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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/28919019/epithelial-to-mesenchymal-transition-epigenetic-reprogramming-driving-cellular-plasticity
#1
REVIEW
Nicolas Skrypek, Steven Goossens, Eva De Smedt, Niels Vandamme, Geert Berx
Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their junctions and polarity to gain a motile mesenchymal phenotype. EMT is essential during embryogenesis and adult physiological processes like wound healing, but is aberrantly activated in pathological conditions like fibrosis and cancer. A series of transcription factors (EMT-inducing transcription factor; EMT-TF) regulate the induction of EMT by repressing the transcription of epithelial genes while activating mesenchymal genes through mechanisms still debated...
September 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28899597/playing-well-with-others-extrinsic-cues-regulate-neural-progenitor-temporal-identity-to-generate-neuronal-diversity
#2
REVIEW
Mubarak Hussain Syed, Brandon Mark, Chris Q Doe
During neurogenesis, vertebrate and Drosophila progenitors change over time as they generate a diverse population of neurons and glia. Vertebrate neural progenitors have long been known to use both progenitor-intrinsic and progenitor-extrinsic cues to regulate temporal patterning. In contrast, virtually all temporal patterning mechanisms discovered in Drosophila neural progenitors (neuroblasts) involve progenitor-intrinsic temporal transcription factor cascades. Recent results, however, have revealed several extrinsic pathways that regulate Drosophila neuroblast temporal patterning: nutritional cues regulate the timing of neuroblast proliferation/quiescence and a steroid hormone cue that is required for temporal transcription factor expression...
September 9, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28888423/transposons-as-tools-for-functional-genomics-in-vertebrate-models
#3
REVIEW
Koichi Kawakami, David A Largaespada, Zoltán Ivics
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes...
September 6, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28887026/beyond-read-counts-ribo-seq-data-analysis-to-understand-the-functions-of-the-transcriptome
#4
REVIEW
Lorenzo Calviello, Uwe Ohler
By mapping the positions of millions of translating ribosomes in the cell, ribosome profiling (Ribo-seq) has established its role as a powerful tool to study gene expression. Several laboratories have introduced modifications to the experimental protocol and expanded the repertoire of biochemical methods to study translation transcriptome-wide. However, the diversity of protocols highlights a need for standardization. At the same time, different computational analysis strategies have used Ribo-seq data to identify the set of translated sequences with high confidence...
September 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28870654/molecular-dependency-impacts-on-the-compensating-ability-of-paralogs
#5
LETTER
Christian R Landry, Guillaume Diss
No abstract text is available yet for this article.
September 1, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28870653/the-new-rna-world-growing-evidence-for-long-noncoding-rna-functionality
#6
REVIEW
Allison Jandura, Henry M Krause
The past decade has seen a major increase in the study of noncoding RNAs (ncRNAs). However, there remains a great deal of confusion and debate over the levels of functionality and mechanisms of action of the majority of these new transcripts. This Opinion article addresses several of these issues, focusing particularly on long ncRNAs (lncRNAs). We reemphasize the unique abilities of RNAs to form myriad structures as well as to interact with other RNAs, DNA, and proteins, which provide them with unique and powerful abilities...
September 1, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28867048/signaling-and-gene-regulatory-networks-in-mammalian-lens-development
#7
REVIEW
Ales Cvekl, Xin Zhang
Ocular lens development represents an advantageous system in which to study regulatory mechanisms governing cell fate decisions, extracellular signaling, cell and tissue organization, and the underlying gene regulatory networks. Spatiotemporally regulated domains of BMP, FGF, and other signaling molecules in late gastrula-early neurula stage embryos generate the border region between the neural plate and non-neural ectoderm from which multiple cell types, including lens progenitor cells, emerge and undergo initial tissue formation...
August 31, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28867047/birth-and-death-of-histone-mrnas
#8
REVIEW
William F Marzluff, Kaitlin P Koreski
In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73...
August 31, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28851604/regulatory-logic-underlying-diversification-of-the-neural-crest
#9
REVIEW
Megan L Martik, Marianne E Bronner
The neural crest is a transient, multipotent population of cells that arises at the border of the developing nervous system. After closure of the neural tube, these cells undergo an epithelial-to-mesenchymal transition (EMT) to delaminate and migrate, often to distant locations in the embryo. Neural crest cells give rise to a diverse array of derivatives including neurons and glia of the peripheral nervous system, melanocytes, and bone and cartilage of the face. A gene regulatory network (GRN) controls the specification, delamination, migration, and differentiation of this fascinating cell type...
August 26, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28844699/circadian-clocks-and-metabolism-implications-for-microbiome-and-aging
#10
REVIEW
Georgios K Paschos, Garret A FitzGerald
The circadian clock directs many aspects of metabolism, to separate in time opposing metabolic pathways and optimize metabolic efficiency. The master circadian clock of the suprachiasmatic nucleus synchronizes to light, while environmental cues such as temperature and feeding, out of phase with the light schedule, may synchronize peripheral clocks. This misalignment of central and peripheral clocks may be involved in the development of disease and the acceleration of aging, possibly in a gender-specific manner...
August 24, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28844698/transposable-element-domestication-as-an-adaptation-to-evolutionary-conflicts
#11
REVIEW
Diwash Jangam, Cédric Feschotte, Esther Betrán
Transposable elements (TEs) are selfish genetic units that typically encode proteins that enable their proliferation in the genome and spread across individual hosts. Here we review a growing number of studies that suggest that TE proteins have often been co-opted or 'domesticated' by their host as adaptations to a variety of evolutionary conflicts. In particular, TE-derived proteins have been recurrently repurposed as part of defense systems that protect prokaryotes and eukaryotes against the proliferation of infectious or invasive agents, including viruses and TEs themselves...
August 24, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28826631/multifarious-functions-of-the-fragile-x-mental-retardation-protein
#12
REVIEW
Jenna K Davis, Kendal Broadie
Fragile X syndrome (FXS), a heritable intellectual and autism spectrum disorder (ASD), results from the loss of Fragile X mental retardation protein (FMRP). This neurodevelopmental disease state exhibits neural circuit hyperconnectivity and hyperexcitability. Canonically, FMRP functions as an mRNA-binding translation suppressor, but recent findings have enormously expanded its proposed roles. Although connections between burgeoning FMRP functions remain unknown, recent advances have extended understanding of its involvement in RNA, channel, and protein binding that modulate calcium signaling, activity-dependent critical period development, and the excitation-inhibition (E/I) neural circuitry balance...
August 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28823576/gene-duplicates-agents-of-fragility-a-reply-to-landry-and-diss
#13
LETTER
Reiner A Veitia
No abstract text is available yet for this article.
August 17, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28818345/mobile-group-ii-introns-as-ancestral-eukaryotic-elements
#14
REVIEW
Olga Novikova, Marlene Belfort
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes...
August 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28800915/transposable-elements-direct-the-coevolution-between-plants-and-microbes
#15
REVIEW
Michael F Seidl, Bart P H J Thomma
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes...
August 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28800914/aneuploidy-police-detect-chromosomal-imbalance-triggering-immune-crackdown
#16
Emma V Watson, Stephen J Elledge
Aneuploidy is ubiquitous in cancer and plays a pivotal, early role in tumor evolution. It must therefore be avoided, and two recent papers highlight the roles of p53, senescence, and the immune system in preventing the outgrowth of aneuploid clones in tissue culture. These mechanisms are likely to synergize to maintain diploid cell populations.
August 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28797643/l1-mosaicism-in-mammals-extent-effects-and-evolution
#17
REVIEW
Geoffrey J Faulkner, Jose L Garcia-Perez
The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism...
August 7, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28781152/speech-and-language-translating-the-genome
#18
REVIEW
Pelagia Deriziotis, Simon E Fisher
Investigation of the biological basis of human speech and language is being transformed by developments in molecular technologies, including high-throughput genotyping and next-generation sequencing of whole genomes. These advances are shedding new light on the genetic architecture underlying language-related disorders (speech apraxia, specific language impairment, developmental dyslexia) as well as that contributing to variation in relevant skills in the general population. We discuss how state-of-the-art methods are uncovering a range of genetic mechanisms, from rare mutations of large effect to common polymorphisms that increase risk in a subtle way, while converging on neurogenetic pathways that are shared between distinct disorders...
August 3, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28778681/on-the-origin-of-lncrnas-missing-link-found
#19
Joaquín M Espinosa
Non-coding (nc)RNAs known as enhancer-derived RNAs (eRNAs) and as long ncRNAs (lncRNAs) have received much attention, but their true functional specialization and evolutionary origins remain obscure. The recent characterization of Bloodlinc, an eRNA derived from a super-enhancer that also functions as a lncRNA, suggests that lncRNAs can evolve from eRNAs.
August 1, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28764860/crispring-the-regulatory-genome-the-challenge-ahead
#20
Stephanie E Sansbury, Katelyn M Sweeney, Ophir Shalem
CRISPR saturation mutagenesis has the potential to dissect the functional landscape of noncoding regions, but is highly susceptible to false discovery and misinterpretation. As recently published, Canver et al. have now taken the first steps towards addressing these issues by increasing screening resolution and analyzing the effects of off targets on hit calling.
July 29, 2017: Trends in Genetics: TIG
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