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Nature Reviews. Genetics

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https://www.readbyqxmd.com/read/30410101/current-and-future-perspectives-of-liquid-biopsies-in-genomics-driven-oncology
#1
REVIEW
Ellen Heitzer, Imran S Haque, Charles E S Roberts, Michael R Speicher
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence...
November 8, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30390049/the-many-lives-of-kats-detectors-integrators-and-modulators-of-the-cellular-environment
#2
REVIEW
Bilal N Sheikh, Asifa Akhtar
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response...
November 2, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30390048/autism-spectrum-disorder-insights-into-convergent-mechanisms-from-transcriptomics
#3
REVIEW
Mathieu Quesnel-Vallières, Robert J Weatheritt, Sabine P Cordes, Benjamin J Blencowe
Heredity has a major role in autism spectrum disorder (ASD), yet underlying causal genetic variants have been defined only in a fairly small subset of cases. The enormous genetic heterogeneity associated with ASD emphasizes the importance of identifying convergent pathways and molecular mechanisms that are responsible for this disorder. We review how recent transcriptomic analyses have transformed our understanding of pathway convergence in ASD. In particular, deep RNA sequencing coupled with downstream investigations has revealed that a substantial fraction of autistic brains possess distinct transcriptomic signatures...
November 2, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30385867/the-causes-of-evolvability-and-their-evolution
#4
REVIEW
Joshua L Payne, Andreas Wagner
Evolvability is the ability of a biological system to produce phenotypic variation that is both heritable and adaptive. It has long been the subject of anecdotal observations and theoretical work. In recent years, however, the molecular causes of evolvability have been an increasing focus of experimental work. Here, we review recent experimental progress in areas as different as the evolution of drug resistance in cancer cells and the rewiring of transcriptional regulation circuits in vertebrates. This research reveals the importance of three major themes: multiple genetic and non-genetic mechanisms to generate phenotypic diversity, robustness in genetic systems, and adaptive landscape topography...
November 1, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30367165/organizational-principles-of-3d-genome-architecture
#5
REVIEW
M Jordan Rowley, Victor G Corces
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically organized into large compartments composed of smaller domains called topologically associating domains (TADs). Recent evidence suggests that compartments are smaller than previously thought and that the transcriptional or chromatin state is responsible for interactions leading to the formation of small compartmental domains in all organisms. In vertebrates, CTCF forms loop domains, probably via an extrusion process involving cohesin...
October 26, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30367164/spotlight-on-nucleosomes
#6
Dorothy Clyde
No abstract text is available yet for this article.
October 26, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30356165/coaching-from-the-sidelines-the-nuclear-periphery-in-genome-regulation
#7
REVIEW
Abigail Buchwalter, Jeanae M Kaneshiro, Martin W Hetzer
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation...
October 24, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30348998/going-to-the-negative-genomics-for-optimized-medical-prescription
#8
Greg Gibson
Personalized medicine promises to advance and improve health by targeting the right medication to the right person at the right time, thus maximizing the proportion of treated patients who achieve an effective response to therapy. This Comment article makes the complementary argument that equally important benefits will derive from negative prediction, namely by identifying those individuals who are either not actually in need of, or unlikely to respond to, a drug. Reduction of unnecessary prescription could conceivably save health-care systems many billions of dollars with very little detrimental impact on outcomes...
October 22, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30348997/uk-biobank-a-new-era-in-genomic-medicine
#9
Orli G Bahcall
No abstract text is available yet for this article.
October 22, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30341441/navigating-mouse-cell-types
#10
Darren J Burgess
No abstract text is available yet for this article.
October 19, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30341440/publisher-correction-base-editing-precision-chemistry-on-the-genome-and-transcriptome-of-living-cells
#11
Holly A Rees, David R Liu
The originally published article contained errors in reference numbering throughout table 1 (DNA base editors and their approximate editing windows) due to the unintended propagation of reference numbering from an earlier version of the table. The article has now been corrected online. The editors apologize for this error.
October 19, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30341439/altered-splicing-in-alzheimer-transcriptomes
#12
Linda Koch
No abstract text is available yet for this article.
October 19, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30327497/publisher-correction-towards-quantitative-and-multiplexed-in-vivo-functional-cancer-genomics
#13
Ian P Winters, Christopher W Murray, Monte M Winslow
The originally published article failed to acknowledge the equal first authorship contribution of I. P. Winters and C. W. Murray. The article has now been corrected online. The editors apologize for this error.
October 16, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30323312/base-editing-precision-chemistry-on-the-genome-and-transcriptome-of-living-cells
#14
REVIEW
Holly A Rees, David R Liu
RNA-guided programmable nucleases from CRISPR systems generate precise breaks in DNA or RNA at specified positions. In cells, this activity can lead to changes in DNA sequence or RNA transcript abundance. Base editing is a newer genome-editing approach that uses components from CRISPR systems together with other enzymes to directly install point mutations into cellular DNA or RNA without making double-stranded DNA breaks. DNA base editors comprise a catalytically disabled nuclease fused to a nucleobase deaminase enzyme and, in some cases, a DNA glycosylase inhibitor...
October 15, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30305704/the-phylogenomics-of-evolving-virus-virulence
#15
REVIEW
Jemma L Geoghegan, Edward C Holmes
How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study...
October 10, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30283055/the-importance-of-genetic-counselling-in-genome-wide-sequencing
#16
Alison M Elliott, Jan M Friedman
No abstract text is available yet for this article.
October 3, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30279525/putting-genetic-variants-to-a-fitness-test
#17
Michelle Trenkmann
No abstract text is available yet for this article.
October 2, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30267031/towards-quantitative-and-multiplexed-in-vivo-functional-cancer-genomics
#18
REVIEW
Ian P Winters, Christopher W Murray, Monte M Winslow
Large-scale sequencing of human tumours has uncovered a vast array of genomic alterations. Genetically engineered mouse models recapitulate many features of human cancer and have been instrumental in assigning biological meaning to specific cancer-associated alterations. However, their time, cost and labour-intensive nature limits their broad utility; thus, the functional importance of the majority of genomic aberrations in cancer remains unknown. Recent advances have accelerated the functional interrogation of cancer-associated alterations within in vivo models...
September 28, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30228295/progress-and-potential-in-organoid-research
#19
REVIEW
Giuliana Rossi, Andrea Manfrin, Matthias P Lutolf
Tissue and organ biology are very challenging to study in mammals, and progress can be hindered, particularly in humans, by sample accessibility and ethical concerns. However, advances in stem cell culture have made it possible to derive in vitro 3D tissues called organoids, which capture some of the key multicellular, anatomical and even functional hallmarks of real organs at the micrometre to millimetre scale. Recent studies have demonstrated that organoids can be used to model organ development and disease and have a wide range of applications in basic research, drug discovery and regenerative medicine...
September 18, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/30154482/full-speed-ahead-for-single-cell-analysis
#20
Darren J Burgess
No abstract text is available yet for this article.
August 28, 2018: Nature Reviews. Genetics
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