Tài liệu miễn phí Sinh học
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Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome
Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo.
4/6/2023 6:36:01 AM +00:00
MetaGen: Reference-free learning with multiple metagenomic samples
A major goal of metagenomics is to identify and study the entire collection of microbial species in a set of targeted samples. We describe a statistical metagenomic algorithm that simultaneously identifies microbial species and estimates their abundances without using reference genomes.
4/6/2023 6:35:50 AM +00:00
Systematic identification of regulatory variants associated with cancer risk
Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically identify the SNPs that affect gene expression by modulating activities of distal regulatory elements, we adapt the self-transcribing active regulatory region sequencing (STARR-seq) strategy, a high-throughput technique to functionally quantify enhancer activities.
4/6/2023 6:35:39 AM +00:00
The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading
The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing.
4/6/2023 6:35:27 AM +00:00
From structure to function, how bioinformatics help to reveal functions of our genomes
The International Bioinformatics Workshop (IBW), held every other year in China since 2003, has grown into an international forum for showcasing the most important breakthroughs in bioinformatics-related fields.
4/6/2023 6:35:15 AM +00:00
Alignment-free sequence comparison: Benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis.
4/6/2023 6:35:07 AM +00:00
Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage
The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of targets still generate considerable off-target effects.
4/6/2023 6:34:55 AM +00:00
Genomic imprinting beyond DNA methylation: A role for maternal histones
Genomic imprinting is an epigenetic phenomenon that allows monoallelic expression of a subset of genes dependent on parental origin and is canonically regulated by DNA methylation.
4/6/2023 6:34:43 AM +00:00
McEnhancer: Predicting gene expression via semi-supervised assignment of enhancers to target genes
Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target genes to putative enhancers via a semi-supervised learning algorithm that predicts gene expression patterns based on enriched sequence features.
4/6/2023 6:34:35 AM +00:00
Massive A-to-I RNA editing is common across the Metazoa and correlates with dsRNA abundance
Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by the ADAR (adenosine deaminase that acts on RNA) enzymes, which are ubiquitously expressed among metazoans. Technical requirements have limited systematic mapping of editing sites to a small number of organisms.
4/6/2023 6:34:28 AM +00:00
DNA methylation dynamics during early plant life
Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown.
4/6/2023 6:34:20 AM +00:00
Genome build information is an essential part of genomic track files
Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Although not a substitute for best practices, we also provide a tool to predict the genome build version of genomic track files.
4/6/2023 6:34:12 AM +00:00
SiFit: Inferring tumor trees from single-cell sequencing data under finite-sites models
Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models.
4/6/2023 6:34:01 AM +00:00
Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation
The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs.
4/6/2023 6:33:50 AM +00:00
DESMAN: A new tool for de novo extraction of strains from metagenomes
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation.
4/6/2023 6:33:42 AM +00:00
Evidence of reduced recombination rate in human regulatory domains
Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate.
4/6/2023 6:33:30 AM +00:00
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A
DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression.
4/6/2023 6:33:24 AM +00:00
Splatter: Simulation of single-cell RNA sequencing data
As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, their similarity to real data is not demonstrated, or reproducible code is not available.
4/6/2023 6:33:17 AM +00:00
Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis
Piwi-interacting RNAs (piRNAs) are a class of short (~26–31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs).
4/6/2023 6:33:06 AM +00:00
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition.
4/6/2023 6:32:57 AM +00:00
Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis
Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential role for recoding by ADAR1 has not been demonstrated.
4/6/2023 6:32:50 AM +00:00
New skin for the old RNA-Seq ceremony: The age of single-cell multi-omics
While we are taught to never judge a book by its cover, covers may actually be revealing. In the case of a cell, the surface proteins on its “cover” are unique to particular cell types: for example, CD3 for T cells and CD19 for B cells. With such markers in hand, populations of cells can be classified into the cell types they contain, in particular using fluorescence-activated cell sorting (FACS) analysis with a panel of antibodies.
4/6/2023 6:32:43 AM +00:00
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.
4/6/2023 6:32:30 AM +00:00
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites.
4/6/2023 6:32:19 AM +00:00
BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells
Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction.
4/6/2023 6:32:10 AM +00:00
Sparse conserved under-methylated CpGs are associated with high-order chromatin structure
Whole-genome bisulfite sequencing (WGBS) is the gold standard for studying landscape DNA methylation. Current computational methods for WGBS are mainly designed for gene regulatory regions with multiple under-methylated CpGs (UMCs), such as promoters and enhancers.
4/6/2023 6:31:59 AM +00:00
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes
Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs.
4/6/2023 6:31:49 AM +00:00
Conservation and divergence of small RNA pathways and microRNAs in land plants
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants.
4/6/2023 6:31:42 AM +00:00
A tandem simulation framework for predicting mapping quality
Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality.
4/6/2023 6:31:35 AM +00:00
Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation
Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phenotypic diversity beyond changes to nucleotide sequence. Previous research has looked at the rate at which spontaneous epialleles arise but it is currently unknown how they are maintained across generations.
4/6/2023 6:31:27 AM +00:00