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Journals Current Opinion in Genetics & ...

Current Opinion in Genetics & Development

https://read.qxmd.com/read/38266394/emergence-of-the-circadian-clock-oscillation-during-the-developmental-process-in-mammals
#21
REVIEW
Kazuhiro Yagita
The circadian clocks are cell-autonomous intrinsic oscillators existing throughout the body to coordinate intracellular and intercellular functions of each organ or tissue. The circadian clock oscillation gradually emerges during mid-to-late gestation in the mammalian developmental process. Recently, it has been revealed that the in vitro differentiation of mouse ES cells recapitulates the circadian clock development. Moreover, reprogramming of the cells results in the redisappearance of the clock, indicating that circadian clocks are tightly coupled with cellular differentiation...
January 23, 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38237456/what-are-tethering-elements
#22
REVIEW
Xiao Li, Michael Levine
High-resolution Micro-C maps identified a specialized class of regulatory DNAs termed 'tethering elements' (TEs) in Drosophila. These 300-500-bp elements facilitate specific long-range genomic associations or loops. The POZ-containing transcription factor GAF (GAGA-associated factor) contributes to loop formation. Tether-tether interactions accelerate Hox gene activation by distal enhancers, and coordinate transcription of duplicated genes (paralogs) through promoter-promoter associations. Some TEs engage in ultra-long-range enhancer-promoter and promoter-promoter interactions (meta-loops) in the Drosophila brain...
January 17, 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38215626/on-the-edge-how-nuclear-pore-complexes-rule-genome-stability
#23
REVIEW
Marie-Noëlle Simon, Karine Dubrana, Benoit Palancade
Nuclear organization has emerged as a critical layer in the coordination of DNA repair activities. Distinct types of DNA lesions have notably been shown to relocate at the vicinity of nuclear pore complexes (NPCs), where specific repair pathways are favored, ultimately safeguarding genome integrity. Here, we review the most recent progress in this field, notably highlighting the increasingly diverse types of DNA structures undergoing repositioning, and the signaling pathways involved. We further discuss our growing knowledge of the molecular mechanisms underlying the choice of repair pathways at NPCs, and their conservation - or divergences...
January 11, 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38199063/the-stem-cell-zoo-for-comparative-studies-of-developmental-tempo
#24
REVIEW
Jorge Lázaro, Jaroslaw Sochacki, Miki Ebisuya
The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species...
January 9, 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38171044/deciphering-microglia-phenotypes-in-health-and-disease
#25
REVIEW
Christopher D Balak, Claudia Z Han, Christopher K Glass
Microglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent transcription factors interact to select and regulate the ensembles of enhancers that determine microglia development and function...
January 2, 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38447236/safeguarding-the-epigenome-through-the-cell-cycle-a-multitasking-game
#26
REVIEW
Valentin Flury, Anja Groth
Sustaining cell identity and function across cell division is germane to human development, healthspan, and cancer avoidance. This relies significantly on propagation of chromatin organization between cell generations, as chromatin presents a barrier to cell fate and cell state conversions. Inheritance of chromatin states across the many cell divisions required for development and tissue homeostasis represents a major challenge, especially because chromatin is disrupted to allow passage of the DNA replication fork to synthesize the two daughter strands...
April 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38430840/inheritance-of-epigenetic-transcriptional-memory
#27
REVIEW
Tiffany Ge, Jason H Brickner
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future...
April 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38428317/somatic-hypermutation-mechanisms-during-lymphomagenesis-and-transformation
#28
REVIEW
Max C Lauring, Uttiya Basu
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma...
April 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38176333/loops-crosstalk-and-compartmentalization-it-takes-many-layers-to-regulate-dna-methylation
#29
REVIEW
Guanghui Xu, Julie A Law
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome...
February 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38128453/exploring-new-roles-for-rna-binding-proteins-in-epigenetic-and-gene-regulation
#30
REVIEW
Pedro Avila-Lopez, Shannon M Lauberth
A significant portion of the human proteome comprises RNA-binding proteins (RBPs) that play fundamental roles in numerous biological processes. In the last decade, there has been a staggering increase in RBP identification and classification, which has fueled interest in the evolving roles of RBPs and RBP-driven molecular mechanisms. Here, we focus on recent insights into RBP-dependent regulation of the epigenetic and transcriptional landscape. We describe advances in methodologies that define the RNA-protein interactome and machine-learning algorithms that are streamlining RBP discovery and predicting new RNA-binding regions...
December 20, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38091876/polycomb%C3%A2-repressive-complex-2-accessory-factors-rheostats-for-cell-fate-decision
#31
REVIEW
Hina Bharti, Sungwook Han, Han-Wen Chang, Danny Reinberg
Epigenetic reprogramming during development is key to cell identity and the activities of the Polycomb repressive complexes are vital for this process. We focus on polycomb repressive complex 2 (PRC2), which catalyzes H3K27me1/2/3 and safeguards cellular integrity by ensuring proper gene repression. Notably, various accessory factors associate with PRC2, strongly influencing cell fate decisions, and their deregulation contributes to various illnesses. Yet, the exact role of these factors during development and carcinogenesis is not fully understood...
December 12, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38052116/topical-section-embryonic-models-2023-for-current-opinion-in-genetics-development
#32
REVIEW
Charlotte E Handford, Sergi Junyent, Victoria Jorgensen, Magdalena Zernicka-Goetz
Stem cell-based mammalian embryo models facilitate the discovery of developmental mechanisms because they are more amenable to genetic and epigenetic perturbations than natural embryos. Here, we highlight exciting recent advances that have yielded a plethora of models of embryonic development. Imperfections in these models highlight gaps in our current understanding and outline future research directions, ushering in an exciting new era for embryology.
December 4, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38052115/human-blastoid-as-an-in-vitro-model-of-human-blastocysts
#33
REVIEW
Xiaodong Liu, Jose M Polo
Human development is a highly coordinated process, with any abnormalities during the early embryonic stages that can often have detrimental consequences. The complexity and nuances of human development underpin its significance in embryo research. However, this research is often hindered by limited availability and ethical considerations associated with the use of donated blastocysts from in vitro fertilization (IVF) surplus. Human blastoids offer promising alternatives as they can be easily generated and manipulated in the laboratory while preserving key characteristics of human blastocysts...
December 4, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37897953/modifying-gastruloids-to-dissect-mechanisms-of-tissue-specific-induction
#34
REVIEW
David A Turner, Jennifer Nichols
How functional organisms arise from a single cell is a fundamental question in biology with direct relevance to understanding developmental defects and diseases. Dissecting developmental processes provides the basic, critical framework for understanding disease progression and treatment. Bottom-up approaches to recapitulate formation of various components of the embryo have been effective to probe symmetry-breaking, self-organisation, tissue patterning and morphogenesis. However, these studies have been mostly concerned with axial patterning, which is essentially longitudinal...
December 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37866057/editorial-overview-conflicts-conflicts-everywhere
#35
EDITORIAL
Harmit S Malik, Judith E Mank
No abstract text is available yet for this article.
December 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37839315/overcoming-muscle-stem-cell-aging
#36
REVIEW
Sebastian Memczak, Juan Ci Belmonte
Reduced muscle strength and mass is one of the hallmarks of physiological aging in humans and can result in severe impairment of the quality of life. In part this is caused by a functional loss of the highly specialized muscle stem cells (MuSCs), which in healthy conditions provide maintenance, growth, and regeneration. Recent progress in understanding of the stem cell niche and results from single cell technologies reveal exciting insights at unprecedented detail into MuSCs and muscle biology during aging...
December 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37951138/-enhancing-skeletal-muscle-and-stem-cells-in-three-dimensional-genome-regulation-of-skeletal-muscle-in-development-and-disease
#37
REVIEW
Matthew A Romero, April D Pyle
The noncoding genome imparts important regulatory control over gene expression. In particular, gene enhancers represent a critical layer of control that integrates developmental and differentiation signals outside the cell into transcriptional outputs inside the cell. Recently, there has been an explosion in genomic techniques to probe enhancer control, function, and regulation. How enhancers are regulated and integrate signals in stem cell development and differentiation is largely an open question. In this review, we focus on the role gene enhancers play in muscle stem cell specification, differentiation, and progression...
November 9, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37931583/somatic-mutation-burden-in-relation-to-aging-and-functional-life-span-implications-for-cellular-reprogramming-and-rejuvenation
#38
REVIEW
Alexander Y Maslov, Jan Vijg
The accrual of somatic mutations has been implicated as causal factors in aging since the 1950s. However, the quantitative analysis of somatic mutations has posed a major challenge due to the random nature of de novo mutations in normal tissues, which has limited analysis to tumors and other clonal lineages. Advances in single-cell and single-molecule next-generation sequencing now allow to obtain, for the first time, detailed insights into the landscape of somatic mutations in different human tissues and cell types as a function of age under various conditions...
November 4, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37864936/divergent-outcomes-of-genetic-conflict-on-the-uv-sex-chromosomes-of-marchantia-polymorpha-and-ceratodon-purpureus
#39
REVIEW
Stuart F McDaniel
In species with separate sexes, the genome must produce two distinct developmental programs. Sexually dimorphic development may be controlled by either sex-limited loci or biased expression of loci transmitted through both sexes. Variation in the gene content of sex-limited chromosomes demonstrates that eukaryotic species differ markedly in the roles of these two mechanisms in governing sexual dimorphism. The bryophyte model systems Marchantia polymorpha and Ceratodon purpureus provide a particularly striking contrast...
October 19, 2023: Current Opinion in Genetics & Development
https://read.qxmd.com/read/37862835/insights-and-applications-of-direct-neuronal-reprogramming
#40
REVIEW
Katie Schaukowitch, Justyna A Janas, Marius Wernig
Direct neuronal reprogramming converts somatic cells of a defined lineage into induced neuronal cells without going through a pluripotent intermediate. This approach not only provides access to the otherwise largely inaccessible cells of the brain for neuronal disease modeling, but also holds great promise for ultimately enabling neuronal cell replacement without the use of transplantation. To improve efficiency and specificity of direct neuronal reprogramming, much of the current efforts aim to understand the mechanisms that safeguard cell identities and how the reprogramming cells overcome the barriers resisting fate changes...
October 18, 2023: Current Opinion in Genetics & Development
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