Tài liệu miễn phí Sinh học
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Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding
The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown.
4/6/2023 6:31:20 AM +00:00
Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. Results: Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls.
4/6/2023 6:31:13 AM +00:00
Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes.
4/6/2023 6:31:03 AM +00:00
SuperTranscripts: A data driven reference for analysis and visualisation of transcriptomes
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence.
4/6/2023 6:30:55 AM +00:00
Searching for cancer vulnerabilities amid genetic chaos
Cancer is an extremely complex disease. Recent largescale studies have revealed fascinating insights into the genetic make-up of multiple tumor entities, but numerous challenges remain.
4/6/2023 6:30:49 AM +00:00
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance
Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characterization of the mechanism of action of drugs. Furthermore, screening the expression of these genes in the tumor tissue may suggest the best course of chemotherapy or a combination of drugs to overcome drug resistance.
4/6/2023 6:30:41 AM +00:00
Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation. In addition, many agricultural and horticultural species are derived from interspecific hybridization.
4/6/2023 6:30:29 AM +00:00
Selection plays the hand it was dealt: Evidence that human adaptation commonly targets standing genetic variation
Adaptation by natural selection is responsible for the extraordinary diversity of life on Earth, as well as the striking matching of organisms to their environments. Yet the role of adaptation in recent human evolution remains controversial.
4/6/2023 6:30:23 AM +00:00
An interaction map of circulating metabolites, immune gene networks, and their genetic regulation
Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic control is still lacking.
4/6/2023 6:30:12 AM +00:00
Large scale genomic reorganization of topological domains at the HoxD locus
The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts.
4/6/2023 6:30:01 AM +00:00
StageR: A general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene level. We propose stageR, a two-stage testing paradigm that leverages the increased power of aggregated gene-level tests and allows post hoc assessment for significant genes.
4/6/2023 6:29:51 AM +00:00
Understanding the genetics behind complex human disease with large-scale iPSC collections
Three recent studies analyzing large-scale collections of human induced pluripotent stem cell lines provide valuable insight into how genetic regulatory variation affects cellular and molecular traits.
4/6/2023 6:29:44 AM +00:00
Characterization of background noise in capture-based targeted sequencing data
Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred during specific steps of the capture-based targeted sequencing process.
4/6/2023 6:29:33 AM +00:00
A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)- creating mutation
Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations associated with the multisystem disorder linked to the gene.
4/6/2023 6:29:21 AM +00:00
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers.
4/6/2023 6:29:11 AM +00:00
A statistical framework for analyzing deep mutational scanning data
Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error estimates for each measurement, capturing both sampling error and consistency between replicates.
4/6/2023 6:29:00 AM +00:00
Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis
The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease.
4/6/2023 6:28:52 AM +00:00
Population and allelic variation of A-to-I RNA editing in human transcriptomes
A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing.
4/6/2023 6:28:45 AM +00:00
MATCHER: Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics
Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type.
4/6/2023 6:28:38 AM +00:00
Canonical mRNA is the exception, rather than the rule
Investigations into gene regulation and disease pathogenesis have been protein-centric for decades. However, in recent years there has been a profound expansion in our knowledge of the variety and complexity of eukaryotic RNA species, particularly the non-coding RNA families.
4/6/2023 6:28:31 AM +00:00
ReMixT: Clone-specific genomic structure estimation in cancer
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes.
4/6/2023 6:28:23 AM +00:00
Identification of novel prostate cancer drivers using RegNetDriver: A framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network.
4/6/2023 6:28:11 AM +00:00
Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility.
4/6/2023 6:28:00 AM +00:00
The three-dimensional genome organization of Drosophila melanogaster through data integration
Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization.
4/6/2023 6:27:48 AM +00:00
Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations.
4/6/2023 6:27:42 AM +00:00
Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wide association studies results
The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how many of the SNPs in the block, and which ones, are causative.
4/6/2023 6:27:34 AM +00:00
MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity
Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we determine whether microbial-associated molecular pattern-triggered gene expression involves modifications at the chromatin level.
4/6/2023 6:27:22 AM +00:00
Chromatin marks and ambient temperature-dependent flowering strike up a novel liaison
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
4/6/2023 6:27:11 AM +00:00
Benchmarking: Contexts and details matter
Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Biology.
4/6/2023 6:27:04 AM +00:00
Data normalization considerations for digital tumor dissection
In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The Cancer Genome Atlas.
4/6/2023 6:26:56 AM +00:00