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Paramecium Genetics, Genomics, and Evolution Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-12-12 Hongan Long, Parul Johri, Jean-Francois Gout, Jiahao Ni, Yue Hao, Timothy Licknack, Yaohai Wang, Jiao Pan, Berenice Jiménez-Marín, Michael Lynch
The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently
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The Clockwork Embryo: Mechanisms Regulating Developmental Rate Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-12-12 Margarete Diaz-Cuadros, Olivier Pourquié
Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental
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Meiosis: Dances Between Homologs Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-10-03 Denise Zickler, Nancy Kleckner
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding
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Programmed Cell Death in Unicellular Versus Multicellular Organisms Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-19 Madhura Kulkarni, J. Marie Hardwick
Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms
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Manipulating the Destiny of Wild Populations Using CRISPR Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-19 Robyn Raban, John M. Marshall, Bruce A. Hay, Omar S. Akbari
Genetic biocontrol aims to suppress or modify populations of species to protect public health, agriculture, and biodiversity. Advancements in genome engineering technologies have fueled a surge in research in this field, with one gene editing technology, CRISPR, leading the charge. This review focuses on the current state of CRISPR technologies for genetic biocontrol of pests and highlights the progress
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RNA Repair: Hiding in Plain Sight Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-19 Stewart Shuman
Enzymes that phosphorylate, dephosphorylate, and ligate RNA 5′ and 3′ ends were discovered more than half a century ago and were eventually shown to repair purposeful site-specific endonucleolytic breaks in the RNA phosphodiester backbone. The pace of discovery and characterization of new candidate RNA repair activities in taxa from all phylogenetic domains greatly exceeds our understanding of the
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Unlocking the Complex Cell Biology of Coral–Dinoflagellate Symbiosis: A Model Systems Approach Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-19 Marie R. Jacobovitz, Elizabeth A. Hambleton, Annika Guse
Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular
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Interplay Between Antimicrobial Resistance and Global Environmental Change Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-14 María Mercedes Zambrano
Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from
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Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-09-14 Ayodeji Adegunsoye, Natalia M. Gonzales, Yoav Gilad
Many human phenotypes are impossible to recapitulate in model organisms or immortalized human cell lines. Induced pluripotent stem cells (iPSCs) offer a way to study disease mechanisms in a variety of differentiated cell types while circumventing ethical and practical issues associated with finite tissue sources and postmortem states. Here, we discuss the broad utility of iPSCs in genetic medicine
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Integrating Complex Life Cycles in Comparative Developmental Biology Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-16 Laurent Formery, Christopher J. Lowe
The goal of comparative developmental biology is identifying mechanistic differences in embryonic development between different taxa and how these evolutionary changes have led to morphological and organizational differences in adult body plans. Much of this work has focused on direct-developing species in which the adult forms straight from the embryo and embryonic modifications have direct effects
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How to Build a Fire: The Genetics of Autoinflammatory Diseases Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-10 Jiahui Zhang, Pui Y. Lee, Ivona Aksentijevich, Qing Zhou
Systemic autoinflammatory diseases (SAIDs) are a heterogeneous group of disorders caused by excess activation of the innate immune system in an antigen-independent manner. Starting with the discovery of the causal gene for familial Mediterranean fever, more than 50 monogenic SAIDs have been described. These discoveries, paired with advances in immunology and genomics, have allowed our understanding
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Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-10 Mark A.A. Minow, Alexandre P. Marand, Robert J. Schmitz
The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants
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Pooled Genome-Scale CRISPR Screens in Single Cells Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-10 Daniel Schraivogel, Lars M. Steinmetz, Leopold Parts
Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas
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Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-10 You Chen, Mauricio I. Paramo, Yingying Zhang, Li Yao, Sagar R. Shah, Yiyang Jin, Junke Zhang, Xiuqi Pan, Haiyuan Yu
Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and evaluate their regulatory effects. Here, we review the latest advances
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Transcription–Replication Conflicts as a Source of Genome Instability Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-08 Liana Goehring, Tony T. Huang, Duncan J. Smith
Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription–replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete
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Asymmetric Stem Cell Division and Germline Immortality Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-08-08 Yukiko M. Yamashita
Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular
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Mechanisms Underlying the Formation and Evolution of Vertebrate Color Patterns Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-07-25 Claudius F. Kratochwil, Ricardo Mallarino
Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of
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Coral Reef Population Genomics in an Age of Global Change Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-06-29 Malin L. Pinsky, René D. Clark, Jaelyn T. Bos
Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together
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Microglial Transcriptional Signatures in the Central Nervous System: Toward A Future of Unraveling Their Function in Health and Disease Annu. Rev. Genet. (IF 11.1) Pub Date : 2023-06-29 Haley A. Vecchiarelli, Marie-Ève Tremblay
Microglia, the resident immune cells of the central nervous system (CNS), are primarily derived from the embryonic yolk sac and make their way to the CNS during early development. They play key physiological and immunological roles across the life span, throughout health, injury, and disease. Recent transcriptomic studies have identified gene transcript signatures expressed by microglia that may provide
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Quiescence in Saccharomyces cerevisiae Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-11-30 Linda L. Breeden, Toshio Tsukiyama
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered
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The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-11-30 Peng Liu, Diego Cuerda-Gil, Saima Shahid, R. Keith Slotkin
Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression
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A Half Century Defining the Logic of Cellular Life Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-11-30 Lucy Shapiro
Over more than fifty years, I have studied how the logic that controls and integrates cell function is built into the dynamic architecture of living cells. I worked with a succession of exceptionally talented students and postdocs, and we discovered that the bacterial cell is controlled by an integrated genetic circuit in which transcriptional and translational controls are interwoven with the three-dimensional
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Enhancer Function and Evolutionary Roles of Human Accelerated Regions Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-07 Sean Whalen, Katherine S. Pollard
Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome. When HARs were discovered in 2006, their function was mysterious due to scant annotation of the noncoding genome. Diverse technologies, from transgenic animals to machine learning, have consistently shown that HARs function as gene regulatory enhancers with significant enrichment in neurodevelopment. It is now
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Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-07 Mashiat Rabbani, Xianing Zheng, Gabe L. Manske, Alexander Vargo, Adrienne N. Shami, Jun Z. Li, Saher Sue Hammoud
Spermatogenesis is a complex differentiation process coordinated spatiotemporally across and along seminiferous tubules. Cellular heterogeneity has made it challenging to obtain stage-specific molecular profiles of germ and somatic cells using bulk transcriptomic analyses. This has limited our ability to understand regulation of spermatogenesis and to integrate knowledge from model organisms to humans
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Scalable Functional Assays for the Interpretation of Human Genetic Variation Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-03 Daniel Tabet, Victoria Parikh, Prashant Mali, Frederick P. Roth, Melina Claussnitzer
Scalable sequence–function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies
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Mechanisms Underlying Circuit Dysfunction in Neurodevelopmental Disorders Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-03 David Exposito-Alonso, Beatriz Rico
Recent advances in genomics have revealed a wide spectrum of genetic variants associated with neurodevelopmental disorders at an unprecedented scale. An increasing number of studies have consistently identified mutations—both inherited and de novo—impacting the function of specific brain circuits. This suggests that, during brain development, alterations in distinct neural circuits, cell types, or
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Errors of the Egg: The Establishment and Progression of Human Aneuploidy Research in the Maternal Germline Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-02 Jennifer R. Gruhn, Eva R. Hoffmann
Meiosis, a key process in the creation of haploid gametes, is a complex cellular division incorporating unique timing and intricate chromosome dynamics. Abnormalities in this elaborate dance can lead to the production of aneuploid gametes, i.e., eggs containing an incorrect number of chromosomes, many of which cannot generate a viable pregnancy. For many decades, research has been attempting to address
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The 3D-Evo Space: Evolution of Gene Expression and Alternative Splicing Regulation Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-02 Federica Mantica, Manuel Irimia
Animal species present relatively high levels of gene conservation, and yet they display a great variety of cell type and tissue phenotypes. These diverse phenotypes are mainly specified through differential gene usage, which relies on several mechanisms. Two of the most relevant mechanisms are regulated gene transcription, usually referred to as gene expression (rGE), and regulated alternative splicing
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The Four Causes: The Functional Architecture of Centromeres and Kinetochores Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-02 Andrew D. McAinsh, Adele L. Marston
Kinetochores are molecular machines that power chromosome segregation during the mitotic and meiotic cell divisions of all eukaryotes. Aristotle explains how we think we have knowledge of a thing only when we have grasped its cause. In our case, to gain understanding of the kinetochore, the four causes correspond to questions that we must ask: ( a) What are the constituent parts, ( b) how does it assemble
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Transcription-Translation Coupling in Bacteria Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-09-02 Gregor M. Blaha, Joseph T. Wade
In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at the dawn of molecular biology, yet the interplay between the two key players, the RNA polymerase and ribosome, remains elusive. Genetic data indicate
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APOBEC-Induced Mutagenesis in Cancer Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-08-27 Tony M. Mertz, Christopher D. Collins, Madeline Dennis, Margo Coxon, Steven A. Roberts
The initiation, progression, and relapse of cancers often result from mutations occurring within somatic cells. Consequently, processes that elevate mutation rates accelerate carcinogenesis and hinder the development of long-lasting therapeutics. Recent sequencing of human cancer genomes has identified patterns of mutations, termed mutation signatures, many of which correspond to specific environmentally
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Genome Protection by DNA Polymerase θ Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-08-27 Richard D. Wood, Sylvie Doublié
DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase–like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development
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The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-08-17 Shruthi Balachandra, Sharanya Sarkar, Amanda A. Amodeo
Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control
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Genome Maintenance in Mammalian Stem Cells Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-08-17 John C. Schimenti, Rui Huang, Liangdao Li, Ryan James
Various stem cells in the body are tasked with maintaining tissue homeostasis throughout the life of an organism and thus must be resilient to intrinsic and extrinsic challenges such as infection and injury. Crucial to these challenges is genome maintenance because a high mutational load and persistent DNA lesions impact the production of essential gene products at proper levels and compromise optimal
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Asymmetric Histone Inheritance: Establishment, Recognition, and Execution Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-07-29 Jennifer A. Urban, Rajesh Ranjan, Xin Chen
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone
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Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-07-25 Tina L. Sing, Gloria A. Brar, Elçin Ünal
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription
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The Awesome Power of Human Genetics of Infectious Disease Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-06-13 Kyle D. Gibbs, Benjamin H. Schott, Dennis C. Ko
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility
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The Genetics of Autophagy in Multicellular Organisms Annu. Rev. Genet. (IF 11.1) Pub Date : 2022-06-09 Hong Zhang
Autophagy, a lysosome-mediated degradation process evolutionarily conserved from yeast to mammals, is essential for maintaining cellular homeostasis and combating diverse cellular stresses. Autophagy involves de novo synthesis of a double-membrane autophagosome, sequestration of selected cellular contents, and subsequent delivery of sequestrated contents to the vacuole (in yeasts and plants) or to
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Genetics of Shoot Meristem and Shoot Regeneration Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Leor Eshed Williams
Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL
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Museum Genomics Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Daren C. Card, Beth Shapiro, Gonzalo Giribet, Craig Moritz, Scott V. Edwards
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics—genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations—has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of
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Green Algal Models for Multicellularity Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 James Umen, Matthew D. Herron
The repeated evolution of multicellularity across the tree of life has profoundly affected the ecology and evolution of nearly all life on Earth. Many of these origins were in different groups of photosynthetic eukaryotes, or algae. Here, we review the evolution and genetics of multicellularity in several groups of green algae, which include the closest relatives of land plants. These include millimeter-scale
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Variation and Evolution of Human Centromeres: A Field Guide and Perspective Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Karen H. Miga, Ivan A. Alexandrov
We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites,
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Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Baptiste Libé-Philippot, Pierre Vanderhaeghen
The cerebral cortex is at the core of brain functions that are thought to be particularly developed in the human species. Human cortex specificities stem from divergent features of corticogenesis, leading to increased cortical size and complexity. Underlying cellular mechanisms include prolonged patterns of neuronal generation and maturation, as well as the amplification of specific types of stem/progenitor
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Drosophila sechellia: A Genetic Model for Behavioral Evolution and Neuroecology Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Thomas O. Auer, Michael P. Shahandeh, Richard Benton
Defining the mechanisms by which animals adapt to their ecological niche is an important problem bridging evolution, genetics, and neurobiology. We review the establishment of a powerful genetic model for comparative behavioral analysis and neuroecology, Drosophila sechellia. This island-endemic fly species is closely related to several cosmopolitan generalists, including Drosophila melanogaster, but
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Architecture and Dynamics of Meiotic Chromosomes Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Sarah N. Ur, Kevin D. Corbett
The specialized two-stage meiotic cell division program halves a cell's chromosome complement in preparation for sexual reproduction. This reduction in ploidy requires that in meiotic prophase, each pair of homologous chromosomes (homologs) identify one another and form physical links through DNA recombination. Here, we review recent advances in understanding the complex morphological changes that
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Plant Cell Identity in the Era of Single-Cell Transcriptomics Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Kook Hui Ryu, Yan Zhu, John Schiefelbein
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell
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Perfecting Targeting in CRISPR Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Hainan Zhang, Tong Li, Yidi Sun, Hui Yang
CRISPR-based genome editing holds promise for genome engineering and other applications in diverse organisms. Defining and improving the genome-wide and transcriptome-wide specificities of these editing tools are essential for realizing their full potential in basic research and biomedical therapeutics. This review provides an overview of CRISPR-based DNA- and RNA-editing technologies, methods to quantify
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How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Franziska Böwer, Arp Schnittger
One of the major cell fate transitions in eukaryotes is entry into meiosis. While in single-celled yeast this decision is triggered by nutrient starvation, in multicellular eukaryotes, such as plants, it is under developmental control. In contrast to animals, plants have only a short germline and instruct cells to become meiocytes in reproductive organs late in development. This situation argues for
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Functional Diversification of Chromatin on Rapid Evolutionary Timescales Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Cara L. Brand, Mia T. Levine
Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat–packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of
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Cold Shock Response in Bacteria Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Yan Zhang, Carol A. Gross
Bacteria often encounter temperature fluctuations in their natural habitats and must adapt to survive. The molecular response of bacteria to sudden temperature upshift or downshift is termed the heat shock response (HSR) or the cold shock response (CSR), respectively. Unlike the HSR, which activates a dedicated transcription factor that predominantly copes with heat-induced protein folding stress,
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Seq Your Destiny: Neural Crest Fate Determination in the Genomic Era Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Shashank Gandhi, Marianne E. Bronner
Neural crest stem/progenitor cells arise early during vertebrate embryogenesis at the border of the forming central nervous system. They subsequently migrate throughout the body, eventually differentiating into diverse cell types ranging from neurons and glia of the peripheral nervous system to bones of the face, portions of the heart, and pigmentation of the skin. Along the body axis, the neural crest
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Genomic and Epigenetic Foundations of Neocentromere Formation Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Evon M. DeBose-Scarlett, Beth A. Sullivan
Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations
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DREAM On: Cell Cycle Control in Development and Disease Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Hayley Walston, Audra N. Iness, Larisa Litovchick
Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle–regulated gene expression, including multisubunit
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DNA End Resection: Mechanism and Control Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Petr Cejka, Lorraine S. Symington
DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genome integrity and cell viability. Typically, cells repair DSBs by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The relative use of these two pathways depends on many factors, including cell cycle stage and the nature of the DNA ends. A critical determinant of repair pathway selection is the initiation
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Prevalence and Adaptive Impact of Introgression Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Nathaniel B. Edelman, James Mallet
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically
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Genetic Regulation of RIPK1 and Necroptosis Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Daichao Xu, Chengyu Zou, Junying Yuan
The receptor-interacting protein kinase 1 (RIPK1) is recognized as a master upstream regulator that controls cell survival and inflammatory signaling as well as multiple cell death pathways, including apoptosis and necroptosis. The activation of RIPK1 kinase is extensively modulated by ubiquitination and phosphorylation, which are mediated by multiple factors that also control the activation of the
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Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Nikhil Mishra, Carl-Philipp Heisenberg
Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically
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A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Julio D. Perez, Claudia M. Fusco, Erin M. Schuman
Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein
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Revelations About Aging and Disease from Unconventional Vertebrate Model Organisms Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Yang Zhao, Andrei Seluanov, Vera Gorbunova
Aging is a major risk factor for multiple diseases. Understanding the underlying mechanisms of aging would help to delay and prevent age-associated diseases. Short-lived model organisms have been extensively used to study the mechanisms of aging. However, these short-lived species may be missing the longevity mechanisms that are needed to extend the lifespan of an already long-lived species such as
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Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria Annu. Rev. Genet. (IF 11.1) Pub Date : 2021-11-23 Brent W. Anderson, Danny K. Fung, Jue D. Wang
Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism