Tài liệu miễn phí Sinh học
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Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution.
4/6/2023 7:08:10 AM +00:00
Meta-analysis of RNA-seq expression data across species, tissues and studies
Differences in gene expression drive phenotypic differences between species, yet major organs and tissues generally have conserved gene expression programs. Several comparative transcriptomic studies have observed greater similarity in gene expression between homologous tissues from different vertebrate species than between diverse tissues of the same species.
4/6/2023 7:08:03 AM +00:00
3CPET: Finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process
Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control, making it a valuable downstream analysis tool in chromatin conformation studies.
4/6/2023 7:07:50 AM +00:00
Circlator: Automated circularization of genome assemblies using long sequencing reads
The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved.
4/6/2023 7:07:43 AM +00:00
Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling
RNA levels detected at steady state are the consequence of multiple dynamic processes within the cell. In addition to synthesis and decay, transcripts undergo processing. Metabolic tagging with a nucleotide analog is one way of determining the relative contributions of synthesis, decay and conversion processes globally.
4/6/2023 7:07:37 AM +00:00
Transcriptome analysis in calorie-restricted rats implicates epigenetic and posttranslational mechanisms in neuroprotection and aging
Caloric restriction (CR) can increase longevity in rodents and improve memory function in humans. α-Lipoic acid (LA) has been shown to improve memory function in rats, but not longevity. While studies have looked at survival in rodents after switching from one diet to another, the underlying mechanisms of the beneficial effects of CR and LA supplementation are unknown.
4/6/2023 7:07:30 AM +00:00
Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency
Single-guide RNA (sgRNA) is one of the two key components of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome-editing system. The current commonly used sgRNA structure has a shortened duplex compared with the native bacterial CRISPR RNA (crRNA)–transactivating crRNA (tracrRNA) duplex and contains a continuous sequence of thymines, which is the pause signal for RNA polymerase III and thus could potentially reduce transcription efficiency.
4/6/2023 7:07:23 AM +00:00
MAST: A flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features.
4/6/2023 7:07:16 AM +00:00
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions.
4/6/2023 7:07:09 AM +00:00
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction
Genetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects.
4/6/2023 7:07:03 AM +00:00
The microbiome quality control project: Baseline study design and future directions
Microbiome research has grown exponentially over the past several years, but studies have been difficult to reproduce across investigations. Relevant variation in measurements between laboratories, from a variety of sources, has not been systematically assessed.
4/6/2023 7:06:56 AM +00:00
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Open chromatin regions are correlated with active regulatory elements in development and are dysregulated in diseases. The BAF (SWI/SNF) complex is essential for development, and has been demonstrated to remodel reconstituted chromatin in vitro and to control the accessibility of a few individual regions in vivo.
4/6/2023 7:06:49 AM +00:00
Transcriptome-wide high-throughput deep m6 A-seq reveals unique differential m6 A methylation patterns between three organs in Arabidopsis thaliana
Transcriptome-wide m6 A patterns in Arabidopsis have been assayed recently. However, differential m6 A patterns between organs have not been well characterized. Results: Over two-third of the transcripts in Arabidopsis are modified by m6 A. In contrast to a recent observation of m6 A enrichment in 5′ mRNA, we find that m6 A is distributed predominantly near stop codons.
4/6/2023 7:06:42 AM +00:00
A genome-wide survey of DNA methylation in hexaploid wheat
DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat.
4/6/2023 7:06:36 AM +00:00
Genomic legacy of the African cheetah, Acinonyx jubatus
Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs.
4/6/2023 7:06:29 AM +00:00
Mineotaur: A tool for high-content microscopy screen sharing and visual analytics
High-throughput/high-content microscopy-based screens are powerful tools for functional genomics, yielding intracellular information down to the level of single-cells for thousands of genotypic conditions. However, accessing their data requires specialized knowledge and most often that data is no longer analyzed after initial publication.
4/6/2023 7:06:23 AM +00:00
Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2
Fibroblast growth factor-19 (FGF19) is an intestinal hormone that mediates postprandial metabolic responses in the liver. The unusual orphan nuclear receptor, small heterodimer partner (SHP), acts as a co-repressor for many transcriptional factors and has been implicated in diverse biological pathways including FGF19-mediated repression of bile acid synthesis.
4/6/2023 7:06:16 AM +00:00
Metagenome-assembled genomes uncover a global brackish microbiome
Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them.
4/6/2023 7:06:09 AM +00:00
Genetic determination of height-mediated mate choice
Numerous studies have reported positive correlations among couples for height. This suggests that humans find individuals of similar height attractive. However, the answer to whether the choice of a mate with a similar phenotype is genetically or environmentally determined has been elusive.
4/6/2023 7:06:02 AM +00:00
Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization
The impact of signal-dependent transcription factors, such as glucocorticoid receptor and nuclear factor kappa-b, on the three-dimensional organization of chromatin remains a topic of discussion. The possible scenarios range from remodeling of higher order chromatin architecture by activated transcription factors to recruitment of activated transcription factors to pre-established long-range interactions.
4/6/2023 7:05:55 AM +00:00
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps.
4/6/2023 7:05:48 AM +00:00
Boosting plant immunity with CRISPR/Cas
CRISPR/Cas has recently been transferred to plants to make them resistant to geminiviruses, a damaging family of DNA viruses. We discuss the potential and the limitations of this method.
4/6/2023 7:05:41 AM +00:00
Lifetime stress accelerates epigenetic aging in an urban, African American cohort: Relevance of glucocorticoid signaling
Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. Results: We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock.
4/6/2023 7:05:34 AM +00:00
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models
Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.
4/6/2023 7:05:27 AM +00:00
Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease
The RNA-guided Cas9 system represents a flexible approach for genome editing in plants. This method can create specific mutations that knock-out or alter target gene function. It provides a valuable tool for plant research and offers opportunities for crop improvement.
4/6/2023 7:05:20 AM +00:00
Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells
Mutations in myosin chaperones Unc45b and Hsp90aa1.1 as well as in the Unc45b-binding protein Smyd1b impair formation of myofibrils in skeletal muscle and lead to the accumulation of misfolded myosin.
4/6/2023 7:05:13 AM +00:00
The Cpf1 CRISPR-Cas protein expands genome-editing tools
CRISPR-Cas systems have immense biotechnological utility. A recent study reveals the potential of the Cpf1 nuclease to complement and extend the existing CRISPR-Cas9 genome-editing tools.
4/6/2023 7:05:06 AM +00:00
Resources for the design of CRISPR gene editing experiments
CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tools and resources currently available to assist users of this technology.
4/6/2023 7:04:55 AM +00:00
Using genomics to combat infectious diseases on a global scale
The work presented spanned novel applications of genomics to human health, as well as aspects of mathematics, web development, molecular biology, and classic phylogenetics to target a range of pathogens: Bacteria, viruses, and parasites.
4/6/2023 7:04:49 AM +00:00
Identification of low abundance microbiome in clinical samples using whole genome sequencing
Identifying the microbiome composition from primary tissues directly affords an opportunity to study the causative relationships between the host microbiome and disease. However, this is challenging due the low abundance of microbial DNA relative to the host.
4/6/2023 7:04:36 AM +00:00