidney R. KushnerRecent studies suggest that poly(A) polymerase I (PAP I)-mediated polyadenylation in Escherichia coli is highly prevalent among mRNAs as well as tRNA precursors. Primary tRNA transcripts are initially processed endonucleolytically to generate pre-tRNA species, which undergo 5′-end maturation by the ribozyme RNase P. Subsequently, a group of 3′ → 5′ exonucleases mature the 3′ ends of the majority of tRNAs with few exceptions. PAP I competes with the 3′ → 5′ exo...
Source: Trends in Genetics - April 28, 2019 Category: Genetics & Stem Cells Source Type: research

Perspectives on PARPs in S Phase
Publication date: Available online 26 April 2019Source: Trends in GeneticsAuthor(s): Hana Hanzlikova, Keith W. CaldecottAccurate copying of DNA during S phase is essential for genome stability and cell viability. During genome duplication, the progression of the DNA replication machinery is challenged by limitations in nucleotide supply and physical barriers in the DNA template that include naturally occurring DNA lesions and secondary structures that are difficult to replicate. To ensure correct and complete replication of the genome, cells have evolved several mechanisms that protect DNA replication forks and thus mainta...
Source: Trends in Genetics - April 28, 2019 Category: Genetics & Stem Cells Source Type: research

Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity
Publication date: Available online 18 April 2019Source: Trends in GeneticsAuthor(s): Gonzalo Sabarís, Ian Laiker, Ella Preger-Ben Noon, Nicolás FrankelThe current paradigm in the field of gene regulation postulates that regulatory information for generating gene expression is organized into modules (enhancers), each containing the information for driving gene expression in a single spatiotemporal context. This modular organization is thought to facilitate the evolution of gene expression by minimizing pleiotropic effects. Here we review recent studies that provide evidence of quite the opposite: (i) enhancers...
Source: Trends in Genetics - April 19, 2019 Category: Genetics & Stem Cells Source Type: research

Models and Nomenclature for Cytoplasmic Incompatibility: Caution over Premature Conclusions – A Response to Beckmann et al.
Publication date: Available online 16 April 2019Source: Trends in GeneticsAuthor(s): J. Dylan Shropshire, Brittany Leigh, Sarah R. Bordenstein, Anne Duplouy, Markus Riegler, Jeremy C. Brownlie, Seth R. Bordenstein (Source: Trends in Genetics)
Source: Trends in Genetics - April 17, 2019 Category: Genetics & Stem Cells Source Type: research

Editorial Board and Contents
Publication date: May 2019Source: Trends in Genetics, Volume 35, Issue 5Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - April 17, 2019 Category: Genetics & Stem Cells Source Type: research

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Publication date: May 2019Source: Trends in Genetics, Volume 35, Issue 5Author(s): (Source: Trends in Genetics)
Source: Trends in Genetics - April 17, 2019 Category: Genetics & Stem Cells Source Type: research

Caution Does Not Preclude Predictive and Testable Models of Cytoplasmic Incompatibility: A Reply to Shropshire et al.
Publication date: Available online 9 April 2019Source: Trends in GeneticsAuthor(s): John F. Beckmann, Manon Bonneau, Hongli Chen, Mark Hochstrasser, Denis Poinsot, Hervé Merçot, Mylène Weill, Mathieu Sicard, Sylvain Charlat (Source: Trends in Genetics)
Source: Trends in Genetics - April 9, 2019 Category: Genetics & Stem Cells Source Type: research

Tools To Live By: Bacterial DNA Structures Illuminate Cancer
Publication date: Available online 5 April 2019Source: Trends in GeneticsAuthor(s): Jun Xia, Qian Mei, Susan M. RosenbergHolliday junctions (HJs) are DNA intermediates in homology-directed DNA repair and replication stalling, but until recently were undetectable in living cells. We review how an engineered protein that traps and labels HJs in Escherichia coli illuminates the biology of DNA and cancer. HJ chromatin immunoprecipitation with deep sequencing (ChIP-seq) analysis showed the directionality of double-strand break (DSB) repair in the E. coli genome. Quantification of HJs as fluorescent foci in live cells revealed t...
Source: Trends in Genetics - April 6, 2019 Category: Genetics & Stem Cells Source Type: research

The Promise of Paleogenomics Beyond Our Own Species
Publication date: Available online 4 April 2019Source: Trends in GeneticsAuthor(s): Katherine Brunson, David ReichPaleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics ca...
Source: Trends in Genetics - April 5, 2019 Category: Genetics & Stem Cells Source Type: research