Tài liệu miễn phí Sinh học
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DeconstructSigs: Delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution
Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample.
4/6/2023 7:11:58 AM +00:00
The aspirin-induced long non-coding RNA OLA1P2 blocks phosphorylated STAT3 homodimer formation
Although the chemopreventive effects of aspirin have been extensively investigated, the roles of many cell components, such as long non-coding RNAs, in these effects are still not completely understood.
4/6/2023 7:11:50 AM +00:00
Trapping the intruder - immune receptor domain fusions provide new molecular leads for improving disease resistance in plants
A new study uses genomics to show that fusions of plant immune receptors and other protein domains occur in significant numbers. This finding will generate many new research hypotheses and provide new opportunities for breeding resistant plant varieties.
4/6/2023 7:11:43 AM +00:00
Genome-wide introgression among distantly related Heliconius butterfly species
The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna.
4/6/2023 7:11:32 AM +00:00
Classification of low quality cells from single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical research. One of the key challenges is to ensure that only single, live cells are included in downstream analysis, as the inclusion of compromised cells inevitably affects data interpretation.
4/6/2023 7:11:25 AM +00:00
External signals shape the epigenome
A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3–STAT6 pathway, which causes dendritic-cell-specific DNA demethylation.
4/6/2023 7:11:18 AM +00:00
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.
4/6/2023 7:11:10 AM +00:00
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay
Chromatin accessibility captures in vivo protein-chromosome binding status, and is considered an informative proxy for protein-DNA interactions. DNase I and Tn5 transposase assays require thousands to millions of fresh cells for comprehensive chromatin mapping.
4/6/2023 7:11:00 AM +00:00
A survey of best practices for RNA-seq data analysis
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
4/6/2023 7:10:50 AM +00:00
Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs
Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown.
4/6/2023 7:10:43 AM +00:00
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. Much of the research effort in this area has examined proximal promoter regions and epigenetic alterations at other loci are not well characterized.a
4/6/2023 7:10:37 AM +00:00
Widespread RNA binding by chromatinassociated proteins
Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression.
4/6/2023 7:10:25 AM +00:00
The contribution of Alu exons to the human proteome
Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial.
4/6/2023 7:10:18 AM +00:00
Proteome diversification by genomic parasites
Alu elements can integrate into human genes and lead to the generation of primate-specific isoforms. A new study examines their contribution to the human proteome. An estimated 2000 human exons have been generated from the inclusion of primate-specific Alu elements into mRNA transcripts. These Alu exons are extensively transcribed, but the prevailing view in recent years has been that they are rarely translated into proteins.
4/6/2023 7:10:10 AM +00:00
Expanding the diversity of DNA base modifications with N6 -methyldeoxyadenosine
Vertebrate DNA is subjected to epigenetic base modifications that have been thought to be limited to methylated and other modified forms of cytidine. A recent study shows that methylation of adenine to form N6 -methyladenine is a rare but readily detectable modification that can be mapped to distinct genomic sites in vertebrates.
4/6/2023 7:10:03 AM +00:00
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans
Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs.
4/6/2023 7:09:57 AM +00:00
H1 gets the genome in shape
By performing high-throughput chromosome conformation capture analyses in embryonic stem cells depleted of the linker histone H1, Geeven and colleagues have uncovered exciting new evidence concerning a role for this histone in modulating three-dimensional genome architecture and chromatin organization.
4/6/2023 7:09:50 AM +00:00
Variation in 5-hydroxymethylcytosine across human cortex and cerebellum
The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite; however, this method cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals.
4/6/2023 7:09:43 AM +00:00
A glimpse into the future of genomeenabled plant biology from the shores of Cold Spring Harbor
The breadth and depth of exciting, unpublished work towards discovering fundamental principles and direct applications in agriculture is impossible to capture in a short meeting report. Therefore, here we highlight some transformative areas whose potential impact is likely to reach beyond plant biology.
4/6/2023 7:09:37 AM +00:00
The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes
Ranking human genes based on their tolerance to functional genetic variation can greatly facilitate patient genome interpretation. It is well established, however, that different parts of proteins can have different functions, suggesting that it will ultimately be more informative to focus attention on functionally distinct portions of genes. Here we evaluate the intolerance of genic sub-regions using two biological sub-region classifications.
4/6/2023 7:09:31 AM +00:00
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.
4/6/2023 7:09:24 AM +00:00
Ancient DNA and the rewriting of human history: Be sparing with Occam’s razor
Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.
4/6/2023 7:09:18 AM +00:00
CIDANE: Comprehensive isoform discovery and abundance estimation
We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools.
4/6/2023 7:09:08 AM +00:00
Functional analysis of androgen receptor mutations that confer anti-androgen resistance identified in circulating cell-free DNA from prostate cancer patients
The androgen receptor (AR) is a pivotal drug target for the treatment of prostate cancer, including its lethal castration-resistant (CRPC) form. All current non-steroidal AR antagonists, such as hydroxyflutamide, bicalutamide, and enzalutamide, target the androgen binding site of the receptor, competing with endogenous androgenic steroids.
4/6/2023 7:09:01 AM +00:00
IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
The role of cytokines in establishing specific transcriptional programmes in innate immune cells has long been recognized. However, little is known about how these extracellular factors instruct innate immune cell epigenomes to engage specific differentiation states.
4/6/2023 7:08:54 AM +00:00
Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is the detection of changes in transcript usage between experimental conditions. For example, discovery of pathological alternative splicing may allow the development of new treatments or better management of patients.
4/6/2023 7:08:48 AM +00:00
FBXO32, encoding a member of the SCF complex, is mutated in dilated cardiomyopathy
Dilated cardiomyopathy (DCM) is a common form of cardiomyopathy causing systolic dysfunction and heart failure. Rare variants in more than 30 genes, mostly encoding sarcomeric proteins and proteins of the cytoskeleton, have been implicated in familial DCM to date.
4/6/2023 7:08:41 AM +00:00
Towards a new era in medicine: Therapeutic genome editing
Genome editing is the process of precisely modifying the nucleotide sequence of the genome. It has provided a powerful approach to research questions but, with the development of a new set of tools, it is now possible to achieve frequencies of genome editing that are high enough to be useful therapeutically. G
4/6/2023 7:08:35 AM +00:00
KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome
Joubert syndrome (JBTS) and related disorders are defined by cerebellar malformation (molar tooth sign), together with neurological symptoms of variable expressivity. The ciliary basis of Joubert syndrome related disorders frequently extends the phenotype to tissues such as the eye, kidney, skeleton and craniofacial structures.
4/6/2023 7:08:28 AM +00:00
Local compartment changes and regulatory landscape alterations in histone H1-depleted cells
Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure.
4/6/2023 7:08:21 AM +00:00