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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/29132689/raw-genomic-data-storage-access-and-sharing
#1
Mahsa Shabani, Danya Vears, Pascal Borry
Patients are increasingly being encouraged and supported to access and control their own medical and genomic data. We argue that well-established and transparent raw genomic data retention and returning policies are imperative to enable patients to practice their rights to access and control raw data.
November 10, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29103876/intergenerational-transmission-of-gene-regulatory-information-in-caenorhabditis-elegans
#2
REVIEW
Olga Minkina, Craig P Hunter
Epigenetic mechanisms can stably maintain gene expression states even after the initiating conditions have changed. Often epigenetic information is transmitted only to daughter cells, but evidence is emerging, in both vertebrate and invertebrate systems, for transgenerational epigenetic inheritance (TEI), the transmission of epigenetic gene regulatory information across generations. Each new description of TEI helps uncover the properties, molecular mechanisms and biological roles for TEI. The nematode Caenorhabditis elegans has been particularly instrumental in the effort to understand TEI, as multiple environmental and genetic triggers can initiate an epigenetic signal that can alter the expression of both transgenes and endogenous loci...
November 2, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29102406/keeping-neurons-young-and-foxy-foxos-promote-neuronal-plasticity
#3
REVIEW
Colleen N McLaughlin, Heather T Broihier
Any adult who has tried to take up the piano or learn a new language is faced with the sobering realization that acquiring such skills is more challenging as an adult than as a child. Neuronal plasticity, or the malleability of brain circuits, declines with age. Young neurons tend to be more adaptable and can alter the size and strength of their connections more readily than can old neurons. Myriad circuit- and synapse-level mechanisms that shape plasticity have been identified. Yet, molecular mechanisms setting the overall competence of young neurons for distinct forms of plasticity remain largely obscure...
November 1, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29107345/functional-genomics-of-host-microbiome-interactions-in-humans
#4
REVIEW
Francesca Luca, Sonia S Kupfer, Dan Knights, Alexander Khoruts, Ran Blekhman
The human microbiome has been linked to various host phenotypes and has been implicated in many complex human diseases. Recent genome-wide association studies (GWASs) have used microbiome variation as a complex trait and have uncovered human genetic variants that are associated with the microbiome. Here we summarize results from these studies and illustrate potential regulatory mechanisms by which host genetic variation can interact with microbiome composition. We argue that, similar to human GWASs, it is important to use functional genomics techniques to gain a mechanistic understanding of causal host-microbiome interactions and their role in human disease...
October 26, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29107344/faithful-artificial-chromosome-propagation-using-spermatogonial-stem-cells
#5
M Yamada, M Seandel
Artificial chromosomes are useful in making functional vectors for very large genes, studying chromosome physiology, and modeling chromosomal disorders. Shinohara et al. have succeeded for the first time in creating transchromosomic mice by manipulating spermatogonial stem cells (SSCs), which exhibited superior chromosomal stability compared with embryonic stem cells (ESCs).
October 26, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29061469/development-and-evolution-through-the-lens-of-global-gene-regulation
#6
REVIEW
Itai Yanai
Evolution and development are two inherently intertwined processes. As the embryo develops it does so in ways that both reflect past constraints and bias the future evolution of the species. While research exploiting this insight typically studies individual genes, transcriptomic analyses have sparked a new wave of discoveries. In this opinion piece, I review the evidence arising from transcriptomics on the topics of the evolution of germ layers, the phylotypic stage, and developmental constraints. The spatiotemporal pattern of gene expression across germ layers provides evidence that the endoderm was the first germ layer to evolve...
October 20, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29037439/caenorhabditis-elegans-dosage-compensation-insights-into-condensin-mediated-gene-regulation
#7
REVIEW
Sarah Elizabeth Albritton, Sevinç Ercan
Recent work demonstrating the role of chromosome organization in transcriptional regulation has sparked substantial interest in the molecular mechanisms that control chromosome structure. Condensin, an evolutionarily conserved multisubunit protein complex, is essential for chromosome condensation during cell division and functions in regulating gene expression during interphase. In Caenorhabditis elegans, a specialized condensin forms the core of the dosage compensation complex (DCC), which specifically binds to and represses transcription from the hermaphrodite X chromosomes...
October 13, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29037438/tag-team-roles-of-mirnas-and-proteolytic-regulators-in-ensuring-robust-gene-expression-dynamics
#8
REVIEW
Benjamin P Weaver, Min Han
Lack of prominent developmental defects arising from loss of many individual miRNAs is consistent with the observations of collaborative networks between miRNAs and roles for miRNAs in regulating stress responses. However, these characteristics may only partially explain the seemingly nonessential nature of many miRNAs. Non-miRNA gene expression regulatory mechanisms also collaborate with miRNA-induced silencing complex (miRISC) to support robust gene expression dynamics. Genetic enhancer screens have revealed roles of miRNAs and other gene repressive mechanisms in development or other cellular processes that were masked by genetic redundancy...
October 13, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29029851/arresting-evolution
#9
REVIEW
James J Bull, Jeffrey E Barrick
Evolution in the form of selective breeding has long been harnessed as a useful tool by humans. However, rapid evolution can also be a danger to our health and a stumbling block for biotechnology. Unwanted evolution can underlie the emergence of drug and pesticide resistance, cancer, and weeds. It makes live vaccines and engineered cells inherently unreliable and unpredictable, and therefore potentially unsafe. Yet, there are strategies that have been and can possibly be used to stop or slow many types of evolution...
October 10, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28988701/choosing-the-active-x-the-human-version-of-x-inactivation
#10
REVIEW
Barbara R Migeon
Humans and rodents differ in how they carry out X inactivation (XI), the mammalian method to compensate for the different number of X chromosomes in males and females. Evolutionary changes in staging embryogenesis and in mutations within the XI center alter the process among mammals. The mouse model of XI is predicated on X counting and subsequently choosing the X to 'inactivate'. However, new evidence suggests that humans initiate XI by protecting one X in both sexes from inactivation by XIST, the noncoding RNA that silences the inactive X...
October 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28987266/the-genetics-of-multiple-sclerosis-from-0-to-200-in-50-years
#11
REVIEW
Sergio E Baranzini, Jorge R Oksenberg
Multiple sclerosis (MS) is a common autoimmune disease that targets myelin in the central nervous system (CNS). Multiple genome-wide association studies (GWAS) over the past 10 years have uncovered more than 200 loci that independently contribute to disease pathogenesis. As with many other complex diseases, risk of developing MS is driven by multiple common variants whose biological effects are not immediately clear. Here, we present a historical perspective on the progress made in MS genetics and discuss current work geared towards creating a more complete model that accurately represents the genetic landscape of MS susceptibility...
October 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28969871/alternative-lengthening-of-telomeres-dna-repair-pathways-converge
#12
REVIEW
Alexander P Sobinoff, Hilda A Pickett
Telomeres shorten during each cellular division, with cumulative attrition resulting in telomeric damage and replicative senescence. Bypass of replicative senescence precipitates catastrophic telomere shortening or crisis, and is characterized by widespread genomic instability. Activation of a telomere maintenance mechanism (TMM) is necessary to stabilise the genome and establish cellular immortality through the reconstitution of telomere capping function. The alternative lengthening of telomeres (ALT) pathway is a TMM frequently activated in tumors of mesenchymal or neuroepithelial origin...
September 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28969870/samhd1-sheds-moonlight-on-dna-double-strand-break-repair
#13
Maria Jose Cabello-Lobato, Siyue Wang, Christine Katrin Schmidt
SAMHD1 (sterile α motif and histidine (H) aspartate (D) domain-containing protein 1) is known for its antiviral activity of hydrolysing deoxynucleotides required for virus replication. Daddacha et al. identify a hydrolase-independent, moonlighting function of SAMHD1 that facilitates homologous recombination of DNA double-strand breaks (DSBs) by promoting recruitment of C-terminal binding protein interacting protein (CTIP), a DNA-end resection factor, to damaged DNA. These findings could benefit anticancer treatment...
September 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28947158/stay-connected-a-germ-cell-strategy
#14
REVIEW
Kevin Lu, Lindy Jensen, Lei Lei, Yukiko M Yamashita
Germ cells develop as a cyst of interconnected sibling cells in a broad range of organisms in both sexes. A well-established function of intercellular connectivity is to transport cytoplasmic materials from 'nurse' cells to oocytes, a critical process for developing functional oocytes in ovaries of many species. However, there are situations where connectivity exists without a nursing mechanism, and the biological meaning of such connectivity remains obscure. In this review, we summarize current knowledge on the formation of intercellular connectivity, and discuss its meaning by visiting multiple examples of germ cell connectivity observed in evolutionarily distant species...
September 22, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28919019/epithelial-to-mesenchymal-transition-epigenetic-reprogramming-driving-cellular-plasticity
#15
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
#16
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/28887026/beyond-read-counts-ribo-seq-data-analysis-to-understand-the-functions-of-the-transcriptome
#17
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
#18
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
#19
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/28987267/the-mobile-world-of-transposable-elements
#20
EDITORIAL
Caryn Navarro
No abstract text is available yet for this article.
November 2017: Trends in Genetics: TIG
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