Trends in Genetics

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  1. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics.

    Trends in Genetics 32(6):360 (2016) PMID 27129983

    The discovery of cell-free tumor and fetal DNA molecules in the plasma of cancer patients and pregnant women, respectively, has opened up exciting opportunities in molecular diagnosis. The understanding of the biological properties of circulating cell-free DNA (cfDNA) molecules would be essentia...
  2. Escape Artists of the X Chromosome.

    Trends in Genetics 32(6):348 (2016) PMID 27103486

    Inactivation of one X chromosome in mammalian females achieves dosage compensation between XX females and XY males; however, over 15% of human X-linked genes continue to be expressed from the inactive X chromosome. New genomic methodologies have improved our identification and characterization o...
  3. To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins.

    Trends in Genetics 32(6):334 (2016) PMID 27066866 PMCID PMC4875764

    Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding...
  4. Expanding the Regulatory Network for Meristem Size in Plants.

    Trends in Genetics 32(6):372 (2016) PMID 27129984

    The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop ...
  5. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.

    Trends in Genetics 32(6):320 (2016) PMID 27050931

    N(6)-Methyladenosine (m(6)A) is emerging as a chemical mark that broadly affects the flow of genetic information in various biological processes in eukaryotes. Recently, Xiao et al. reported that the nuclear m(6)A reader protein YTHDC1 impacts mRNA splicing, providing a transcriptome-wide glance...
  6. Participatory Genomic Testing as an Educational Experience.

    Trends in Genetics 32(6):317 (2016) PMID 27117243

    Several institutions have incorporated participatory genomic testing into their curricula to engage students in experiential learning, and this has raised ethical concerns. We summarize strategies for managing these concerns and review evidence of the influence of this experiential approach on s...
  7. The Determinants of Directionality in Transcriptional Initiation.

    Trends in Genetics 32(6):322 (2016) PMID 27066865 PMCID PMC4874897

    A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA ha...
  8. Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping.

    Trends in Genetics 32(5):256 (2016) PMID 27017185

    Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and f...
  9. Understanding Celiac Disease by Genomics.

    Trends in Genetics 32(5):295 (2016) PMID 26972670

    Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we n...
  10. Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

    Trends in Genetics 32(5):251 (2016) PMID 27005445

    The emergence of collective creative enterprise such as large scientific consortia is a unique feature in modern scientific research. We analyzed the temporal co-authorship network structures of ENCODE and modENCODE consortia. Our analysis revealed that the consortium members work closely as a c...
  11. Circular RNA Expression: Its Potential Regulation and Function.

    Trends in Genetics 32(5):309 (2016) PMID 27050930

    In 2012, a new feature of eukaryotic gene expression emerged: ubiquitous expression of circular RNA (circRNA) from genes traditionally thought to express messenger or linear noncoding (nc)RNA only. CircRNAs are covalently closed, circular RNA molecules that typically comprise exonic sequences an...
  12. New Insights into the Regulation of Heterochromatin.

    Trends in Genetics 32(5):284 (2016) PMID 27005444 PMCID PMC4842111

    All living organisms are constantly exposed to stresses from internal biological processes and surrounding environments, which induce many adaptive changes in cellular physiology and gene expression programs. Unexpectedly, constitutive heterochromatin, which is generally associated with the stab...
  13. Evolution of Epigenetic Regulation in Vertebrate Genomes.

    Trends in Genetics 32(5):269 (2016) PMID 27080453 PMCID PMC4842087

    Empirical models of sequence evolution have spurred progress in the field of evolutionary genetics for decades. We are now realizing the importance and complexity of the eukaryotic epigenome. While epigenome analysis has been applied to genomes from single-cell eukaryotes to human, comparative a...
  14. The Ties that Bind (the Igh Locus).

    Trends in Genetics 32(5):253 (2016) PMID 27012539 PMCID PMC4842146

    Immunoglobulin heavy-chain locus V(D)J recombination requires a 3D chromatin organization which permits widely distributed variable (V) gene segments to contact distant diversity (D) and joining (J) gene segments. A recent study has identified key nodes in the locus interactome, paving the way f...
  15. The Limits of Natural Selection in a Nonequilibrium World.

    Trends in Genetics 32(4):201 (2016) PMID 26874998

    Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assu...
  16. Deciphering ENCODE.

    Trends in Genetics 32(4):238 (2016) PMID 26962025

    The ENCODE project represents a major leap from merely describing and comparing genomic sequences to surveying them for direct indicators of function. The astounding quantity of data produced by the ENCODE consortium can serve as a map to locate specific landmarks, guide hypothesis generation, a...
  17. Breaking TADs: How Alterations of Chromatin Domains Result in Disease.

    Trends in Genetics 32(4):225 (2016) PMID 26862051

    Spatial organization is an inherent property of the vertebrate genome to accommodate the roughly 2m of DNA in the nucleus of a cell. In this nonrandom organization, topologically associating domains (TADs) emerge as a fundamental structural unit that is thought to guide regulatory elements to th...
  18. The Emerging Function and Mechanism of ceRNAs in Cancer.

    Trends in Genetics 32(4):211 (2016) PMID 26922301 PMCID PMC4805481

    Complex diseases, such as cancer, are often associated with aberrant gene expression at both the transcriptional and post-transcriptional level. Over the past several years, competing endogenous RNAs (ceRNAs) have emerged as an important class of post-transcriptional regulators that alter gene e...
  19. Manipulating Bacterial Communities by in situ Microbiome Engineering.

    Trends in Genetics 32(4):189 (2016) PMID 26916078 PMCID PMC4828914

    Microbial communities inhabit our entire planet and have a crucial role in biogeochemical processes, agriculture, biotechnology, and human health. Here, we argue that 'in situ microbiome engineering' represents a new paradigm of community-scale genetic and microbial engineering. We discuss conte...
  20. Autism and Cancer Share Risk Genes, Pathways, and Drug Targets.

    Trends in Genetics 32(3):139 (2016) PMID 26830258 PMCID PMC4769654

    Autism is a neurodevelopmental disorder, diagnosed behaviorally by social and communication deficits, repetitive behaviors, and restricted interests. Recent genome-wide exome sequencing has revealed extensive overlap in risk genes for autism and for cancer. Understanding the genetic commonalitie...