Tài liệu miễn phí Sinh học
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P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis
P16 DNA methylation is well known to be the most frequent event in cancer development. It has been reported that genetic inactivation of P16 drives cancer growth and metastasis, however, whether P16 DNA methylation is truly a driver in cancer metastasis remains unknown.
4/6/2023 7:04:29 AM +00:00
Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements
To expand the repertoire of Cas9s available for genome targeting, we present a new in vitro method for the simultaneous examination of guide RNA and protospacer adjacent motif (PAM) requirements. The method relies on the in vitro cleavage of plasmid libraries containing a randomized PAM as a function of Cas9-guide RNA complex concentration.
4/6/2023 7:04:23 AM +00:00
Characterization of Staphylococcus aureus Cas9: A smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications
CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the smaller, 1053 amino acid nuclease Staphylococcus aureus Cas9.
4/6/2023 7:04:16 AM +00:00
The estrous cycle surpasses sex differences in regulating the transcriptome in the rat medial prefrontal cortex and reveals an underlying role of early growth response 1
Males and females differ in cognitive functions and emotional processing, which in part have been associated with baseline sex differences in gene expression in the medial prefrontal cortex. Nevertheless, a growing body of evidence suggests that sex differences in medial prefrontal cortex-dependent cognitive functions are attenuated by hormonal fluctuations within the menstrual cycle.
4/6/2023 7:04:09 AM +00:00
Understanding Brassicaceae evolution through ancestral genome reconstruction
Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed. Results: We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula.
4/6/2023 7:04:02 AM +00:00
Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining
Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to developmental arrest in the liver and allowing the host to launch a protective immune response.
4/6/2023 7:03:56 AM +00:00
Pop in, pop out: A novel gene-targeting strategy for use with CRISPR-Cas9
The CRISPR-Cas9 system is frequently used to create small deletions in the genomes of mammalian cells, but the isolation of precisely targeted mutants is still challenging. A new, two-step ‘pop in & out’ targeting approach facilitates this task.
4/6/2023 7:03:49 AM +00:00
CRISPR/Cas9-mediated viral interference in plants
The CRISPR/Cas9 system provides bacteria and archaea with molecular immunity against invading phages and conjugative plasmids. Recently, CRISPR/Cas9 has been used for targeted genome editing in diverse eukaryotic species.
4/6/2023 7:03:41 AM +00:00
A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression
To facilitate indefinite proliferation, stem cells and most cancer cells require the activity of telomerase, which counteracts the successive shortening of telomeres caused by incomplete DNA replication at the very end of each chromosome.
4/6/2023 7:03:34 AM +00:00
Genomic screens identify a new phytobacterial microbe-associated molecular pattern and the cognate Arabidopsis receptor-like kinase that mediates its immune elicitation
The recognition of microbe-associated molecular patterns during infection is central to the mounting of an effective immune response. In spite of their importance, it remains difficult to identify these molecules and the host receptors required for their perception, ultimately limiting our understanding of the role of these molecules in the evolution of host-pathogen relationships.
4/6/2023 7:03:26 AM +00:00
Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes.
4/6/2023 7:03:19 AM +00:00
DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases
Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inflammation may reveal novel pathways or therapeutic targets for inflammation.
4/6/2023 7:03:13 AM +00:00
The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
4/6/2023 7:03:06 AM +00:00
Epigenomics: Dissecting hybridization and polyploidization
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.
4/6/2023 7:02:55 AM +00:00
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
Human pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states.
4/6/2023 7:02:48 AM +00:00
Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean
Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products.
4/6/2023 7:02:18 AM +00:00
“Like sugar in milk”: Reconstructing the genetic history of the Parsi population
The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA).
4/6/2023 7:02:08 AM +00:00
MicroRNAs control mRNA fate by compartmentalization based on 3′ UTR length in male germ cells
Post-transcriptional regulation of gene expression can be achieved through the control of mRNA stability, cytoplasmic compartmentalization, 3′ UTR length and translational efficacy. Spermiogenesis, a process through which haploid male germ cells differentiate into spermatozoa, represents an ideal model for studying posttranscriptional regulation in vivo because it involves a large number of transcripts that are physically sequestered in ribonucleoprotein particles (RNPs) and thus subjected to delayed translation.
4/6/2023 7:02:01 AM +00:00
Differentiated demographic histories and local adaptations between Sherpas and Tibetans
The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two groups, we analyzed genome-wide data in 111 Sherpas (Tibet and Nepal) and 177 Tibetans (Tibet and Qinghai), together with available data from present-day human populations.
4/6/2023 7:01:53 AM +00:00
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD.
4/6/2023 7:01:46 AM +00:00
Unexpected consequences: Exon skipping caused by CRISPR-generated mutations
A new study finds that splicing disruption is a frequent consequence of mutations generated by CRISPR/Cas9 gene-editing technology, and alleles designed to be null can express aberrant proteins. This new information allows enhanced quality control procedures to select the best mutant alleles generated by CRISPR/Cas9.
4/6/2023 7:01:40 AM +00:00
Unreeling the chromatin thread: A genomic perspective on organization around the periphery of the Arabidopsis nucleus
The first genome-wide examination of the chromatin landscape at the periphery of the plant cell nucleus reveals substantial enrichment of heterochromatin and Polycomb-based repressive chromatin.
4/6/2023 7:01:34 AM +00:00
Going beyond genetics to discover cancer targets
Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.
4/6/2023 7:01:27 AM +00:00
CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion
CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exons. For example, CRISPR-mediated editing of β-catenin exon 3, which encodes an autoinhibitory domain, induces partial skipping of the in-frame exon and nuclear accumulation of β-catenin.
4/6/2023 7:01:20 AM +00:00
Emerging roles of chromatin in the maintenance of genome organization and function in plants
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus.
4/6/2023 7:01:14 AM +00:00
Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants
Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood.
4/6/2023 7:01:07 AM +00:00
Correspondence on Lovell et al.: Response to Bornelöv et al
While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that specific groups of syntenic protein-coding genes are missing in birds.
4/6/2023 7:01:01 AM +00:00
EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets.
4/6/2023 7:00:54 AM +00:00
Correspondence on Lovell et al.: Identification of chicken genes previously assumed to be evolutionarily lost
Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases.
4/6/2023 7:00:47 AM +00:00
An evolutionary case for functional gene body methylation in plants and animals
Cytosine methylation is a covalent modification of DNA that is shared by plants, animals, and other eukaryotes [1]. The most frequently methylated sequences in plant genomes are symmetrical CG dinucleotides, and this methylation is maintained across cell divisions by the MET1 family of methyltransferases.
4/6/2023 7:00:41 AM +00:00