Tài liệu miễn phí Sinh học
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Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons
Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding.
4/6/2023 7:00:31 AM +00:00
Developmental transitions: Integrating environmental cues with hormonal signaling in the chromatin landscape in plants
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants.
4/6/2023 7:00:24 AM +00:00
Missing heritability and where to find it
High-throughput and affordable genomic technologies have spawned several large-scale genetic studies on human disease populations. What might have been disparate disciplines a decade ago, including clinical medicine, biology, and computer science, are now converging with the goal of understanding the complex basis of human disease.
4/6/2023 7:00:18 AM +00:00
The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci
The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana.
4/6/2023 7:00:12 AM +00:00
N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration
Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion.
4/6/2023 7:00:04 AM +00:00
Millstone: Software for multiplex microbial genome analysis and engineering
Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples.
4/6/2023 6:59:58 AM +00:00
Translational contributions to tissue specificity in rhythmic and constitutive gene expression
The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood.
4/6/2023 6:59:51 AM +00:00
The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana
Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels.
4/6/2023 6:59:44 AM +00:00
Easi-CRISPR: A robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins
Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes.
4/6/2023 6:59:38 AM +00:00
Longitudinal study of Plasmodium pathogens identifies new loci associated with artemisinin resistance
A longitudinal analysis of malaria parasite genomes has revealed new markers that can be used in public health efforts to limit the spread of multidrug-resistant malaria.
4/6/2023 6:59:31 AM +00:00
Challenges and emerging directions in single-cell analysis
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease.
4/6/2023 6:59:25 AM +00:00
Optimizing complex phenotypes through model-guided multiplex genome engineering
We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.ΔA.
4/6/2023 6:59:17 AM +00:00
Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data
Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essential to design fine-mapping experiments for complex traits and diseases.
4/6/2023 6:59:10 AM +00:00
Multi-omics approaches to disease
High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which gave rise to the field of “integrative genetics”. Other omics technologies, such as proteomics and
4/6/2023 6:59:02 AM +00:00
Horizontal gene transfer is not a hallmark of the human genome
Crisp et al. recently reported that 145 human genes have been horizontally transferred from distant species. Here, I re-analyze those genes listed by Crisp et al. as having the highest certainty of having been horizontally transferred, as well as 17 further genes from the 2001 human genome article, and find little or no evidence to support claims of horizontal gene transfer (HGT).
4/6/2023 6:58:56 AM +00:00
A comparative evaluation of genome assembly reconciliation tools
The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity.
4/6/2023 6:58:49 AM +00:00
The impact of rare and low-frequency genetic variants in common disease
Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits.
4/6/2023 6:58:43 AM +00:00
PRC2 represses transcribed genes on the imprinted inactive X chromosome in mice
Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing.
4/6/2023 6:58:36 AM +00:00
Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana
Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species.
4/6/2023 6:58:29 AM +00:00
The MHC locus and genetic susceptibility to autoimmune and infectious diseases
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases.
4/6/2023 6:58:23 AM +00:00
Proximal methylation features associated with nonrandom changes in gene body methylation
Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability.
4/6/2023 6:58:16 AM +00:00
Structuring supplemental materials in support of reproducibility
Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable, and reusable (i.e., “FAIR”). Moreover, properly off-loading to them the data and detail in a paper could make the main text more readable.
4/6/2023 6:58:10 AM +00:00
Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance
Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance.
4/6/2023 6:58:03 AM +00:00
Multiple gene movements into and out of haploid sex chromosomes
Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution.
4/6/2023 6:57:56 AM +00:00
SCALE: Modeling allele-specific gene expression by single-cell RNA sequencing
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting.
4/6/2023 6:57:50 AM +00:00
Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations
The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture.
4/6/2023 6:57:43 AM +00:00
H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity
Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2.
4/6/2023 6:57:36 AM +00:00
The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens.
4/6/2023 6:57:30 AM +00:00
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae, we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins.
4/6/2023 6:57:22 AM +00:00
Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort
The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finnish men from the Metabolic Syndrome In Men (METSIM) study.
4/6/2023 6:57:16 AM +00:00