Tài liệu miễn phí Sinh học
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Dissecting indirect genetic effects from peers in laboratory mice
The phenotype of an individual can be affected not only by the individual’s own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown.
4/6/2023 5:14:22 AM +00:00
Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states.
4/6/2023 5:14:09 AM +00:00
Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease
Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and nongenetic host factors.
4/6/2023 5:13:58 AM +00:00
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2.
4/6/2023 5:13:51 AM +00:00
The dynamics of N6 -methyladenine RNA modification in interactions between rice and plant viruses
N6 -methyladenosine (m6 A) is the most common RNA modification in eukaryotes and has been implicated as a novel epigenetic marker that is involved in various biological processes. The pattern and functional dissection of m6 A in the regulation of several major human viral diseases have already been reported.
4/6/2023 5:13:40 AM +00:00
Evolution of mouse circadian enhancers from transposable elements
Transposable elements are increasingly recognized as a source of cisregulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into functional enhancers regulating host gene expression.
4/6/2023 5:13:31 AM +00:00
Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep
The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.
4/6/2023 5:13:17 AM +00:00
SMOOTH-seq: Single-cell genome sequencing of human cells on a thirdgeneration sequencing platform
There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based single-cell whole-genome sequencing (scWGS) method named SMOOTH-seq (single-molecule real-time sequencing of long fragments amplified through transposon insertion).
4/6/2023 5:13:10 AM +00:00
SPARK-X: Non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method for rapid and effective detection of spatially expressed genes in large spatial transcriptomic studies.
4/6/2023 5:12:57 AM +00:00
GxEsum: A novel approach to estimate the phenotypic variance explained by genomewide GxE interaction based on GWAS summary statistics for biobank-scale data
Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. However, existing methods are computationally demanding and infeasible to handle biobank-scale data.
4/6/2023 5:12:50 AM +00:00
Positive natural selection of N6- methyladenosine on the RNAs of processed pseudogenes
Canonical nonsense-mediated decay (NMD) is an important splicingdependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms.
4/6/2023 5:12:41 AM +00:00
Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in the cell-free DNA of human blood and could possibly be harnessed as a new cancer biomarker
4/6/2023 5:12:33 AM +00:00
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines.
4/6/2023 5:12:24 AM +00:00
Chromosome-level genome assembly of a regenerable maize inbred line A188
The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.
4/6/2023 5:12:17 AM +00:00
GUNC: Detection of chimerism and contamination in prokaryotic genomes
Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome’s full complement of genes.
4/6/2023 5:12:10 AM +00:00
Annotation of snoRNA abundance across human tissues reveals complex snoRNAhost gene relationships
Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extraribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns.
4/6/2023 5:12:02 AM +00:00
Transcription shapes DNA replication initiation to preserve genome integrity
Early DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question of how early DNA replication coordinates with transcription to avoid collisions and DNA damage.
4/6/2023 5:11:55 AM +00:00
Targeted mutagenesis in mouse cells and embryos using an enhanced prime editor
Prime editors, novel genome-editing tools consisting of a CRISPR-Cas9 nickase and an engineered reverse transcriptase, can induce targeted mutagenesis. Nevertheless, much effort is required to optimize and improve the efficiency of prime-editing.
4/6/2023 5:11:48 AM +00:00
Gene set enrichment analysis for genomewide DNA methylation data
DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions.
4/6/2023 5:11:41 AM +00:00
BUTTERFLY: Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated molecules, thereby facilitating the counting of distinct molecules from sequenced reads.
4/6/2023 5:11:30 AM +00:00
N6 -methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner
Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6 A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits.
4/6/2023 5:11:21 AM +00:00
Characterization of structural variation in Tibetans reveals new evidence of highaltitude adaptation and introgression
Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far.
4/6/2023 5:11:13 AM +00:00
Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures
Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown.
4/6/2023 5:11:04 AM +00:00
GRiNCH: Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units.
4/6/2023 5:10:56 AM +00:00
A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks
Lung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development.
4/6/2023 5:10:47 AM +00:00
Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood.
4/6/2023 5:10:33 AM +00:00
The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation
4/6/2023 5:10:25 AM +00:00
MichiGAN: Sampling from disentangled representations of single-cell data using generative adversarial networks
Deep generative models such as variational autoencoders (VAEs) and generative adversarial networks (GANs) generate and manipulate high-dimensional images. We systematically assess the complementary strengths and weaknesses of these models on single-cell gene expression data.
4/6/2023 5:10:15 AM +00:00
Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood.
4/6/2023 5:10:05 AM +00:00
The genetic mechanism of heterosis utilization in maize improvement
In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits.
4/6/2023 5:09:57 AM +00:00