Tài liệu miễn phí Sinh học
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Chloroplast genomes: Diversity, evolution, and applications in genetic engineering
Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication.
4/6/2023 7:24:15 AM +00:00
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin assortativity, to integrate the epigenomic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts.
4/6/2023 7:24:04 AM +00:00
Retrozymes are a unique family of nonautonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs
Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA pathogens.
4/6/2023 7:23:56 AM +00:00
In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine
Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair.
4/6/2023 7:23:50 AM +00:00
Blood lipids influence DNA methylation in circulating cells
Cells can be primed by external stimuli to obtain a long-term epigenetic memory. We hypothesize that long-term exposure to elevated blood lipids can prime circulating immune cells through changes in DNA methylation, a process that may contribute to the development of atherosclerosis.
4/6/2023 7:23:43 AM +00:00
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia
Altered metabolism is a hallmark of cancer. However, the role of genomic changes in metabolic genes driving the tumour metabolic shift remains to be elucidated. Here, we have investigated the genomic and transcriptomic changes underlying this shift across ten different cancer types.
4/6/2023 7:23:32 AM +00:00
Mash: Fast genome and metagenome distance estimation using MinHash
Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
4/6/2023 7:23:25 AM +00:00
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
Mitochondrial heteroplasmy, the presence of more than one mitochondrial DNA (mtDNA) variant in a cell or individual, is not as uncommon as previously thought. It is mostly due to the high mutation rate of the mtDNA and limited repair mechanisms present in the mitochondrion. Motivated by mitochondrial diseases, much focus has been placed into studying this phenomenon in human samples and in medical contexts.
4/6/2023 7:23:18 AM +00:00
Widespread parainflammation in human cancer
Chronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly promotes mouse gut tumorigenesis upon p53 loss.
4/6/2023 7:23:11 AM +00:00
OncodriveFML: A general framework to identify coding and non-coding regions with cancer driver mutations
Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here we present OncodriveFML, a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis.
4/6/2023 7:23:04 AM +00:00
Resolving complex structural genomic rearrangements using a randomized approach
Complex chromosomal rearrangements are structural genomic alterations involving multiple instances of deletions, duplications, inversions, or translocations that co-occur either on the same chromosome or represent different overlapping events on homologous chromosomes.
4/6/2023 7:22:57 AM +00:00
CHiCAGO: Robust detection of DNA looping interactions in Capture Hi-C data
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques.
4/6/2023 7:22:50 AM +00:00
Tracing the expression of circular RNAs in human pre-implantation embryos
PolyA– RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA– RNA, has not been characterized during human pre-implantation development.
4/6/2023 7:22:42 AM +00:00
Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses have become important tools to identify new avenues for therapies.
4/6/2023 7:22:31 AM +00:00
MUFFINN: Cancer gene discovery via network analysis of somatic mutation data
A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors).
4/6/2023 7:22:24 AM +00:00
Computing tumor trees from single cells
Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical oncology.
4/6/2023 7:22:17 AM +00:00
The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence
The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism.
4/6/2023 7:22:10 AM +00:00
Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types
For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the extent to which it is involved in control of mammalian gene expression and its relationship to chromatin structure remain poorly understood.
4/6/2023 7:22:03 AM +00:00
High type II error and interpretation inconsistencies when attempting to refute transgenerational epigenetic inheritance
A recently published article in Genome Biology attempts to refute important aspects of the phenomenon of transgenerational epigenetic inheritance (TEI). An alternative explanation of the data is offered here, showing that TEI is indeed not contradicted.
4/6/2023 7:21:53 AM +00:00
High type I error and misrepresentations in search for transgenerational epigenetic inheritance: Response to Guerrero-Bosagna
In a recent paper, we described our efforts in search for evidence supporting epigenetic transgenerational inheritance caused by endocrine disrupter chemicals. One aspect of our study was to compare genome-wide DNA methylation changes in the vinclozolin-exposed fetal male germ cells (n = 3) to control samples (n = 3), their counterparts in the next, unexposed, generation (n = 3 + 3) and also in adult spermatozoa (n = 2 + 2) in both generations.
4/6/2023 7:21:47 AM +00:00
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. Using simulated data, we demonstrate that MDSINE significantly outperforms the existing inference method.
4/6/2023 7:21:39 AM +00:00
Taking the RISC of exiting naïve pluripotency
A new study shows how RNA-induced silencing complex (RISC)-mediated posttranscriptional regulation of chromatin remodelers allows for tight control of the naïve-to-primed pluripotency transition.
4/6/2023 7:21:32 AM +00:00
Response to “Variable directionality of gene expression changes across generations does not constitute negative evidence of epigenetic inheritance” Sharma, A. Environmental Epigenetics, 2015, 1-5
Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generation is significant in our study.
4/6/2023 7:21:25 AM +00:00
Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons
Alzheimer’s disease (AD) is a neurodegenerative disease of the brain and the most common form of dementia in the elderly. Aneuploidy, a state in which cells have an abnormal number of chromosomes, has been proposed to play a role in neurodegeneration in AD patients.
4/6/2023 7:21:12 AM +00:00
SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
Single cell experiments provide an unprecedented opportunity to reconstruct a sequence of changes in a biological process from individual “snapshots” of cells. However, nonlinear gene expression changes, genes unrelated to the process, and the possibility of branching trajectories make this a challenging problem.
4/6/2023 7:21:06 AM +00:00
The Ensembl variant effect predictor
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results.
4/6/2023 7:20:58 AM +00:00
Vcfanno: Fast, flexible annotation of genetic variants
The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file.
4/6/2023 7:20:50 AM +00:00
Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all lymphoma cells.
4/6/2023 7:20:39 AM +00:00
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling, which limits their scope and generality. We propose a novel method that compares and clusters cells based on their transcript-compatibility read counts rather than on the transcript or gene quantifications used in standard analysis pipelines.
4/6/2023 7:20:30 AM +00:00
Taxonomer: An interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.
4/6/2023 7:20:18 AM +00:00