Tài liệu miễn phí Sinh học

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Invasive DNA elements modify the nuclear architecture of their insertion site by KNOTlinked silencing in Arabidopsis thaliana

The three-dimensional (3D) organization of chromosomes is linked to epigenetic regulation and transcriptional activity. However, only few functional features of 3D chromatin architecture have been described to date.

4/6/2023 10:30:21 PM +00:00

Chromatin accessibility plays a key role in selective targeting of Hox proteins

Hox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking.

4/6/2023 10:30:13 PM +00:00

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single algorithm can call every type of SVs with high precision and high recall.

4/6/2023 10:30:04 PM +00:00

OSCA: A tool for omic-data-based complex trait analysis

The rapid increase of omic data has greatly facilitated the investigation of associations between omic profiles such as DNA methylation (DNAm) and complex traits in large cohorts. Here, we propose a mixed-linear-model-based method called MOMENT that tests for association between a DNAm probe and trait with all other distal probes fitted in multiple random-effect components to account for unobserved confounders.

4/6/2023 10:29:56 PM +00:00

A practical guide to methods controlling false discoveries in computational biology

In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error rate control. While classic FDR methods use only p values as input, more modern FDR methods have been shown to increase power by incorporating complementary information as informative covariates to prioritize, weight, and group hypotheses.

4/6/2023 10:29:48 PM +00:00

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches

Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples.

4/6/2023 10:29:41 PM +00:00

Haplotype-aware diplotyping from noisy long reads

Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking.

4/6/2023 10:29:33 PM +00:00

Systematic analysis of dark and camouflaged genes reveals diseaserelevant genes hiding in plain sight

The human genome contains “dark” gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease.

4/6/2023 10:29:25 PM +00:00

ChiCMaxima: A robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C

Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable.

4/6/2023 10:29:15 PM +00:00

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals.

4/6/2023 10:29:08 PM +00:00

Human cleaving embryos enable robust homozygotic nucleotide substitutions by base editors

Base editing installs a precise nucleotide change in specific gene loci without causing a double-strand break. Its efficiency in human embryos is generally low, limiting its utility in functional genetic studies.

4/6/2023 10:29:01 PM +00:00

Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex

Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of complex traits and diseases.

4/6/2023 10:28:54 PM +00:00

Addressing confounding artifacts in reconstruction of gene co-expression networks

Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifacts in gene expression data confound commonly used network reconstruction algorithms.

4/6/2023 10:28:45 PM +00:00

WhoGEM: An admixture-based prediction machine accurately predicts quantitative functional traits in plants

The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) that overcomes some of the bottlenecks limiting the current methods.

4/6/2023 10:28:37 PM +00:00

The inherited variations of a p53- responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression

Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechanisms of cancers.

4/6/2023 10:28:30 PM +00:00

Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both plants and animals, the nuclear periphery is a functional compartment enriched with heterochromatin.

4/6/2023 10:28:18 PM +00:00

Measuring sequencer size bias using REcount: A novel method for highly accurate Illumina sequencing-based quantification

Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error.

4/6/2023 10:28:11 PM +00:00

TransLiG: A de novo transcriptome assembler that uses line graph iteration

We present TransLiG, a new de novo transcriptome assembler, which is able to integrate the sequence depth and pair-end information into the assembling procedure by phasing paths and iteratively constructing line graphs starting from splicing graphs.

4/6/2023 10:28:01 PM +00:00

Bazam: A rapid method for read extraction and realignment of high-throughput sequencing data

The vast quantities of short-read sequencing data being generated are often exchanged and stored as aligned reads. However, aligned data becomes outdated as new reference genomes and alignment methods become available.

4/6/2023 10:27:55 PM +00:00

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio

Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. Results: Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families.

4/6/2023 10:27:48 PM +00:00

Translation of the circular RNA circβ-catenin promotes liver cancer cell growth through activation of the Wnt pathway

Circular RNAs are a class of regulatory RNA transcripts, which are ubiquitously expressed in eukaryotes. In the current study, we evaluate the function of a novel circRNA derived from the β-catenin gene locus, circβ-catenin.

4/6/2023 10:27:40 PM +00:00

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level. The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.

4/6/2023 10:27:29 PM +00:00

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication.

4/6/2023 10:27:23 PM +00:00

DegNorm: Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias.

4/6/2023 10:27:15 PM +00:00

SCRABBLE: Single-cell RNA-seq imputation constrained by bulk RNA-seq data

Single-cell RNA-seq data contain a large proportion of zeros for expressed genes. Such dropout events present a fundamental challenge for various types of data analyses. Here, we describe the SCRABBLE algorithm to address this problem.

4/6/2023 10:27:08 PM +00:00

CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors

Increasing genetic diversity via directed evolution holds great promise to accelerate trait development and crop improvement. We developed a CRISPR/Cas-based directed evolution platform in plants to evolve the rice (Oryza sativa) SF3B1 spliceosomal protein for resistance to splicing inhibitors.

4/6/2023 10:27:01 PM +00:00

Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses

Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses. Recently, the bacterial CRISPR/Cas9 system has been transferred to plants to target and confer immunity to geminiviruses.

4/6/2023 10:26:55 PM +00:00

Comparative analysis of sequencing technologies for single-cell transcriptomics

Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins.

4/6/2023 10:26:45 PM +00:00

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations.

4/6/2023 10:26:37 PM +00:00

Topconfects: A package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list

Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purpose.

4/6/2023 10:26:30 PM +00:00