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Nature Reviews. Genetics

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https://www.readbyqxmd.com/read/28649135/synthetic-lethality-and-cancer
#1
REVIEW
Nigel J O'Neil, Melanie L Bailey, Philip Hieter
A synthetic lethal interaction occurs between two genes when the perturbation of either gene alone is viable but the perturbation of both genes simultaneously results in the loss of viability. Key to exploiting synthetic lethality in cancer treatment are the identification and the mechanistic characterization of robust synthetic lethal genetic interactions. Advances in next-generation sequencing technologies are enabling the identification of hundreds of tumour-specific mutations and alterations in gene expression that could be targeted by a synthetic lethality approach...
June 26, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28649134/cancer-epigenetics-therapy-induced-transcription-is-cryptically-widespread
#2
Darren J Burgess
No abstract text is available yet for this article.
June 26, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28649133/disease-genetics-repeat-expansion-disorders-going-through-a-phase
#3
Dorothy Clyde
No abstract text is available yet for this article.
June 26, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28626224/reference-standards-for-next-generation-sequencing
#4
REVIEW
Simon A Hardwick, Ira W Deveson, Tim R Mercer
Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is being readily applied for the diagnosis of disease-associated genetic features. However, the interpretation of NGS data remains challenging owing to the size and complexity of the genome and the technical errors that are introduced during sample preparation, sequencing and analysis. These errors can be understood and mitigated through the use of reference standards - well-characterized genetic materials or synthetic spike-in controls that help to calibrate NGS measurements and to evaluate diagnostic performance...
June 19, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28607512/network-propagation-a-universal-amplifier-of-genetic-associations
#5
REVIEW
Lenore Cowen, Trey Ideker, Benjamin J Raphael, Roded Sharan
Biological networks are powerful resources for the discovery of genes and genetic modules that drive disease. Fundamental to network analysis is the concept that genes underlying the same phenotype tend to interact; this principle can be used to combine and to amplify signals from individual genes. Recently, numerous bioinformatic techniques have been proposed for genetic analysis using networks, based on random walks, information diffusion and electrical resistance. These approaches have been applied successfully to identify disease genes, genetic modules and drug targets...
June 12, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28607511/technique-sizing-up-tumours-with-tuba-seq
#6
Michelle Trenkmann
No abstract text is available yet for this article.
June 12, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28555659/human-y-chromosome-variation-in-the-genome-sequencing-era
#7
REVIEW
Mark A Jobling, Chris Tyler-Smith
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail...
May 30, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28555658/tet-mediated-active-dna-demethylation-mechanism-function-and-beyond
#8
REVIEW
Xiaoji Wu, Yi Zhang
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation...
May 30, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28529337/dynamic-chromatin-technologies-from-individual-molecules-to-epigenomic-regulation-in-cells
#9
REVIEW
Olivier Cuvier, Beat Fierz
The establishment and maintenance of chromatin states involves multiscale dynamic processes integrating transcription factor and multiprotein effector dynamics, cycles of chemical chromatin modifications, and chromatin structural organization. Recent developments in genomic technologies are emerging that are enabling a view beyond ensemble- and time-averaged properties and are revealing the importance of dynamic chromatin states for cell fate decisions, differentiation and reprogramming at the single-cell level...
May 22, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28479598/the-origin-of-metazoa-a-unicellular-perspective
#10
REVIEW
Arnau Sebé-Pedrós, Bernard M Degnan, Iñaki Ruiz-Trillo
The first animals evolved from an unknown single-celled ancestor in the Precambrian period. Recently, the identification and characterization of the genomic and cellular traits of the protists most closely related to animals have shed light on the origin of animals. Comparisons of animals with these unicellular relatives allow us to reconstruct the first evolutionary steps towards animal multicellularity. Here, we review the results of these investigations and discuss their implications for understanding the earliest stages of animal evolution, including the origin of metazoan genes and genome function...
May 8, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28579607/plant-genetics-branching-out-for-crop-improvement
#11
Darren J Burgess
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28555657/associating-cellular-epigenetic-models-with-human-phenotypes
#12
REVIEW
Tuuli Lappalainen, John M Greally
Epigenetic association studies have been carried out to test the hypothesis that environmental perturbations trigger cellular reprogramming, with downstream effects on cellular function and phenotypes. There have now been numerous studies of the potential molecular mediators of epigenetic changes by epigenome-wide association studies (EWAS). However, a challenge for the field is the interpretation of the results obtained. We describe a second-generation EWAS approach, which focuses on the possible cellular models of epigenetic perturbations, studied by rigorous analysis and interpretation of genomic data...
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28529336/stem-cells-the-different-flavours-of-ips-cells
#13
Katharine H Wrighton
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28529335/cancer-genomics-tracking-cancer-evolution
#14
Carolina Perdigoto
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28529334/plant-genetics-spatial-transcriptomics-in-plants
#15
Liesbet Lieben
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28502977/the-evolutionary-significance-of-polyploidy
#16
REVIEW
Yves Van de Peer, Eshchar Mizrachi, Kathleen Marchal
Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential...
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28502976/technology-nucleic-acid-detection-it-s-elementary-with-sherlock
#17
Dorothy Clyde
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28479597/genetic-testing-the-diagnostic-power-of-rna-seq
#18
Katharine H Wrighton
No abstract text is available yet for this article.
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28479595/comparative-transcriptomics-in-human-and-mouse
#19
REVIEW
Alessandra Breschi, Thomas R Gingeras, Roderic Guigó
Cross-species comparisons of genomes, transcriptomes and gene regulation are now feasible at unprecedented resolution and throughput, enabling the comparison of human and mouse biology at the molecular level. Insights have been gained into the degree of conservation between human and mouse at the level of not only gene expression but also epigenetics and inter-individual variation. However, a number of limitations exist, including incomplete transcriptome characterization and difficulties in identifying orthologous phenotypes and cell types, which are beginning to be addressed by emerging technologies...
July 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28344341/functional-variomics-and-network-perturbation-connecting-genotype-to-phenotype-in-cancer
#20
REVIEW
Song Yi, Shengda Lin, Yongsheng Li, Wei Zhao, Gordon B Mills, Nidhi Sahni
Proteins interact with other macromolecules in complex cellular networks for signal transduction and biological function. In cancer, genetic aberrations have been traditionally thought to disrupt the entire gene function. It has been increasingly appreciated that each mutation of a gene could have a subtle but unique effect on protein function or network rewiring, contributing to diverse phenotypic consequences across cancer patient populations. In this Review, we discuss the current understanding of cancer genetic variants, including the broad spectrum of mutation classes and the wide range of mechanistic effects on gene function in the context of signalling networks...
July 2017: Nature Reviews. Genetics
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