scholarly journals DNA-RNA hybrid (R-loop): from a unified picture of the mammalian telomere to the genome-wide

2020 ◽  
Author(s):  
Minoo Rassoulzadegan ◽  
Ali Sharifi-Zarchi ◽  
Leila Kianmehr
Keyword(s):  
Human Cancer ◽  
Future Generation ◽  
Mouse Cell ◽  
Entire Genome ◽  
Physical Isolation ◽  
Double Stranded Dna ◽  
Human Genomes ◽  
Genome Wide ◽  
Normal Human ◽  
Complex Genome

SummaryLocal three-stranded DNA-RNA hybrid regions of the genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for the mouse and human telomeres, clearly suggested by the identification of the complementary RNA TERRA. It was, however, evidenced by DRIP exclusively in human cancer and not in normal human nor in any mouse cell. Based on the observation that in several fractionation procedures, DNA-RNA hybrids copurify with double-stranded DNA, we developed a preparative approach that allows detection of stable DNA-RNA triplexes in a complex genome, their physical isolation and their RNA nucleotide sequence. We then define in the normal mouse and human genomes the notion of terminal R-loop complexes including TERRA molecules synthesized from local promoters of every chromosome. In addition to the telomeric structures since, the finding of the RNA peak, applied in addition to the whole murine sperm genomes, has highlighted a reproducible profile of the R-loop complexes from entire genome suggesting a defined profile for a future generation.

scholarly journals DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1556
Author(s):  
Minoo Rassoulzadegan ◽  
Ali Sharifi-Zarchi ◽  
Leila Kianmehr
Keyword(s):  
Normal Mouse ◽  
Human Sperm ◽  
Telomeric Repeat ◽  
Chromosomal Dna ◽  
Physical Isolation ◽  
Genome Wide ◽  
Cellular Extract ◽  
New Strategy ◽  
Complex Genome

Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular extract without antibody that allows their physical isolation and determination of their RNA nucleotide sequence. We then define in the normal mouse and human sperm genomes the notion of stable DNA associated RNA terminal R-loop complexes, including TERRA molecules synthesized from local promoters of every chromosome. Furthermore, the first strong evidence of all telomeric structures, applied additionally to the whole murine sperm genome compared to the testes, showed reproducible R-loop complexes of the whole genome and suggesting a defined profile in the sperm genome for the next generation.

scholarly journals Antioxidants, Phytochemicals, and Cytotoxicity Studies onPhaleria macrocarpa(Scheff.) Boerl Seeds

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Ma Ma Lay ◽  
Saiful Anuar Karsani ◽  
Behrooz Banisalam ◽  
Sadegh Mohajer ◽  
Sri Nurestri Abd Malek
Keyword(s):  
Human Cancer ◽  
Cytotoxic Effects ◽  
Nutritional Values ◽  
Water Fraction ◽  
Human Cancer Cells ◽  
Fiber Protein ◽  
Cytotoxicity Studies ◽  
Normal Human ◽  
Lung Cell Line ◽  
Mcf 7

In recent years, the utilization of certain medicinal plants as therapeutic agents has drastically increased.Phaleria macrocarpa(Scheff.) Boerl is frequently used in traditional medicine. The present investigation was undertaken with the purpose of developing pharmacopoeial standards for this species. Nutritional values such as ash, fiber, protein, fat, and carbohydrate contents were investigated, and phytochemical screenings with different reagents showed the presence of flavonoids, glycosides, saponin glycosides, phenolic compounds, steroids, tannins, and terpenoids. Our results also revealed that the water fraction had the highest antioxidant activity compared to the methanol extract and other fractions. The methanol and the fractionated extracts (hexane, chloroform, ethyl acetate, and water) ofP. macrocarpaseeds were also investigated for their cytotoxic effects on selected human cancer cells lines (MCF-7, HT-29, MDA-MB231, Ca Ski, and SKOV-3) and a normal human fibroblast lung cell line (MRC-5). Information from this study can be applied for future pharmacological and therapeutic evaluations of the species, and may assist in the standardization for quality, purity, and sample identification. To the best of our knowledge, this is the first report on the phytochemical screening and cytotoxic effect of the crude and fractionated extracts ofP. macrocarpaseeds on selected cells lines.

scholarly journals A curated dataset of modern and ancient high-coverage shotgun human genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pierpaolo Maisano Delser ◽  
Eppie R. Jones ◽  
Anahit Hovhannisyan ◽  
Lara Cassidy ◽  
Ron Pinhasi ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome ◽  
Reference Dataset ◽  
High Coverage ◽  
Sample Distribution ◽  
Human Samples ◽  
Human Genomes ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Computationally Intensive

AbstractOver the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10–18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

scholarly journals CRISPR enriches for cells with mutations in a p53-related interactome, and this can be inhibited

2021 ◽  
Author(s):  
Long Jiang ◽  
Katrine Ingelshed ◽  
Yunbing Shen ◽  
Sanjaykumar V. Boddul ◽  
Vaishnavi Srinivasan Iyer ◽  
...  
Keyword(s):  
Cellular Response ◽  
Human Cancer ◽  
Genetic Alterations ◽  
Dna Breaks ◽  
Data Set ◽  
Human Cancer Cell Lines ◽  
Cycle Arrest ◽  
Double Stranded Dna ◽  
A Cell

CRISPR/Cas9 can be used to inactivate or modify genes by inducing double-stranded DNA breaks1–3. As a protective cellular response, DNA breaks result in p53-mediated cell cycle arrest and activation of cell death programs4,5. Inactivating p53 mutations are the most commonly found genetic alterations in cancer, highlighting the important role of the gene6–8. Here, we show that cells deficient in p53, as well as in genes of a core CRISPR-p53 tumor suppressor interactome, are enriched in a cell population when CRISPR is applied. Such enrichment could pose a challenge for clinical CRISPR use. Importantly, we identify that transient p53 inhibition suppresses the enrichment of cells with these mutations. Furthermore, in a data set of >800 human cancer cell lines, we identify parameters influencing the enrichment of p53 mutated cells, including strong baseline CDKN1A expression as a predictor for an active CRISPR-p53 axis. Taken together, our data identify strategies enabling safe CRISPR use.

scholarly journals An ancestral recombination graph of human, Neanderthal, and Denisovan genomes

2021 ◽  
Vol 7 (29) ◽  
pp. eabc0776
Author(s):  
Nathan K. Schaefer ◽  
Beth Shapiro ◽  
Richard E. Green
Keyword(s):  
Incomplete Lineage Sorting ◽  
Simulated Data ◽  
Modern Human ◽  
Ancestral Recombination Graph ◽  
Lineage Sorting ◽  
Human Genomes ◽  
Genome Wide ◽  
A Genome ◽  
Graph Inference ◽  
And Function

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.

scholarly journals Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

2020 ◽  
Author(s):  
Jouni Sirén ◽  
Jean Monlong ◽  
Xian Chang ◽  
Adam M. Novak ◽  
Jordan M. Eizenga ◽  
...  
Keyword(s):  
Human Populations ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Human Genomes ◽  
Genome Wide ◽  
Sequence Graph ◽  
Long Read ◽  
Comparable Accuracy ◽  
Single Nucleotide Variations ◽  
Allelic Variations

ABSTRACTWe introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg)1, maps reads to thousands of human genomes at around the same speed BWA-MEM2 maps reads to a single reference genome, while maintaining comparable accuracy to VG-MAP, vg’s original mapper. We have developed efficient genotyping pipelines using Giraffe. We demonstrate improvements in genotyping for single nucleotide variations (SNVs), insertions and deletions (indels) and structural variations (SVs) genome-wide. We use Giraffe to genotype and phase 167 thousands structural variations ascertained from long read studies in 5,202 human genomes sequenced with short reads, including the complete 1000 Genomes Project dataset, at an average cost of $1.50 per sample. We determine the frequency of these variations in diverse human populations, characterize their complex allelic variations and identify thousands of expression quantitative trait loci (eQTLs) driven by these variations.

scholarly journals PREDICTION OF PHENOTYPIC AND GENOTYPIC VALUES BY BLUP/GWS AND NEURAL NETWORKS

2018 ◽  
Vol 31 (3) ◽  
pp. 532-540 ◽  
Author(s):  
ALISSON ESDRAS COUTINHO ◽  
DIOGO GONÇALVES NEDER ◽  
MAIRYKON COÊLHO DA SILVA ◽  
ELIANE CRISTINA ARCELINO ◽  
SILVAN GOMES DE BRITO ◽  
...  
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Breeding Cycle ◽  
Prediction Methods ◽  
Best Linear Unbiased Predictor ◽  
Entire Genome ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Genome Wide ◽  
Best Linear Unbiased

ABSTRACT Genome-wide selection (GWS) uses simultaneously the effect of the thousands markers covering the entire genome to predict genomic breeding values for individuals under selection. The possible benefits of GWS are the reduction of the breeding cycle, increase in gains per unit of time, and decrease of costs. However, the success of the GWS is dependent on the choice of the method to predict the effects of markers. Thus, the objective of this work was to predict genomic breeding values (GEBV) through artificial neural networks (ANN), based on the estimation of the effect of the markers, compared to the Ridge Regression-Best Linear Unbiased Predictor/Genome Wide Selection (RR-BLUP/GWS). Simulations were performed by software R to provide correlations concerning ANN and RR-BLUP/GWS. The prediction methods were evaluated using correlations between phenotypic and genotypic values and predicted GEBV. The results showed the superiority of the ANN in predicting GEBV in simulations with higher and lower marker densities, with higher levels of linkage disequilibrium and heritability.

New evidence on the relationship between Microsporidia and Fungi: a genome-wide analysis by DarkHorse software

2014 ◽  
Vol 60 (9) ◽  
pp. 557-568 ◽  
Author(s):  
Heng Xiang ◽  
Ruizhi Zhang ◽  
David De Koeyer ◽  
Guoqing Pan ◽  
Tian Li ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Enterocytozoon Bieneusi ◽  
Entire Genome ◽  
Encephalitozoon Intestinalis ◽  
Genome Wide ◽  
A Genome ◽  
Fungal Genes ◽  
Eukaryotic Organisms ◽  
New Evidence ◽  
The Relationship

Microsporidia are a group of obligate intracellular eukaryotic parasites that infect a wide variety of species, including humans. Phylogenetic analysis indicates a relationship between the Microsporidia and the Fungi. However, most results are based on the analysis of relatively few genes. DarkHorse analysis involves the transformation of BLAST results into a lineage probability index (LPI) value and allows for the comparison of genes for an entire genome with those of other genomes. Thus, we can see which genes from the microsporidia score most closely based on the LPI with other eukaryotic organisms. In this analysis, we calculated the LPI for each gene from the genomes of 7 Microsporidia, Antonospora locustae, Enterocytozoon bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis, Nosema bombycis, Nosema ceranae, and Nematocida parisii, to analyze the genetic relationships between Microsporidia and other species. It was found that many (91%) genes were most closely correlated with genes from other microsporidial genomes and had the highest mean LPI (0.985), indicating a monophyletic origin of the Microsporidia. In a subsequent analysis, we excluded the other Microsporidia from the analysis to look for relationships before the divergence of Microsporidia, and found that 43% of the microsporidial genes scored highest with fungal genes, and a higher mean LPI was found with Fungi than with other kingdoms, suggesting that Microsporidia is closely related to Fungi at the genomic level. Microsporidial genes were functionally clustered based on the KOG (Eukaryotic COG) database, and the possible lineages for each gene family were discussed in concert with the DarkHorse results.

scholarly journals Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

GigaScience ◽  
2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Miriam Payá-Milans ◽  
Laura Poza-Viejo ◽  
Patxi San Martín-Uriz ◽  
David Lara-Astiaso ◽  
Mark D Wilkinson ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Model Systems ◽  
Epigenetic Mark ◽  
Protein Coding ◽  
Brassica Crops ◽  
Genome Wide ◽  
Floral Regulatory Genes ◽  
Complex Genome

Abstract Background Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. Findings We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3′-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. Conclusions We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.

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