scholarly journals DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks

Cell Reports ◽  
2020 ◽  
Vol 33 (13) ◽  
pp. 108569
Author(s):  
Sourav Saha ◽  
Yilun Sun ◽  
Shar-yin Naomi Huang ◽  
Simone Andrea Baechler ◽  
Lorinc Sandor Pongor ◽  
...  
Keyword(s):  
Rna Cleavage ◽  
Repair Pathway ◽  
Dna And Rna ◽  
Protein Crosslinks ◽  
Rna And Dna

scholarly journals Topoisomerase 3B (TOP3B) DNA and RNA Cleavage Complexes and Pathway to Repair TOP3B-Linked RNA and DNA Breaks

2020 ◽  
Author(s):  
Sourav Saha ◽  
Yilun Sun ◽  
Shar-Yin Huang ◽  
Ukhyun Jo ◽  
Hongliang Zhang ◽  
...  
Keyword(s):  
Rna Cleavage ◽  
Dna Breaks ◽  
Dna And Rna ◽  
Rna And Dna

scholarly journals Characteristic of HPV Integration in the Genome and Transcriptome of Cervical Cancer Tissues

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Weiyang Li ◽  
Yanwei Qi ◽  
Xiaofang Cui ◽  
Qing Huo ◽  
Liangxi Zhu ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Adherens Junction ◽  
Cholinergic Synapse ◽  
Cervical Cancers ◽  
Dna And Rna ◽  
Chi Squared ◽  
Integration Sites ◽  
Cancer Tissues ◽  
High Risk Hpv ◽  
Rna And Dna

High-risk HPV is clearly associated with cervical cancer. HPV integration has been confirmed to promote carcinogenesis in the previous studies. In our study, a total of 285 DNA breakpoints and 287 RNA breakpoints were collected. We analyzed the characteristic of HPV integration in the DNA and RNA samples. The results revealed that the patterns of HPV integration in RNA and DNA samples differ significantly. FHIT, KLF5, and LINC00392 were the hotspot genes integrated by HPV in the DNA samples. RAD51B, CASC8, CASC21, ERBB2, TP63, TEX41, RAP2B, and MYC were the hotspot genes integrated by HPV in RNA samples. Breakpoints of DNA samples were significantly prone to the region of INTRON (P < 0.01, Chi-squared test), whereas in the RNA samples, the breakpoints were prone to EXON. Pathway analysis had revealed that the breakpoints of RNA samples were enriched in the pathways of transcriptional misregulation in cancer, cancer pathway, and pathway of adherens junction. Breakpoints of DNA samples were enriched in the pathway of cholinergic synapse. In summary, our data helped to gain insights into the HPV integration sites in DNA and RNA samples of cervical cancer. It had provided theoretical basis for understanding the mechanism of tumorigenesis from the perspective of HPV integration in the HPV-associated cervical cancers.

scholarly journals Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

2005 ◽  
Vol 71 (6) ◽  
pp. 3235-3247 ◽  
Author(s):  
Heath J. Mills ◽  
Robert J. Martinez ◽  
Sandra Story ◽  
Patricia A. Sobecky
Keyword(s):  
Phylogenetic Analysis ◽  
Microbial Community ◽  
Gulf Of Mexico ◽  
Gas Hydrate ◽  
Phylogenetic Analyses ◽  
Active Fraction ◽  
Clone Libraries ◽  
Dna And Rna ◽  
Rna And Dna

ABSTRACT The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.

scholarly journals Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amanda L. Gavin ◽  
Deli Huang ◽  
Tanya R. Blane ◽  
Therese C. Thinnes ◽  
Yusuke Murakami ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Inflammatory Diseases ◽  
Type I ◽  
Multiple Sensors ◽  
Dna And Rna ◽  
Elevated Type ◽  
Minor Contribution ◽  
Ifn Γ ◽  
A Minor ◽  
Rna And Dna

AbstractPhospholipase D3 (PLD3) and PLD4 polymorphisms have been associated with several important inflammatory diseases. Here, we show that PLD3 and PLD4 digest ssRNA in addition to ssDNA as reported previously. Moreover, Pld3−/−Pld4−/− mice accumulate small ssRNAs and develop spontaneous fatal hemophagocytic lymphohistiocytosis (HLH) characterized by inflammatory liver damage and overproduction of Interferon (IFN)-γ. Pathology is rescued in Unc93b13d/3dPld3−/−Pld4−/− mice, which lack all endosomal TLR signaling; genetic codeficiency or antibody blockade of TLR9 or TLR7 ameliorates disease less effectively, suggesting that both RNA and DNA sensing by TLRs contributes to inflammation. IFN-γ made a minor contribution to pathology. Elevated type I IFN and some other remaining perturbations in Unc93b13d/3dPld3−/−Pld4−/− mice requires STING (Tmem173). Our results show that PLD3 and PLD4 regulate both endosomal TLR and cytoplasmic/STING nucleic acid sensing pathways and have implications for the treatment of nucleic acid-driven inflammatory disease.

scholarly journals GeTallele: a method for integrative analysis and visualization of DNA and RNA allele frequencies

2018 ◽  
Author(s):  
Piotr Słowiński ◽  
Muzi Li ◽  
Paula Restrepo ◽  
Nawaf Alomran ◽  
Liam F. Spurr ◽  
...  
Keyword(s):  
Gene Dosage ◽  
Transcriptional Response ◽  
Structural Features ◽  
Integrative Analysis ◽  
Allele Frequencies ◽  
Biological Traits ◽  
Specific Expression ◽  
Dna And Rna ◽  
Wide Range ◽  
Rna And Dna

AbstractBackgroundAsymmetric allele expression typically indicates functional and/or structural features associated with the underlying genetic variants. When integrated, RNA and DNA allele frequencies can reveal patterns characteristic of a wide-range of biological traits, including ploidy changes, genome admixture, allele-specific expression and gene-dosage transcriptional response.ResultsTo assess RNA and DNA allele frequencies from matched sequencing datasets, we introduce a method for generating model distributions of variant allele frequencies (VAF) with a given variant read probability. In contrast to other methods, based on whole sequences or single SNV, proposed methodology uses continuous multi-SNV genomic regions. The methodology is implemented in a GeTallele toolbox that provides a suite of functions for integrative analysis, statistical assessment and visualization of Genome and Transcriptome allele frequencies. Using model VAF probabilities, GeTallele allows estimation and comparison of variant read probabilities (VAF distributions) in a sequencing dataset. We demonstrate this functionality across cancer DNA and RNA sequencing datasets.ConclusionBased on our evaluation, variant read probabilities can serve as a dependable indicator to assess gene and chromosomal allele asymmetries and to aid calls of genomic events in matched sequencing RNA and DNA [email protected]

Concurrent targeted resequencing for translocations and mutations in tumor samples.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e14597-e14597
Author(s):  
Li Chen
Keyword(s):  
Lung Tumor ◽  
Variant Calling ◽  
Limited Information ◽  
Tissue Samples ◽  
Single Tube ◽  
Targeted Resequencing ◽  
Pik3ca Mutations ◽  
Dna And Rna ◽  
Exon 19 Deletion ◽  
Rna And Dna

e14597 Background: Genetic variations are diverse, and proper nucleic acid templates should be analyzed for optimal outcomes. Previous NGS assays separately treat DNA and/or RNA, and are costly and produce limited information. Here we present a concurrent assay simultaneously converting both RNA and DNA templates in a single-tube format to streamline variant detection process. Methods: We developed a high-throughput targeted resequencing assay utilizing both DNA and RNA templates for mutation and fusion detection, and applied to a cohort of over 1000 lung tumor samples. Total nucleic acids from tissue samples were processed in a single-tube format throughout, and post-assay data analysis split RNA and DNA signals for corresponding variant calling. Sensitivity and specificity were sufficient for tissue samples. Results: In addition to common EGFR, KRAS, BRAF, PIK3CA mutations and ALK, ROS1, RET fusions and MET Exon 14 skipping, we also identified rare HLA-DRB1---MET and MSN---NTRK2 fusions. We found that MET exon 14 skipping was abundant, and that EGFR T790M is more associated with Exon 19 deletion than with L858R. We also found baseline mutation frequency for FFPE samples at 4-5%. Conclusions: Overall, this method is robust and convenient for clinical molecular diagnosis for tissue samples where variant types are diverse and time and budgets are constrained. Extreme caution is suggested for making positive calls below 5% MAF.

Comparing Ion Distributions around RNA and DNA Helical and Loop-loop Motifs

2008 ◽  
Vol 1130 ◽  
Author(s):  
Andrey V Semichaevsky ◽  
Ashley E Marlowe ◽  
Yaroslava G Yingling
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Assembly Process ◽  
Dna Motifs ◽  
Dna And Rna ◽  
Ion Distributions ◽  
Concentration Of Ions ◽  
The Stability ◽  
Dynamics Simulations ◽  
Rna And Dna

AbstractNucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this paper we use explicit molecular dynamics simulations to examine the variations in cationic distributions around DNA and RNA helices and loop-loop interactions with identical sequence except for Thymine to Uracil substitution. Our simulations show that the ionic distributions are different around RNA and DNA motifs which could be related to the discrepancy in stability of loop-loop complexes.

scholarly journals Transfer of Conditionability Between Planaria Through DNA and RNA

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Cecilia Schiavoni ◽  
Jessica Genter
Keyword(s):  
Genetic Material ◽  
Neural Mechanism ◽  
Control Group ◽  
Memory Retention ◽  
Donor Group ◽  
Control Donor ◽  
Dna And Rna ◽  
Rna And Dna

This experiment examined whether the transfer of DNA or RNA from conditioned planaria could make the recipients more susceptible to similar conditioning. It has been shown in prior experiments that cephalization is not necessary for memory retention in planaria, so there must be another, non-neural mechanism for memory. Thus, changes in DNA or RNA may be responsible for memory retention, and introducing these changes to naive planaria could transfer the "memory" of the conditioned donor. This study included 3 groups of 11 planaria: the control group, the DNA receival group, and the RNA receival group. After the control group was conditioned, each planarian’s RNA and DNA were extracted and given to its genetically identical counterparts in the DNA and RNA receival groups. The number of trials it took to condition the planaria in each group was measured and compared to see if the transfer of RNA or DNA made the recipients more easily conditionable than the control donor group. The results show that the transfer of RNA and DNA made insignificant changes to the conditionability of recipients. However, further research may be able to identify the location of memory bearing molecules, which, if applied to experiments similar to this one, would ensure that the planaria received a high enough concentration of genetic material for any changes present to make a significant effect.

scholarly journals The Nucleic Acid Binding Activity of Bleomycin Hydrolase Is Involved in Bleomycin Detoxification

1998 ◽  
Vol 18 (6) ◽  
pp. 3580-3585 ◽  
Author(s):  
Wenjin Zheng ◽  
Stephen Albert Johnston
Keyword(s):  
Nucleic Acid ◽  
Binding Activity ◽  
Dual Function ◽  
Nucleic Acid Binding ◽  
Peptide Cleavage ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Bleomycin Hydrolase ◽  
Nucleic Acid Binding Activity ◽  
Rna And Dna

ABSTRACT Yeast bleomycin hydrolase, Gal6p, is a cysteine peptidase that detoxifies the anticancer drug bleomycin. Gal6p is a dual-function protein capable of both nucleic acid binding and peptide cleavage. We now demonstrate that Gal6p exhibits sequence-independent, high-affinity binding to single-stranded DNA, nicked double-stranded DNA, and RNA. A region of the protein that is involved in binding both RNA and DNA substrates is delineated. Immunolocalization reveals that the Gal6 protein is chiefly cytoplasmic and thus may be involved in binding cellular RNAs. Variant Gal6 proteins that fail to bind nucleic acid also exhibit reduced ability to protect cells from bleomycin toxicity, suggesting that the nucleic acid binding activity of Gal6p is important in bleomycin detoxification and may be involved in its normal biological functions.

Sign in / Sign up

Export Citation Format

Share Document