Tài liệu miễn phí Sinh học
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Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation.
4/6/2023 5:43:32 AM +00:00
STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions
STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content.
4/6/2023 5:43:20 AM +00:00
The evolution of relapse of adult T cell acute lymphoblastic leukemia
Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent.
4/6/2023 5:43:12 AM +00:00
DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis
Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription.
4/6/2023 5:43:05 AM +00:00
A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos
During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored.
4/6/2023 5:42:57 AM +00:00
Convergent network effects along the axis of gene expression during prostate cancer progression
Tumor-specific genomic aberrations are routinely determined by highthroughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels and consequently biochemical states of tumor tissues.
4/6/2023 5:42:46 AM +00:00
Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activityrelated therapeutic targets in cancer. However, the underlying mechanism of epigenetic activation and their function in cancer initiation and progression remain largely unknown.
4/6/2023 5:42:39 AM +00:00
Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus
Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of genetic and environmental risk factors contributing to disease development.
4/6/2023 5:42:28 AM +00:00
Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage
Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes.
4/6/2023 5:42:21 AM +00:00
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves.
4/6/2023 5:42:13 AM +00:00
A pitfall for machine learning methods aiming to predict across cell types
Machine learning models that predict genomic activity are most useful when they make accurate predictions across cell types. Here, we show that when the training and test sets contain the same genomic loci, the resulting model may falsely appear to perform well by effectively memorizing the average activity associated with each locus across the training cell types.
4/6/2023 5:42:04 AM +00:00
Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases.
4/6/2023 5:41:52 AM +00:00
High throughput single-cell detection of multiplex CRISPR-edited gene modifications
CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells.
4/6/2023 5:41:44 AM +00:00
Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions
One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood.
4/6/2023 5:41:34 AM +00:00
RNA editing in cancer impacts mRNA abundance in immune response pathways
RNA editing generates modifications to the RNA sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in editing levels across many cancer types, as well as a few specific mechanisms implicating individual sites in tumorigenesis or metastasis.
4/6/2023 5:41:24 AM +00:00
Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize
Prime editing is a novel and universal CRISPR/Cas-derived precision genome-editing technology that has been recently developed. However, low efficiency of prime editing has been shown in transgenic rice lines. We hypothesize that enhancing pegRNA expression could improve prime-editing efficiency.
4/6/2023 5:41:16 AM +00:00
An integrated peach genome structural variation map uncovers genes associated with fruit traits
Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.
4/6/2023 5:41:08 AM +00:00
Mustache: Multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
We present MUSTACHE, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. MUSTACHE employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps.
4/6/2023 5:40:55 AM +00:00
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of ICB response, but elucidating the molecular and cellular drivers of resistance for individual tumors remains challenging.
4/6/2023 5:40:45 AM +00:00
Tissue-specific usage of transposable element-derived promoters in mouse development
Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology.
4/6/2023 5:40:35 AM +00:00
Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis
Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development and must be properly re-established after its decondensation.
4/6/2023 5:40:27 AM +00:00
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications.
4/6/2023 5:40:16 AM +00:00
Metalign: Efficient alignment-based metagenomic profiling via containment min hash
Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignmentbased metagenomic profiling.
4/6/2023 5:40:09 AM +00:00
Haplotype threading: Accurate polyploid phasing from long reads
Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable challenges, especially in regions of collapsing haplotypes.
4/6/2023 5:40:00 AM +00:00
GraphAligner: Rapid and versatile sequence-to-graph alignment
Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph.
4/6/2023 5:39:49 AM +00:00
STARR-seq identifies active, chromatinmasked, and dormant enhancers in pluripotent mouse embryonic stem cells
Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation.
4/6/2023 5:39:38 AM +00:00
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets.
4/6/2023 5:39:30 AM +00:00
GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes.
4/6/2023 5:39:23 AM +00:00
A systematic comparison of chloroplast genome assembly tools
Chloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information.
4/6/2023 5:39:13 AM +00:00
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping.
4/6/2023 5:39:04 AM +00:00