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Trends in Genetics: TIG

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https://www.readbyqxmd.com/read/28196760/polycomb-group-systems-in-fungi-new-models-for-understanding-polycomb-repressive-complex-2
#1
REVIEW
Zachary A Lewis
Polycomb group (PcG) proteins form multiple complexes that direct assembly of transcriptionally repressed chromatin, an essential process for multicellular development. Recent studies in plants and animals have uncovered surprising complexity in the form of multiple, variant PcG complexes governed by an extensive regulatory network. PcG proteins are absent from major yeast models, but recent research revealed minimal PcG systems in several well-studied fungi. In both animals and fungi, PcG complexes are responsive to local chromatin structure, but important aspects of PcG regulation remain unknown...
February 11, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174022/the-evolution-and-genetics-of-carotenoid-processing-in-animals
#2
REVIEW
David P L Toews, Natalie R Hofmeister, Scott A Taylor
Coloration is one of the most conspicuous traits that varies among organisms. Carotenoid pigments are responsible for many of the red, orange, and yellow colors in the natural world and, at least for most animals, these molecules must be acquired from their environment. Identifying genes important for carotenoid transport, deposition, and processing has been difficult, in contrast to the well-characterized genes involved in the melanogenesis pathways. We review recent progress in the genetics of carotenoid processing, advances owing in part to the application of high-throughput sequencing data...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174021/biogenesis-and-function-of-ago-associated-rnas
#3
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...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174020/necessity-is-the-mother-of-invention-ciliates-transposons-and-transgenerational-inheritance
#4
REVIEW
Sarah E Allen, Mariusz Nowacki
Ciliates are a fascinating model system for the study of the interaction between eukaryotic germlines and somatic lines, especially with regard to the invasion and defence against transposable elements. They separate their germline and somatic line into two nuclei within the same cell, and they silence transposons and repetitive elements by way of deleting them from their somatic genome. This large-scale deletion event uses a series of intricate sequence targeting pathways involving small RNAs and transposases, part of which consists of a transnuclear comparison between maternal soma and daughter germline...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174019/understanding-idiopathic-scoliosis-a-new-zebrafish-school-of-thought
#5
REVIEW
Curtis W Boswell, Brian Ciruna
Idiopathic scoliosis (IS) refers to a 3D rotation of the spine that occurs in the absence of underlying vertebral anomalies or obvious physiological defects. Despite affecting approximately 4% of the population, the etiology and pathogenesis of IS remain poorly understood, largely due to genetic heterogeneity and historical lack of appropriate developmental models. Recently, zebrafish has emerged as a powerful system for studying IS, owing to well-developed genetic resources and a natural susceptibility to spinal curvatures...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28174018/evolving-plastic-responses-to-external-and-genetic-environments
#6
Max Reuter, M Florencia Camus, Mark S Hill, Filip Ruzicka, Kevin Fowler
Phenotypic plasticity can mitigate adaptive trade-offs in fluctuating environments but how plasticity arises is little known. New research documents this process in a bacterial system. We highlight remarkable parallels to the evolution of sexual dimorphism and argue that their approach can aid our understanding of adaptive conflicts between the sexes.
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28089370/single-cell-multiomics-multiple-measurements-from-single-cells
#7
REVIEW
Iain C Macaulay, Chris P Ponting, Thierry Voet
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies...
January 12, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28069312/centromeres-drive-a-hard-bargain
#8
REVIEW
Leah F Rosin, Barbara G Mellone
Centromeres are essential chromosomal structures that mediate the accurate distribution of genetic material during meiotic and mitotic cell divisions. In most organisms, centromeres are epigenetically specified and propagated by nucleosomes containing the centromere-specific H3 variant, centromere protein A (CENP-A). Although centromeres perform a critical and conserved function, CENP-A and the underlying centromeric DNA are rapidly evolving. This paradox has been explained by the centromere drive hypothesis, which proposes that CENP-A is undergoing an evolutionary tug-of-war with selfish centromeric DNA...
January 7, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28017398/moral-duties-of-genomics-researchers-why-personalized-medicine-requires-a-collective-approach
#9
REVIEW
Shoko Vos, Johannes J M van Delden, Paul J van Diest, Annelien L Bredenoord
Advances in genome sequencing together with the introduction of personalized medicine offer promising new avenues for research and precision treatment, particularly in the field of oncology. At the same time, the convergence of genomics, bioinformatics, and the collection of human tissues and patient data creates novel moral duties for researchers. After all, unprecedented amounts of potentially sensitive information are being generated. Over time, traditional research ethics principles aimed at protecting individual participants have become supplemented with social obligations related to the interests of society and the research enterprise at large, illustrating that genomic medicine is also a social endeavor...
December 22, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27939750/the-gep-crowd-sourcing-big-data-analysis-with-undergraduates
#10
Sarah C R Elgin, Charles Hauser, Teresa M Holzen, Christopher Jones, Adam Kleinschmit, Judith Leatherman
The era of 'big data' is also the era of abundant data, creating new opportunities for student-scientist research partnerships. By coordinating undergraduate efforts, the Genomics Education Partnership produces high-quality annotated data sets and analyses that could not be generated otherwise, leading to scientific publications while providing many students with research experience.
December 6, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28104289/nuclear-dynamics-of-heterochromatin-repair
#11
REVIEW
Nuno Amaral, Taehyun Ryu, Xiao Li, Irene Chiolo
Repairing double-strand breaks (DSBs) is particularly challenging in pericentromeric heterochromatin, where the abundance of repeated sequences exacerbates the risk of ectopic recombination and chromosome rearrangements. Recent studies in Drosophila cells revealed that faithful homologous recombination (HR) repair of heterochromatic DSBs relies on the relocalization of DSBs to the nuclear periphery before Rad51 recruitment. We summarize here the exciting progress in understanding this pathway, including conserved responses in mammalian cells and surprising similarities with mechanisms in yeast that deal with DSBs in distinct sites that are difficult to repair, including other repeated sequences...
February 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28087167/lingering-questions-about-enhancer-rna-and-enhancer-transcription-coupled-genomic-instability
#12
REVIEW
Gerson Rothschild, Uttiya Basu
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes...
February 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28012572/mammalian-polycistronic-mrnas-and-disease
#13
REVIEW
Timofey A Karginov, Daniel Parviz Hejazi Pastor, Bert L Semler, Christopher M Gomez
Our understanding of gene expression has come far since the 'one-gene one-polypeptide' hypothesis proposed by Beadle and Tatum. In this review, we address the gradual recognition that a growing number of polycistronic genes, originally discovered in viruses, are being identified within the mammalian genome, and that these may provide new insights into disease mechanisms and treatment. We carried out a systematic literature review identifying 13 mammalian genes for which there is evidence for polycistronic expression via translation through an internal ribosome entry site (IRES)...
February 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27939749/mining-the-unknown-assigning-function-to-noncoding-single-nucleotide-polymorphisms
#14
REVIEW
Sierra S Nishizaki, Alan P Boyle
One of the formative goals of genetics research is to understand how genetic variation leads to phenotypic differences and human disease. Genome-wide association studies (GWASs) bring us closer to this goal by linking variation with disease faster than ever before. Despite this, GWASs alone are unable to pinpoint disease-causing single nucleotide polymorphisms (SNPs). Noncoding SNPs, which represent the majority of GWAS SNPs, present a particular challenge. To address this challenge, an array of computational tools designed to prioritize and predict the function of noncoding GWAS SNPs have been developed...
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27939252/a-matter-of-time-small-rnas-regulate-the-duration-of-epigenetic-inheritance
#15
REVIEW
Leah Houri-Zeevi, Oded Rechavi
Small RNAs are increasingly emerging as transgenerational carriers of epigenetic information in Caenorhabditis elegans and in other organisms. Recent studies have identified factors that are required for the inheritance of small RNAs and for heritable RNAi in worms, which typically persist for a finite number of generations. We examine here recent insights into the mechanisms that control the duration of transgenerational inheritance of small RNAs. We discuss current understanding of two types of regulatory mechanisms: those that prolong RNAi inheritance through amplification and maintenance of heritable small RNAs, and those that limit the persistence of ancestral RNAi by, for example, employing negative feedback loops to reset the transmission of epigenetic information...
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27931778/a-magic-spot-in-genome-maintenance
#16
REVIEW
Aviram Rasouly, Bibhusita Pani, Evgeny Nudler
Nucleotide excision repair (NER) is the key DNA repair system that eliminates the majority of DNA helix-distorting lesions. RNA polymerase (RNAP) expedites the recognition of DNA damage by NER components via transcription-coupled DNA repair (TCR). In bacteria, a modified nucleotide ppGpp ('magic spot') is a pleiotropic second messenger that mediates the response to nutrient deficiencies by altering the initiation properties of RNAP. In this review, we discuss newly elucidated roles of guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in transcription elongation that couple this alarmone to DNA damage repair and maintenance...
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27916428/highly-signal-responsive-gene-regulatory-network-governing-myxococcus-development
#17
REVIEW
Lee Kroos
The bacterium Myxococcus xanthus undergoes multicellular development when starved. Thousands of cells build mounds in which some differentiate into spores. This remarkable feat and the genetic tractability of Myxococcus provide a unique opportunity to understand the evolution of gene regulatory networks (GRNs). Recent work has revealed a GRN involving interconnected cascades of signal-responsive transcriptional activators. Initially, starvation-induced intracellular signals direct changes in gene expression...
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27914620/gene-regulation-and-speciation
#18
REVIEW
Katya L Mack, Michael W Nachman
Understanding the genetic architecture of speciation is a major goal in evolutionary biology. Hybrid dysfunction is thought to arise most commonly through negative interactions between alleles at two or more loci. Divergence between interacting regulatory elements that affect gene expression (i.e., regulatory divergence) may be a common route for these negative interactions to arise. We review here how regulatory divergence between species can result in hybrid dysfunction, including recent theoretical support for this model...
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#19
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
January 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27889084/linking-telomere-regulation-to-stem-cell-pluripotency
#20
REVIEW
Lin Liu
Embryonic stem cells (ESCs), somatic cell nuclear transfer ESCs, and induced pluripotent stem cells (iPSCs) represent the most studied group of PSCs. Unlimited self-renewal without incurring chromosomal instability and pluripotency are essential for the potential use of PSCs in regenerative therapy. Telomere length maintenance is critical for the unlimited self-renewal, pluripotency, and chromosomal stability of PSCs. While telomerase has a primary role in telomere maintenance, alternative lengthening of telomere pathways involving recombination and epigenetic modifications are also required for telomere length regulation, notably in mouse PSCs...
January 2017: Trends in Genetics: TIG
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