Tài liệu miễn phí Sinh học
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Insulator-based loops mediate the spreading of H3K27me3 over distant microdomains repressing euchromatin genes
Chromosomes are subdivided spatially to delimit long-range interactions into topologically associating domains (TADs). TADs are often flanked by chromatin insulators and transcription units that may participate in such demarcation. Remarkably, single-cell Drosophila TAD units correspond to dynamic heterochromatin nanocompartments that can self-assemble.
4/6/2023 5:34:07 AM +00:00
Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias.
4/6/2023 5:33:59 AM +00:00
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
4/6/2023 5:33:45 AM +00:00
Splicing-accessible coding 3′UTRs control protein stability and interaction networks
3′-Untranslated regions (3′UTRs) play crucial roles in mRNA metabolism, such as by controlling mRNA stability, translation efficiency, and localization. Intriguingly, in some genes the 3′UTR is longer than their coding regions, pointing to additional, unknown functions.
4/6/2023 5:33:34 AM +00:00
Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues
Mobile elements are a major source of structural variants in the human genome, and some mobile elements can regulate gene expression and transcript splicing. However, the impact of polymorphic mobile element insertions (pMEIs) on gene expression and splicing in diverse human tissues has not been thoroughly studied.
4/6/2023 5:33:27 AM +00:00
Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
Principal component analysis (PCA) is an essential method for analyzing single-cell RNA-seq (scRNA-seq) datasets, but for large-scale scRNA-seq datasets, computation time is long and consumes large amounts of memory.
4/6/2023 5:33:18 AM +00:00
Producing polished prokaryotic pangenomes with the Panaroo pipeline
Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss.
4/6/2023 5:33:11 AM +00:00
CRISPR guides induce gene silencing in plants in the absence of Cas
RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation, and expanded function including antiviral immunity.
4/6/2023 5:33:02 AM +00:00
Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution
Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat.
4/6/2023 5:32:54 AM +00:00
Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration
Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood.
4/6/2023 5:32:46 AM +00:00
Comparative assessment of genes driving cancer and somatic evolution in noncancer tissues: An update of the Network of Cancer Genes (NCG) resource
Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue homeostasis and cancer development.
4/6/2023 5:32:33 AM +00:00
DENA: Training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6 -methyladenosine on RNA
Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by N6 -methyladenosine (m6 A) are likely distorted due to superimposed signals from saturated m6 A residues.
4/6/2023 5:32:26 AM +00:00
Bacon: A comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capturespecific methodologies
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions.
4/6/2023 5:32:18 AM +00:00
Blood-based epigenome-wide analyses of cognitive abilities
Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable.
4/6/2023 5:32:11 AM +00:00
Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice
The daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions underlying the rhythmic gene expression remain unclear.
4/6/2023 5:32:03 AM +00:00
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample
Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data.
4/6/2023 5:31:51 AM +00:00
Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries
Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry.
4/6/2023 5:31:44 AM +00:00
Phiclust: A clusterability measure for singlecell transcriptomics reveals phenotypic subpopulations
The ability to discover new cell phenotypes by unsupervised clustering of single-cell transcriptomes has revolutionized biology. Currently, there is no principled way to decide whether a cluster of cells contains meaningful subpopulations that should be further resolved.
4/6/2023 5:31:36 AM +00:00
Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression
Epigenetic clocks use DNA methylation (DNAm) levels of specific sets of CpG dinucleotides to accurately predict individual chronological age. A popular application of these clocks is to explore whether the deviation of predicted age from chronological age is associated with disease phenotypes, where this deviation is interpreted as a potential biomarker of biological age.
4/6/2023 5:31:27 AM +00:00
Comparison and evaluation of statistical error models for scRNA-seq
Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, including biological variation in cellular state as well as technical variation introduced during experimental processing.
4/6/2023 5:31:19 AM +00:00
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic mock community and construct sequencing libraries with a range of mean read lengths.
4/6/2023 5:31:11 AM +00:00
N4 -acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana
Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6 -methyladenosine (m6A)/N6 -methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively.
4/6/2023 5:31:00 AM +00:00
Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue
Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers.
4/6/2023 5:30:50 AM +00:00
Evolution of the repression mechanisms in circadian clocks
Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of this feedback varies widely between lower and higher organisms.
4/6/2023 5:30:43 AM +00:00
Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data
Constructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization.
4/6/2023 5:30:32 AM +00:00
The economics of organellar gene loss and endosymbiotic gene transfer
The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes.
4/6/2023 5:30:21 AM +00:00
Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis
RNA silencing has an important role mediating sequence-specific virus resistance in plants. The complex interaction of viruses with RNA silencing involves the loading of viral small interfering RNAs (vsiRNAs) into its host ARGONAUTE (AGO) proteins.
4/6/2023 5:30:12 AM +00:00
SPLINK: A hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the presence of cross-study heterogeneity.
4/6/2023 5:30:04 AM +00:00
Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity
Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos.
4/6/2023 5:29:55 AM +00:00
Hidden biases in germline structural variant detection
Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.
4/6/2023 5:29:43 AM +00:00