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Single-cell phylotranscriptomics of developmental and cell type evolution Trends Genet. (IF 11.4) Pub Date : 2024-03-14 Fuqiang Ma, Chaogu Zheng
Single-cell phylotranscriptomics is an emerging tool to reveal the molecular and cellular mechanisms of evolution. We summarize its utility in studying the hourglass pattern of ontogenetic evolution and for understanding the evolutionary history of cell types. The developmental hourglass model suggests that the mid-embryonic stage is the most conserved period of development across species, which is
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Architecture of an RNA polymerase ribozyme illuminates the RNA World Trends Genet. (IF 11.4) Pub Date : 2024-03-13 David M. Shechner
'Ribo-organisms' of the primordial RNA World would have needed ribozymes that catalyze RNA replication. recently revealed how these RNA replicases might have functioned by solving the structure of an artificial polymerase ribozyme. This work illustrates how complex RNA structures evolve, with implications for the origins of life.
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PCNA cycling dynamics during DNA replication and repair in mammals Trends Genet. (IF 11.4) Pub Date : 2024-03-13 Sukhyun Kang, Juyeong Yoo, Kyungjae Myung
Proliferating cell nuclear antigen (PCNA) is a eukaryotic replicative DNA clamp. Furthermore, DNA-loaded PCNA functions as a molecular hub during DNA replication and repair. PCNA forms a closed homotrimeric ring that encircles the DNA, and association and dissociation of PCNA from DNA are mediated by clamp-loader complexes. PCNA must be actively released from DNA after completion of its function. If
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The heterogeneous genetic architectures of orofacial clefts Trends Genet. (IF 11.4) Pub Date : 2024-03-13 Kelsey Robinson, Sarah W. Curtis, Elizabeth J. Leslie
Orofacial clefts (OFCs) are common, affecting 1:1000 live births. OFCs occur across a phenotypic spectrum – including cleft lip (CL), cleft lip and palate (CLP), or cleft palate (CP) – and can be further subdivided based on laterality, severity, or specific structures affected. Herein we review what is known about the genetic architecture underlying each of these subtypes, considering both shared and
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Genetic variation drives differences in obesity-related gene regulation Trends Genet. (IF 11.4) Pub Date : 2024-03-09 Minna U. Kaikkonen
recently demonstrated that genetic variation, rather than dietary changes, governs gene regulation in liver. This finding highlights the impact of noncoding variants on chromatin accessibility, histone modifications, transcription factor binding, and gene expression and has implications for future research directions in understanding the genetic basis of disease.
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Recombination in bdelloid rotifer genomes: asexuality, transfer and stress Trends Genet. (IF 11.4) Pub Date : 2024-03-08 Christopher G. Wilson, Tymoteusz Pieszko, Reuben W. Nowell, Timothy G. Barraclough
Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding
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Dominance and multi-locus interaction Trends Genet. (IF 11.4) Pub Date : 2024-03-07 Juan Li, Claudia Bank
Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes
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Helitrons: genomic parasites that generate developmental novelties Trends Genet. (IF 11.4) Pub Date : 2024-02-29 Daniela Barro-Trastoy, Claudia Köhler
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as ‘peel-and-paste elements’. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for
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Unraveling the diversity and cultural heritage of fruit crops through paleogenomics Trends Genet. (IF 11.4) Pub Date : 2024-02-28 Meirav Meiri, Guy Bar-Oz
Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying
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Genetic adaptations for the oceanic success of fish eggs Trends Genet. (IF 11.4) Pub Date : 2024-02-23 Roderick Nigel Finn, Joan Cerdà
Genetic adaptations of organisms living in extreme environments are fundamental to our understanding of where life can evolve. Water is the single limiting parameter in this regard, yet when released in the oceans, the single-celled eggs of marine bony fishes (teleosts) have no means of acquiring it. They are strongly hyposmotic to seawater and lack osmoregulatory systems. Paradoxically, modern teleosts
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Diverse pathways to speciation revealed by marine snails Trends Genet. (IF 11.4) Pub Date : 2024-02-22 Kerstin Johannesson, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja Marie Westram, Roger K. Butlin, Sean Stankowski
Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails () supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe
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Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges Trends Genet. (IF 11.4) Pub Date : 2024-02-12 Monika Witzenberger, Schraga Schwartz
Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target
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Clocks at sea: the genome-editing tide is rising Trends Genet. (IF 11.4) Pub Date : 2024-02-08 Erica R. Kwiatkowski, Joshua J.C. Rosenthal, Patrick Emery
The coastline is a particularly challenging environment for its inhabitants. Not only do they have to cope with the solar day and the passing of seasons, but they must also deal with tides. In addition, many marine species track the phase of the moon, especially to coordinate reproduction. Marine animals show remarkable behavioral and physiological adaptability, using biological clocks to anticipate
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Finding genes and pathways that underlie coral adaptation Trends Genet. (IF 11.4) Pub Date : 2024-02-06 Oliver Selmoni, Line K. Bay, Moises Exposito-Alonso, Phillip A. Cleves
Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art
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Enhancing plant biotechnology by nanoparticle delivery of nucleic acids Trends Genet. (IF 11.4) Pub Date : 2024-02-05 Jiaxi Yong, Miaomiao Wu, Bernard J. Carroll, Zhi Ping Xu, Run Zhang
Plant biotechnology plays a crucial role in developing modern agriculture and plant science research. However, the delivery of exogenous genetic material into plants has been a long-standing obstacle. Nanoparticle-based delivery systems are being established to address this limitation and are proving to be a feasible, versatile, and efficient approach to facilitate the internalization of functional
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Subscription and Copyright Information Trends Genet. (IF 11.4) Pub Date : 2024-02-05
Abstract not available
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An ocean of diffusible information Trends Genet. (IF 11.4) Pub Date : 2024-02-02 Ashley M. Stein, Steven J. Biller
In the ocean, free-living bacteria exist in a dilute world where direct physical interactions between cells are relatively rare. How then do they exchange genetic information via horizontal gene transfer (HGT)? have explored the world of marine 'protected extracellular DNA' (peDNA), and find that extracellular vesicles (EVs) are likely to play an important role.
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A sea star is only a head Trends Genet. (IF 11.4) Pub Date : 2024-02-01 Andreas Hejnol
Where are the front and back ends in a sea star? recently tackled this long-standing mystery using state-of-the-art molecular tools, leading them to suggest that a sea star may be constructed from components that, in other animals, would constitute only the head.
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How intrinsically disordered proteins order plant gene silencing Trends Genet. (IF 11.4) Pub Date : 2024-01-30 Baoshuan Shang, Changhao Li, Xiuren Zhang
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) possess low sequence complexity of amino acids and display non-globular tertiary structures. They can act as scaffolds, form regulatory hubs, or trigger biomolecular condensation to control diverse aspects of biology. Emerging evidence has recently implicated critical roles of IDPs and IDR-contained proteins
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Duplicated gene networks promote ‘hopeful’ phenotypic variation Trends Genet. (IF 11.4) Pub Date : 2024-01-24 Christian Parisod
The consequences of whole-genome duplication (WGD) remain elusive. A new study by Ebadi et al. simulating duplicated gene networks predicts that WGD immediately generates autopolyploids with extreme phenotypes and increases phenotypic variance. Such theoretical work calls for new experimental studies addressing to what extent WGD may be beneficial under environmental changes.
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Degradation and translation of maternal mRNA for embryogenesis Trends Genet. (IF 11.4) Pub Date : 2024-01-22 Guanghui Yang, Qiliang Xin, Jurrien Dean
Maternal mRNAs accumulate during egg growth and must be judiciously degraded or translated to ensure successful development of mammalian embryos. In this review we integrate recent investigations into pathways controlling rapid degradation of maternal mRNAs during the maternal-to-zygotic transition. Degradation is not indiscriminate, and some mRNAs are selectively protected and rapidly translated after
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Time will tell: comparing timescales to gain insight into transcriptional bursting Trends Genet. (IF 11.4) Pub Date : 2024-01-12 Joseph V.W. Meeussen, Tineke L. Lenstra
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer–promoter (E–P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic
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Subscription and Copyright Information Trends Genet. (IF 11.4) Pub Date : 2024-01-08
Abstract not available
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Gene regulation during meiosis Trends Genet. (IF 11.4) Pub Date : 2024-01-04 Jingyi Gao, Yiwen Qin, John C. Schimenti
Meiosis is essential for gamete production in all sexually reproducing organisms. It entails two successive cell divisions without DNA replication, producing haploid cells from diploid ones. This process involves complex morphological and molecular differentiation that varies across species and between sexes. Specialized genomic events like meiotic recombination and chromosome segregation are tightly
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Uncovering dark matter in cancer by identifying epigenetic drivers Trends Genet. (IF 11.4) Pub Date : 2024-01-03 Jun Zhong, Laufey T. Amundadottir
The complex relationship between chromatin accessibility, transcriptional regulation, and cancer transitions presents a daunting puzzle. Terekhanova et al. created a pan-cancer epigenetic and transcriptomic atlas at single-cell resolution, yielding important insights into the underlying chromatin architecture of cancer transitions and novel discoveries with the potential to advance precision medicine
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The genetic landscape of age-related hearing loss Trends Genet. (IF 11.4) Pub Date : 2023-12-30 Yuzuru Ninoyu, Rick A. Friedman
Age-related hearing loss (ARHL) is a prevalent concern in the elderly population. Recent genome-wide and phenome-wide association studies (GWASs and PheWASs) have delved into the identification of causative variants and the understanding of pleiotropy, highlighting the polygenic intricacies of this complex condition. While recent large-scale GWASs have pinpointed significant SNPs and risk variants
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In search of critical dsRNA targets of ADAR1 Trends Genet. (IF 11.4) Pub Date : 2023-12-29 Erez Y. Levanon, Roni Cohen-Fultheim, Eli Eisenberg
Recent studies have underscored the pivotal role of adenosine-to-inosine RNA editing, catalyzed by ADAR1, in suppressing innate immune interferon responses triggered by cellular double-stranded RNA (dsRNA). However, the specific ADAR1 editing targets crucial for this regulatory function remain elusive. We review analyses of transcriptome-wide ADAR1 editing patterns and their evolutionary dynamics,
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Take a walk on the KRAB side: (Trends in Genetics, 39:11 p:844-857, 2023) Trends Genet. (IF 11.4) Pub Date : 2023-12-30 Olga Rosspopoff, Didier Trono
Abstract not available
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Biobanking animal genetic resources: critical infrastructure and growth opportunities Trends Genet. (IF 11.4) Pub Date : 2023-12-22 Harvey D. Blackburn, Emmanuel Lozada-Soto, Samuel R. Paiva
National animal gene banks have acquired substantial quantities of germplasm that protect and preserve a wide range of livestock breeds. New challenges and growth opportunities are emerging. A key challenge will be increased gene bank use, but this requires increased characterization of phenotypes and genotypes for populations and collections.
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Advances in methods for tRNA sequencing and quantification Trends Genet. (IF 11.4) Pub Date : 2023-12-19 Nigam H. Padhiar, Upendra Katneni, Anton A. Komar, Yuri Motorin, Chava Kimchi-Sarfaty
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications
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TFAM mislocalization during spermatogenesis Trends Genet. (IF 11.4) Pub Date : 2023-11-29 Sam Kavoosi, Martin Picard, Brett A. Kaufman
Mitochondrial DNA (mtDNA) is inherited almost exclusively from the maternal lineage. Paternal destruction of either mtDNA or whole mitochondria has been the dominant model for mtDNA transmission. Recently, Lee et al. provided evidence for mitochondrial transcription factor A (TFAM) import sequence regulation as a potential cause for mtDNA depletion in human sperm before fertilization.
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Metastable epialleles in humans Trends Genet. (IF 11.4) Pub Date : 2023-11-24 Maria Derakhshan, Noah J. Kessler, Garrett Hellenthal, Matt J. Silver
First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across tissues derived from different germ layers within a given individual. This property, termed systemic interindividual variation (SIV), is attributed to stochastic methylation establishment before germ layer differentiation. Evidence
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Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis Trends Genet. (IF 11.4) Pub Date : 2023-11-20 John A. Morris, Jennifer S. Sun, Neville E. Sanjana
Programmable genome-engineering technologies, such as CRISPR (clustered regularly interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens that capitalize on this programmability, have transformed biomedical science. These screens connect genes and noncoding genome elements to disease-relevant phenotypes, but until recently have been limited to individual phenotypes such
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Wildlife endogenous retroviruses: colonization, consequences, and cooption Trends Genet. (IF 11.4) Pub Date : 2023-11-19 Patric Jern, Alex D. Greenwood
Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus–host interactions. These initial forays into broader taxonomic analysis, including sequencing
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Subscription and Copyright Information Trends Genet. (IF 11.4) Pub Date : 2023-11-13
Abstract not available
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A dive into the unknome Trends Genet. (IF 11.4) Pub Date : 2023-11-13 Juri Rappsilber
We may never understand the function of all genes, findings by Freeman, Munro and colleagues suggest, unless we rethink our approaches. They make a thorough attempt at quantifying the unknownness of protein-coding genes and experimentally prove that many neglected genes hold the seed of important discoveries.
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Genome stability from the perspective of telomere length Trends Genet. (IF 11.4) Pub Date : 2023-11-11 Xinyi Lu, Lin Liu
Telomeres and their associated proteins protect the ends of chromosomes to maintain genome stability. Telomeres undergo progressive shortening with each cell division in mammalian somatic cells without telomerase, resulting in genome instability. When telomeres reach a critically short length or are recognized as a damage signal, cells enter a state of senescence, followed by cell cycle arrest, programmed
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Opportunities and tradeoffs in single-cell transcriptomic technologies Trends Genet. (IF 11.4) Pub Date : 2023-11-10 Matilde I. Conte, Azahara Fuentes-Trillo, Cecilia Domínguez Conde
Recent technological and algorithmic advances enable single-cell transcriptomic analysis with remarkable depth and breadth. Nonetheless, a persistent challenge is the compromise between the ability to profile high numbers of cells and the achievement of full-length transcript coverage. Currently, the field is progressing and developing new and creative solutions that improve cellular throughput, gene
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Alternative paths for genetics, then and now: Q&A with Gregory Radick about Disputed Inheritance Trends Genet. (IF 11.4) Pub Date : 2023-11-10 Gregory Radick
Abstract not available
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Strategies for dissecting the complexity of neurodevelopmental disorders Trends Genet. (IF 11.4) Pub Date : 2023-11-08 Jiawan Sun, Serena Noss, Deepro Banerjee, Maitreya Das, Santhosh Girirajan
Neurodevelopmental disorders (NDDs) are associated with a wide range of clinical features, affecting multiple pathways involved in brain development and function. Recent advances in high-throughput sequencing have unveiled numerous genetic variants associated with NDDs, which further contribute to disease complexity and make it challenging to infer disease causation and underlying mechanisms. Herein
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Retrotransposon renaissance in early embryos Trends Genet. (IF 11.4) Pub Date : 2023-11-08 Youjia Guo, Ten D. Li, Andrew J. Modzelewski, Haruhiko Siomi
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding
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Pioneer factors: roles and their regulation in development Trends Genet. (IF 11.4) Pub Date : 2023-11-07 Amandine Barral, Kenneth S. Zaret
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming
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Making sense of proprioception Trends Genet. (IF 11.4) Pub Date : 2023-11-03 Alessandro Santuz, Niccolò Zampieri
Proprioception – the sense of body position in space – is intimately linked to motor control. Here, we briefly review the current knowledge of the proprioceptive system and how advances in the genetic characterisation of proprioceptive sensory neurons in mice promise to dissect its role in health and disease.
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Predicting RNA structures and functions by artificial intelligence Trends Genet. (IF 11.4) Pub Date : 2023-10-26 Jun Zhang, Mei Lang, Yang Zhang
RNA functions by interacting with its intended targets structurally. However, due to the dynamic nature of RNA molecules, RNA structures are difficult to determine experimentally or predict computationally. Artificial intelligence (AI) has revolutionized many biomedical fields and has been progressively utilized to deduce RNA structures, target binding, and associated functionality. Integrating structural
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From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish Trends Genet. (IF 11.4) Pub Date : 2023-10-26 Amruta Swaminathan, Fanning Xia, Nicolas Rohner
How genotype determines phenotype is a well-explored question, but genotype–environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus, comprising surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait
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Chromatin bridges: stochastic breakage or regulated resolution? Trends Genet. (IF 11.4) Pub Date : 2023-10-25 Huadong Jiang, Ying Wai Chan
Genetic material is organized in the form of chromosomes, which need to be segregated accurately into two daughter cells in each cell cycle. However, chromosome fusion or the presence of unresolved interchromosomal linkages lead to the formation of chromatin bridges, which can induce DNA lesions and genome instability. Persistent chromatin bridges are trapped in the cleavage furrow and are broken at
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Small protein plays with big networks Trends Genet. (IF 11.4) Pub Date : 2023-10-24 Valerie A. Tornini
Thousands of small proteins, called microproteins, are encoded in small open reading frames (smORFs) throughout the genome. Despite assumptions that these proteins would be too small to properly fold and function, a recent study by Chen et al. identifies the surprisingly complex roles of one such microprotein.
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Approaches and challenges in genome-wide circular RNA identification and quantification Trends Genet. (IF 11.4) Pub Date : 2023-10-13 Xu-Kai Ma, Si-Nan Zhai, Li Yang
Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied
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Subscription and Copyright Information Trends Genet. (IF 11.4) Pub Date : 2023-10-09
Abstract not available
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Recent insights into eukaryotic double-strand DNA break repair unveiled by single-molecule methods Trends Genet. (IF 11.4) Pub Date : 2023-10-07 Sara De Bragança, Mark S. Dillingham, Fernando Moreno-Herrero
Genome integrity and maintenance are essential for the viability of all organisms. A wide variety of DNA damage types have been described, but double-strand breaks (DSBs) stand out as one of the most toxic DNA lesions. Two major pathways account for the repair of DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Both pathways involve complex DNA transactions catalyzed by proteins
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Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs Trends Genet. (IF 11.4) Pub Date : 2023-09-30 Alan Monziani, Igor Ulitsky
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs)
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Aneuploidy in human cancer: new tools and perspectives Trends Genet. (IF 11.4) Pub Date : 2023-09-29 Asad A. Lakhani, Sarah L. Thompson, Jason M. Sheltzer
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed
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An updated view of the kinetochore architecture Trends Genet. (IF 11.4) Pub Date : 2023-09-27 Mariko Ariyoshi, Tatsuo Fukagawa
The kinetochore is a supramolecular complex that facilitates faithful chromosome segregation by bridging the centromere and spindle microtubules. Recent functional and structural studies on the inner kinetochore subcomplex, constitutive centromere-associated network (CCAN) have updated our understanding of kinetochore architecture. While the CCAN core establishes a stable interface with centromeric
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Protecting axons in grandchildren Trends Genet. (IF 11.4) Pub Date : 2023-09-22 Surojit Sural
Prenatal exposure to environmental agents can influence the fitness of not only the fetus, but also subsequent generations. In a recent study, Wang et al. demonstrated that feeding ursolic acid (UA), a plant-derived compound, to Caenorhabditis elegans mothers during their reproductive period prevented neurodegeneration in not only their offspring, but also the F2 progeny.
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Subscription and Copyright Information Trends Genet. (IF 11.4) Pub Date : 2023-09-11
Abstract not available
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