Tài liệu miễn phí Sinh học
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Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our knowledge regarding translation elongation comes from the sequencing of mRNA fragments protected by single ribosomes by ribo-seq.
4/6/2023 5:48:10 AM +00:00
SPIN reveals genome-wide landscape of nuclear compartmentalization
We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function.
4/6/2023 5:48:01 AM +00:00
A novel protein encoded by circular SMO RNA is essential for Hedgehog signaling activation and glioblastoma tumorigenicity
Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown.
4/6/2023 5:47:52 AM +00:00
N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease
N6-methyladenosine (m6 A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain. We show that m6 A modification displays temporal and spatial dynamics during neurodevelopment and aging.
4/6/2023 5:47:42 AM +00:00
The variant call format provides efficient and robust storage of GWAS summary statistics
GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the possibility of errors in data interpretation and post-GWAS analyses.
4/6/2023 5:47:31 AM +00:00
Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences
Animal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scattered throughout the RNA sequence that correspond to binding sites for small RNAs and RNA binding proteins.
4/6/2023 5:47:21 AM +00:00
Widespread occurrence of microRNAmediated target cleavage on membranebound polysomes
Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular localization has not yet been well studied, thus limiting our mechanistic understanding of sRNA action.
4/6/2023 5:47:13 AM +00:00
Quantitative profiling of N6 - methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
There are no comprehensive methods to identify N6 -methyladenosine (m6 A) at single-base resolution for every single transcript, which is necessary for the estimation of m6 A abundance.
4/6/2023 5:47:04 AM +00:00
Aberrant splicing isoforms detected by fulllength transcriptome sequencing as transcripts of potential neoantigens in nonsmall cell lung cancer
Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens.
4/6/2023 5:46:56 AM +00:00
Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape
Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.
4/6/2023 5:46:48 AM +00:00
SCMC learns biological variation through the alignment of multiple single-cell genomics datasets
Distinguishing biological from technical variation is crucial when integrating and comparing single-cell genomics datasets across different experiments. Existing methods lack the capability in explicitly distinguishing these two variations, often leading to the removal of both variations.
4/6/2023 5:46:40 AM +00:00
In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants
A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose.
4/6/2023 5:46:31 AM +00:00
Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets.
4/6/2023 5:46:21 AM +00:00
Comprehensive integrative profiling of upper tract urothelial carcinomas
Crosstalk between genetic, epigenetic, and immune alterations in upper tract urothelial carcinomas and their role in shaping muscle invasiveness and patient outcome are poorly understood.
4/6/2023 5:46:09 AM +00:00
Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity
Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly for young and healthy monozygotic twins, DNA methylation divergence, if any, may be restricted to stochastic processes occurring post-twinning during embryonic development and early life.
4/6/2023 5:46:01 AM +00:00
Integrated genomic and transcriptomic analysis reveals unique characteristics of hepatic metastases and pro-metastatic role of complement C1q in pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers due to its high metastasis rate in the liver. However, little is known about the molecular features of hepatic metastases due to difficulty in obtaining fresh tissues and low tumor cellularity
4/6/2023 5:45:53 AM +00:00
MethylationToActivity: A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors
Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive.
4/6/2023 5:45:40 AM +00:00
Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits
Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited.
4/6/2023 5:45:32 AM +00:00
Histone modifications during the life cycle of the brown alga Ectocarpus
Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity.
4/6/2023 5:45:21 AM +00:00
FAN-C: A feature-rich framework for the analysis and visualisation of chromosome conformation capture data
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming.
4/6/2023 5:45:14 AM +00:00
GCNG: Graph convolutional networks for inferring gene interaction from spatial transcriptomics data
Most methods for inferring gene-gene interactions from expression data focus on intracellular interactions. The availability of high-throughput spatial expression data opens the door to methods that can infer such interactions both within and between cells. To achieve this, we developed Graph Convolutional Neural networks for Genes (GCNG).
4/6/2023 5:45:06 AM +00:00
An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes
Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to systematically integrate transcriptomic, epigenomic, and cistromic information to accurately define the regulatory networks critical for metastasis.
4/6/2023 5:44:59 AM +00:00
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease.
4/6/2023 5:44:51 AM +00:00
Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome
Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage.
4/6/2023 5:44:43 AM +00:00
Evolution of regulatory networks associated with traits under selection in cichlids
Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated with phenotypic effect across ecologically diverse species.
4/6/2023 5:44:33 AM +00:00
Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual
Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes.
4/6/2023 5:44:24 AM +00:00
Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection
Adenosine-to-inosine (A-to-I) RNA editing plays important roles in diversifying the transcriptome and preventing MDA5 sensing of endogenous dsRNA as nonself. To date, few studies have investigated the population genomic signatures of A-to-I editing due to the lack of editing sites overlapping with SNPs.
4/6/2023 5:44:13 AM +00:00
Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higherorder organization and transcriptional activity in living cells remains unclear.
4/6/2023 5:44:01 AM +00:00
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.
4/6/2023 5:43:51 AM +00:00
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood.
4/6/2023 5:43:42 AM +00:00