journal
https://read.qxmd.com/read/38302301/a-sea-star-is-only-a-head
#21
JOURNAL ARTICLE
Andreas Hejnol
Where are the front and back ends in a sea star? Formery et al. 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.
January 31, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38296708/how-intrinsically-disordered-proteins-order-plant-gene-silencing
#22
REVIEW
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 in nuclear transcription and cytoplasmic post-transcriptional processes, among other molecular functions...
January 30, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38272738/duplicated-gene-networks-promote-hopeful-phenotypic-variation
#23
JOURNAL ARTICLE
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.
January 24, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38262796/degradation-and-translation-of-maternal-mrna-for-embryogenesis
#24
REVIEW
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 fertilization for reprogramming the zygotic genome during early embryogenesis. Oocyte specific cofactors and pathways have been illustrated to control different futures of maternal mRNAs...
January 22, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38216391/time-will-tell-comparing-timescales-to-gain-insight-into-transcriptional-bursting
#25
REVIEW
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 relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells...
January 11, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38177041/gene-regulation-during-meiosis
#26
REVIEW
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 regulated, including preparation for post-meiotic development. Research in model organisms, notably yeast, has shed light on the genetic and molecular aspects of meiosis and its regulation...
January 3, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38171966/uncovering-dark-matter-in-cancer-by-identifying-epigenetic-drivers
#27
JOURNAL ARTICLE
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.
January 2, 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38161109/the-genetic-landscape-of-age-related-hearing-loss
#28
REVIEW
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 associated with ARHL, the detailed mechanisms, encompassing both genetic and epigenetic modifications, remain to be fully elucidated...
December 30, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/38160062/take-a-walk-on-the-krab-side-trends-in-genetics-39-11-p-844-857-2023
#29
Olga Rosspopoff, Didier Trono
No abstract text is available yet for this article.
December 30, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/37926636/making-sense-of-proprioception
#30
JOURNAL ARTICLE
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.
January 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/37879968/small-protein-plays-with-big-networks
#31
JOURNAL ARTICLE
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.
January 2024: Trends in Genetics: TIG
https://read.qxmd.com/read/38160061/in-search-of-critical-dsrna-targets-of-adar1
#32
REVIEW
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, which offer valuable insights into this unresolved query. The growing appreciation of the significance of immunogenic dsRNAs and their editing in inflammatory and autoimmune diseases and cancer calls for a more comprehensive understanding of dsRNA immunogenicity, which may promote our understanding of these diseases and open doors to therapeutic avenues...
December 29, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/38135595/biobanking-animal-genetic-resources-critical-infrastructure-and-growth-opportunities
#33
JOURNAL ARTICLE
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.
December 22, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/38123442/advances-in-methods-for-trna-sequencing-and-quantification
#34
REVIEW
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 and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows...
December 19, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/37743186/protecting-axons-in-grandchildren
#35
JOURNAL ARTICLE
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.
December 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/38036338/tfam-mislocalization-during-spermatogenesis
#36
JOURNAL ARTICLE
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.
November 29, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/38000919/metastable-epialleles-in-humans
#37
REVIEW
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 suggests that some putative human MEs are sensitive to environmental exposures in early development. In this review we introduce key concepts pertaining to human MEs, describe methods used to identify MEs in humans, and review their genomic features...
November 23, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/37989654/next-generation-forward-genetic-screens-uniting-high-throughput-perturbations-with-single-cell-analysis
#38
REVIEW
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 as growth or fluorescent reporters of gene expression. By pairing massively parallel screens with high-dimensional profiling of single-cell types/states, we can now measure how individual genetic perturbations or combinations of perturbations impact the cellular transcriptome, proteome, and epigenome...
November 20, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/37985317/wildlife-endogenous-retroviruses-colonization-consequences-and-cooption
#39
REVIEW
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 of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species...
November 18, 2023: Trends in Genetics: TIG
https://read.qxmd.com/read/37968205/a-dive-into-the-unknome
#40
JOURNAL ARTICLE
Juri Rappsilber
We may never understand the function of all genes, findings by Freeman, Munro and colleagues Rocha et al. 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.
November 13, 2023: Trends in Genetics: TIG
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