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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/28633980/the-genes-that-make-a-good-parent
#1
Reinmar Hager
What is the genetic basis of differences in parental care between promiscuous and monogamous mammal species? A team led by Hopi Hoekstra studied an intercross between deer mice and old-field mice that differ in their mating systems and parental behaviours. The authors discovered 12 genomic regions contributing to those differences and identified vasopressin as a regulator of nestbuilding behaviour.
June 17, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629950/antibiotic-independent-adaptive-effects-of-antibiotic-resistance-mutations
#2
REVIEW
Ruth Hershberg
Antibiotic usage selects for the accumulation and spread of antibiotic-resistant bacteria. However, resistance can also accumulate in the absence of antibiotic exposure. Antibiotics are often designed to target widely distributed regulatory housekeeping genes. The targeting of such genes enables these antibiotics to be useful against a wider variety of pathogens. This review highlights work suggesting that regulatory housekeeping genes of the type targeted by many antibiotics function as hubs of adaptation to conditions unrelated to antibiotic exposure...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#3
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28545962/a-fundamental-unit-of-cell-size-in-bacteria
#4
Suckjoon Jun, Michael J Rust
A new study clarifies a relationship between growth, gene expression, and cell size in cyanobacteria. Quite unexpectedly, cyanobacteria and Escherichia coli appear to share an invariance principle to coordinate growth and chromosome replication. This principle allows quantitative predictions of cell size across a range of growth conditions in both organisms.
May 22, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28535931/the-dimensions-dynamics-and-relevance-of-the-mammalian-noncoding-transcriptome
#5
REVIEW
Ira W Deveson, Simon A Hardwick, Tim R Mercer, John S Mattick
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing...
May 20, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28532625/v-d-j-recombination-exploits-dna-damage-responses-to-promote-immunity
#6
REVIEW
Rahul Arya, Craig H Bassing
It has been recognized for 40 years that the variable (diversity) joining [V(D)J] recombination-mediated assembly of diverse B and T lymphocyte antigen receptor (AgR) genes is not only essential for adaptive immunity, but also a risk for autoimmunity and lymphoid malignancies. Over the past few years, several studies have revealed that recombination-activating gene (RAG) endonuclease-induced DNA double-strand breaks (DSBs) transcend hazardous intermediates during antigen receptor gene assembly. RAG cleavage within the genomes of lymphocyte progenitors and immature lymphocytes regulates the expression of ubiquitous and lymphocyte-specific gene transcripts to control the differentiation and function of both adaptive and innate immune cell lineages...
May 19, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28528721/perspectives-on-gene-regulatory-network-evolution
#7
REVIEW
Marc S Halfon
Animal development proceeds through the activity of genes and their cis-regulatory modules (CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here various aspects of GRN evolution and argue that developmental system drift (DSD), in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution...
May 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28506494/sociomics-using-omic-approaches-to-understand-social-evolution
#8
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/28438343/developmental-and-transmittable-origins-of-obesity-associated-health-disorders
#9
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
#10
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
#11
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
#12
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
#13
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/28457629/mosaicism-in-preimplantation-human-embryos-when-chromosomal-abnormalities-are-the-norm
#14
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...
July 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28499622/m-6-a-in-mrna-an-ancient-mechanism-for-fine-tuning-gene-expression
#15
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...
June 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28495267/the-evolutionary-interplay-between-adaptation-and-self-fertilization
#16
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...
June 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28372848/splicing-factor-mutations-in-myelodysplasias-insights-from-spliceosome-structures
#17
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
#18
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
#19
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
#20
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
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