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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/28506494/sociomics-using-omic-approaches-to-understand-social-evolution
#1
REVIEW
Melanie Ghoul, Sandra B Andersen, Stuart A West
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression...
May 12, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28499622/m-6-a-in-mrna-an-ancient-mechanism-for-fine-tuning-gene-expression
#2
REVIEW
Jean-Yves Roignant, Matthias Soller
Modifications in mRNA constitute ancient mechanisms to regulate gene expression post-transcriptionally. N(6)-methyladenosine (m(6)A) is the most prominent mRNA modification, and is installed by a large methyltransferase complex (the m(6)A 'writer'), not only specifically bound by RNA-binding proteins (the m(6)A 'readers'), but also removed by demethylases (the m(6)A 'erasers'). m(6)A mRNA modifications have been linked to regulation at multiple steps in mRNA processing. In analogy to the regulation of gene expression by miRNAs, we propose that the main function of m(6)A is post-transcriptional fine-tuning of gene expression...
May 9, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28495267/the-evolutionary-interplay-between-adaptation-and-self-fertilization
#3
REVIEW
Matthew Hartfield, Thomas Bataillon, Sylvain Glémin
Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking...
May 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28457629/mosaicism-in-preimplantation-human-embryos-when-chromosomal-abnormalities-are-the-norm
#4
REVIEW
Rajiv C McCoy
Along with errors in meiosis, mitotic errors during post-zygotic cell division contribute to pervasive aneuploidy in human embryos. Relatively little is known, however, about the genesis of these errors or their fitness consequences. Rapid technological advances are helping to close this gap, revealing diverse molecular mechanisms contributing to mitotic error. These include altered cell cycle checkpoints, aberrations of the centrosome, and failed chromatid cohesion, mirroring findings from cancer biology. Recent studies are challenging the idea that mitotic error is abnormal, emphasizing that the fitness impacts of mosaicism depend on its scope and severity...
April 27, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28438343/developmental-and-transmittable-origins-of-obesity-associated-health-disorders
#5
REVIEW
Arin K Oestreich, Kelle H Moley
The current global obesity pandemic is clearly linked to both the increasing prevalence of, and preference for, foods high in calories, specifically fat and sucrose, and declining levels of daily physical activity. A less commonly discussed possible explanation is that risk of obesity begins in utero as a result of developmental plasticity during early life. This idea fits into the broader Developmental Origins of Health and Diseases (DOHAD) hypothesis, which holds that stressful in utero exposure manifests as disease in adulthood...
April 21, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28434610/gene-duplicates-agents-of-robustness-or-fragility
#6
Reiner A Veitia
A recent analysis of paralog deletion in yeast has shown that functional compensation and dependency occur equally. While theory predicts that compensation produces robustness, the authors hypothesized that stabilization of one paralogous protein through interaction with its copy could explain dependency. Here, we provide alternative explanations, such as selection for increased protein dosage and hypofunctionalization.
April 20, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28420493/etiology-of-human-genetic-disease-on-the-fly
#7
REVIEW
Clement Y Chow, Lawrence T Reiter
The model organism Drosophila melanogaster has been at the forefront of genetic studies since before the discovery of DNA. Although human disease modeling in flies may still be rather novel, recent advances in genetic tool design and genome sequencing now confer huge advantages in the fly system when modeling human disease. In this review, we focus on new genomic tools for human gene variant analysis; new uses for the Drosophila Genetic Reference Panel (DGRP) in detection of background alleles that influence a phenotype; and several examples of how multigenic conditions, both complex disorders and duplication and/or deletion syndromes, can be effectively studied in the fly model system...
April 15, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28365141/comparative-approaches-to-genetic-discrimination-chasing-shadows
#8
REVIEW
Yann Joly, Ida Ngueng Feze, Lingqiao Song, Bartha M Knoppers
Genetic discrimination (GD) is one of the most pervasive issues associated with genetic research and its large-scale implementation. An increasing number of countries have adopted public policies to address this issue. Our research presents a worldwide comparative review and typology of these approaches. We conclude with suggestions for public policy development.
March 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28365140/deregulation-of-crtcs-in-aging-and-age-related-disease-risk
#9
REVIEW
Caroline C Escoubas, Carlos G Silva-García, William B Mair
Advances in public health in the past century have seen a sharp increase in human life expectancy. With these changes have come an increased prevalence of age-related pathologies and health burdens in the elderly. Patient age is the biggest risk factor for multiple chronic conditions that often occur simultaneously within a single individual. An alternative to disease-centric therapeutic approaches is that of 'geroscience', which aims to define molecular mechanisms that link age to overall disease risk. One such mechanism is deregulation of CREB-regulated transcriptional coactivators (CRTCs)...
March 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28359583/enhancer-derived-lncrnas-regulate-genome-architecture-fact-or-fiction
#10
Stephanie Fanucchi, Musa M Mhlanga
How does the non-coding portion of the genome contribute to the regulation of genome architecture? A recent paper by Tan et al. focuses on the relationship between cis-acting complex-trait-associated lincRNAs and the formation of chromosomal contacts in topologically associating domains (TADs).
March 27, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28359582/variation-in-recombination-rate-adaptive-or-not
#11
REVIEW
Kathryn R Ritz, Mohamed A F Noor, Nadia D Singh
Rates of meiotic recombination are widely variable both within and among species. However, the functional significance of this variation remains largely unknown. Is the observed within-species variation in recombination rate adaptive? Recent work has revealed new insight into the scale and scope of population-level variation in recombination rate. These data indicate that the magnitude of within-population variation in recombination is similar among taxa. The apparent similarity of the variance in recombination rate among individuals between distantly related species suggests that the relative costs and benefits of recombination that establish the upper and lower bounds may be similar across species...
March 27, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28268034/epistasis-in-neuropsychiatric-disorders
#12
REVIEW
Caleb Webber
The contribution of epistasis to human disease remains unclear. However, several studies have now identified epistatic interactions between common variants that increase the risk of a neuropsychiatric disorder, while there is growing evidence that genetic interactions contribute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in patients. This review discusses the current evidence for epistatic events and genetic interactions in neuropsychiatric disorders, how paradigm shifts in the phenotypic classification of patients would empower the search for epistatic effects, and how network and cellular models might be employed to further elucidate relevant epistatic interactions...
March 3, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28372848/splicing-factor-mutations-in-myelodysplasias-insights-from-spliceosome-structures
#13
REVIEW
Jermaine L Jenkins, Clara L Kielkopf
Somatic mutations of pre-mRNA splicing factors recur among patients with myelodysplastic syndrome (MDS) and related malignancies. Although these MDS-relevant mutations alter the splicing of a subset of transcripts, the mechanisms by which these single amino acid substitutions change gene expression remain controversial. New structures of spliceosome intermediates and associated protein complexes shed light on the molecular interactions mediated by 'hotspots' of the SF3B1 and U2AF1 pre-mRNA splicing factors...
May 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28359585/imaging-translational-and-post-translational-gene-regulatory-dynamics-in-living-cells-with-antibody-based-probes
#14
REVIEW
Kenneth Lyon, Timothy J Stasevich
Antibody derivatives, such as antibody fragments (Fabs) and single-chain variable fragments (scFvs), are now being used to image traditionally hard-to-see protein subpopulations, including nascent polypeptides being translated and post-translationally modified proteins. This has allowed researchers to directly image and quantify, for the first time, translation initiation and elongation kinetics with single-transcript resolution and the temporal ordering and kinetics of post-translational histone and RNA polymerase II modifications...
May 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28359584/specialize-and-divide-twice-functions-of-three-aurora-kinase-homologs-in-mammalian-oocyte-meiotic-maturation
#15
REVIEW
Alexandra L Nguyen, Karen Schindler
The aurora kinases (AURKs) comprise an evolutionarily conserved family of serine/threonine kinases involved in mitosis and meiosis. While most mitotic cells express two AURK isoforms (AURKA and AURKB), mammalian germ cells also express a third, AURKC. Although much is known about the functions of the kinases in mitosis, less is known about how the three isoforms function to coordinate meiosis. This review is aimed at describing what is known about the three isoforms in female meiosis, the similarities and differences between kinase functions, and speculates as to why mammalian germ cells require expression of three AURKs instead of two...
May 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28292534/synonymous-codons-choose-wisely-for-expression
#16
REVIEW
Christina E Brule, Elizabeth J Grayhack
The genetic code, which defines the amino acid sequence of a protein, also contains information that influences the rate and efficiency of translation. Neither the mechanisms nor functions of codon-mediated regulation were well understood. The prevailing model was that the slow translation of codons decoded by rare tRNAs reduces efficiency. Recent genome-wide analyses have clarified several issues. Specific codons and codon combinations modulate ribosome speed and facilitate protein folding. However, tRNA availability is not the sole determinant of rate; rather, interactions between adjacent codons and wobble base pairing are key...
April 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28245910/genomics-of-islet-dys-function-and-type-2-diabetes
#17
REVIEW
Nathan Lawlor, Shubham Khetan, Duygu Ucar, Michael L Stitzel
Pancreatic islet dysfunction and beta cell failure are hallmarks of type 2 diabetes mellitus (T2DM) pathogenesis. In this review, we discuss how genome-wide association studies (GWASs) and recent developments in islet (epi)genome and transcriptome profiling (particularly single cell analyses) are providing novel insights into the genetic, environmental, and cellular contributions to islet (dys)function and T2DM pathogenesis. Moving forward, study designs that interrogate and model genetic variation [e.g., allelic profiling and (epi)genome editing] will be critical to dissect the molecular genetics of T2DM pathogenesis, to build next-generation cellular and animal models, and to develop precision medicine approaches to detect, treat, and prevent islet (dys)function and T2DM...
April 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174021/biogenesis-and-function-of-ago-associated-rnas
#18
REVIEW
Iben Daugaard, Thomas Birkballe Hansen
Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing...
March 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28236503/y-and-w-chromosome-assemblies-approaches-and-discoveries
#19
REVIEW
Marta Tomaszkiewicz, Paul Medvedev, Kateryna D Makova
Hundreds of vertebrate genomes have been sequenced and assembled to date. However, most sequencing projects have ignored the sex chromosomes unique to the heterogametic sex - Y and W - that are known as sex-limited chromosomes (SLCs). Indeed, haploid and repetitive Y chromosomes in species with male heterogamety (XY), and W chromosomes in species with female heterogamety (ZW), are difficult to sequence and assemble. Nevertheless, obtaining their sequences is important for understanding the intricacies of vertebrate genome function and evolution...
February 21, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28222895/the-epigenetic-regulator-smchd1-in-development-and-disease
#20
REVIEW
Natasha Jansz, Kelan Chen, James M Murphy, Marnie E Blewitt
It has very recently become clear that the epigenetic modifier SMCHD1 has a role in two distinct disorders: facioscapulohumoral muscular dystrophy (FSHD) and Bosma arhinia and micropthalmia (BAMS). In the former there are heterozygous loss-of-function mutations, while both gain- and loss-of-function mutations have been proposed to underlie the latter. These findings have led to much interest in SMCHD1 and how it works at the molecular level. We summarise here current understanding of the mechanism of action of SMCHD1, its role in these diseases, and what has been learnt from study of mouse models null for Smchd1 in the decade since the discovery of SMCHD1...
February 17, 2017: Trends in Genetics: TIG
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