scholarly journals ASPECT, an LDA-Based Predictive Algorithm for In Vitro Selection

10.29007/vkrq ◽  
2020 ◽  
Author(s):  
Puzhou Wang
Keyword(s):  
In Vitro Selection ◽  
Latent Dirichlet Allocation ◽  
De Novo ◽  
A Priori ◽  
Sequencing Data ◽  
Rna Sequences ◽  
Predictive Algorithm ◽  
Selection Experiments ◽  
Functional Dna

In vitro selection enables the identification of functional DNA or RNA sequences (i.e., active sequences) out of entirely or partially random pools. Various computational tools have been developed for the analysis of sequencing data from selection experiments. However, most of these tools rely on structure-function relationship that is usually unknown for de novo selection experiments. This largely restricts the applications of these algorithms. In this paper, an active sequence predictor based on Latent Dirichlet allocation (LDA), ASPECT (Active Sequence PrEdiCTor), is proposed. ASPECT is independent of a priori knowledge on the structures of active sequences. Experimental results showed that ASPECT is effective.

In vitro selection of RNA sequences capable of mediating the formation of iron oxide nanoparticles

2009 ◽  
Vol 19 (44) ◽  
pp. 8320 ◽  
Author(s):  
Carly J. Carter ◽  
Magda Dolska ◽  
Alina Owczarek ◽  
Christopher J. Ackerson ◽  
Bruce E. Eaton ◽  
...  
Keyword(s):  
Iron Oxide ◽  
Iron Oxide Nanoparticles ◽  
In Vitro Selection ◽  
Oxide Nanoparticles ◽  
Rna Sequences ◽  
Selection Of

scholarly journals In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole–activated substrates

2020 ◽  
Vol 117 (11) ◽  
pp. 5741-5748 ◽  
Author(s):  
Travis Walton ◽  
Saurja DasGupta ◽  
Daniel Duzdevich ◽  
Seung Soo Oh ◽  
Jack W. Szostak
Keyword(s):  
Origin Of Life ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Bond Formation ◽  
Rna Sequences ◽  
Phosphodiester Bond ◽  
Complex Protein ◽  
The Origin Of Life ◽  
Group 2

The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5′-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide–activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3′-5′ phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.

scholarly journals Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

2017 ◽  
Author(s):  
Michal Bassani-Sternberg ◽  
Chloé Chong ◽  
Philippe Guillaume ◽  
Marthe Solleder ◽  
HuiSong Pak ◽  
...  
Keyword(s):  
A Priori ◽  
Human Leukocyte ◽  
Binding Specificity ◽  
Binding Assays ◽  
Sequencing Data ◽  
Protein Structure Analysis ◽  
Binding Motifs ◽  
Leukocyte Antigen ◽  
Underlying Mechanisms

AbstractThe precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across ten newly generated as well as forty public HLA peptidomics datasets comprising more than 115,000 unique peptides, we show that we can rapidly and accurately identify many HLA-I binding motifs and map them to their corresponding alleles without any a priori knowledge of HLA-I binding specificity. Our approach recapitulates and refines known motifs for 43 of the most frequent alleles, uncovers new motifs for 9 alleles that up to now had less than five known ligands and provides a scalable framework to incorporate additional HLA peptidomics studies in the future. The refined motifs improve neo-antigen and cancer testis antigen predictions, indicating that unbiased HLA peptidomics data are ideal for in silico predictions of neo-antigens from tumor exome sequencing data. The new motifs further reveal allosteric modulation of the binding specificity of HLA-I alleles and we unravel the underlying mechanisms by protein structure analysis, mutagenesis and in vitro binding assays.

scholarly journals Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments

RNA ◽  
2020 ◽  
Vol 26 (8) ◽  
pp. 1060-1068
Author(s):  
Devin P. Bendixsen ◽  
Jessica M. Roberts ◽  
Brent Townshend ◽  
Eric J. Hayden
Keyword(s):  
In Vitro Selection ◽  
Selection Experiments ◽  
Low Diversity

Germline Missense Mutation of Deleted in Malignant Brain Tumor 1 (DMBT1) in Familial Mediastinal Neuroendocrine Cancer and in vitro Effects in Thyroid Cancer Cells

2019 ◽  
Vol 110 (7-8) ◽  
pp. 714-720
Author(s):  
Ning Qu ◽  
Rong-Liang Shi ◽  
Tian Liao ◽  
Sheng-Lin Huang ◽  
Duo Wen ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Missense Mutation ◽  
Sanger Sequencing ◽  
De Novo ◽  
Susceptibility Gene ◽  
Ectopic Expression ◽  
Malignant Brain Tumor ◽  
Sequencing Data ◽  
De Novo Mutations

Background: Neuroendocrine tumors (NETs) rarely occur in the mediastinum and their etiology and pathogenesis are still unclear. Objectives: This study assessed inherited or de novo mutations in familial mediastinal NETs. Method: DNA samples from 4 patients were subjected to the whole-exome sequencing, and Sanger sequencing was used to identify Deleted in malignant brain tumor 1 (DMBT1) mutations in all 45 family members. Results: All patients showed a germline DMBT1 mutation at 4971C. Sanger sequencing data showed that 4 NETs and 2 carriers in the first patient’s family and 2 NETs and 4 carriers in the second patient’s family, respectively, had this DMBT1 mutation. The in vitro data showed that the ectopic expression of DMBT1 reduced tumor cell viability and migration by arresting the G1/S phase of the cell cycle. Conclusions: We identified a germline missense mutation in DMBT1D1657E as a susceptibility gene for familial mediastinal NETs.

scholarly journals Water/Oil Emulsions with Controlled Droplet Sizes for In Vitro Selection Experiments

ACS Omega ◽  
2021 ◽  
Author(s):  
Douglas Magde ◽  
Arvin Akoopie ◽  
Michael D. Magde ◽  
Ulrich F. Müller
Keyword(s):  
In Vitro Selection ◽  
Selection Experiments ◽  
Droplet Sizes ◽  
Oil Emulsions

scholarly journals Selection and Characterization of Pre-mRNA Splicing Enhancers: Identification of Novel SR Protein-Specific Enhancer Sequences

1999 ◽  
Vol 19 (3) ◽  
pp. 1705-1719 ◽  
Author(s):  
Thomas D. Schaal ◽  
Tom Maniatis
Keyword(s):  
In Vitro Selection ◽  
Sr Proteins ◽  
Mrna Splicing ◽  
Sequence Motifs ◽  
Rna Sequences ◽  
Sr Protein ◽  
Enhancer Sequence ◽  
Splicing Enhancer

ABSTRACT Splicing enhancers are RNA sequences required for accurate splice site recognition and the control of alternative splicing. In this study, we used an in vitro selection procedure to identify and characterize novel RNA sequences capable of functioning as pre-mRNA splicing enhancers. Randomized 18-nucleotide RNA sequences were inserted downstream from a Drosophila doublesex pre-mRNA enhancer-dependent splicing substrate. Functional splicing enhancers were then selected by multiple rounds of in vitro splicing in nuclear extracts, reverse transcription, and selective PCR amplification of the spliced products. Characterization of the selected splicing enhancers revealed a highly heterogeneous population of sequences, but we identified six classes of recurring degenerate sequence motifs five to seven nucleotides in length including novel splicing enhancer sequence motifs. Analysis of selected splicing enhancer elements and other enhancers in S100 complementation assays led to the identification of individual enhancers capable of being activated by specific serine/arginine (SR)-rich splicing factors (SC35, 9G8, and SF2/ASF). In addition, a potent splicing enhancer sequence isolated in the selection specifically binds a 20-kDa SR protein. This enhancer sequence has a high level of sequence homology with a recently identified RNA-protein adduct that can be immunoprecipitated with an SRp20-specific antibody. We conclude that distinct classes of selected enhancers are activated by specific SR proteins, but there is considerable sequence degeneracy within each class. The results presented here, in conjunction with previous studies, reveal a remarkably broad spectrum of RNA sequences capable of binding specific SR proteins and/or functioning as SR-specific splicing enhancers.

SRSF6-regulated alternative splicing that promotes tumour progression offers a therapy target for colorectal cancer

Gut ◽  
2017 ◽  
Vol 68 (1) ◽  
pp. 118-129 ◽  
Author(s):  
Ledong Wan ◽  
Wenying Yu ◽  
Enhui Shen ◽  
Wenjie Sun ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Alternative Splicing ◽  
De Novo ◽  
Tumour Progression ◽  
The Cancer Genome Atlas ◽  
Chronic Obstructive ◽  
Binding Motif ◽  
Sequencing Data

ObjectiveTo investigate the molecular function of splicing factor SRSF6 in colorectal cancer (CRC) progression and discover candidate chemicals for cancer therapy through targeting SRSF6.DesignWe performed comprehensive analysis for the expression of SRSF6 in 311 CRC samples, The Cancer Genome Atlas and Gene Expression Omnibus (GEO) database. Functional analysis of SRSF6 in CRC was performed in vitro and in vivo. SRSF6-regulated alternative splicing (AS) and its binding motif were identified by next-generation RNA-sequencing and RNA immunoprecipitation sequencing (RIP-seq), which was validated by gel shift and minigene reporter assay. ZO-1 exon23 AS was investigated to mediate the function of SRSF6 in vitro and in vivo. Based on the analysis of domain-specific role, SRSF6-targeted inhibitor was discovered de novoby virtual screening in 4855 FDA-approved drugs and its antitumour effects were evaluated in vitroand in vivo.ResultsSRSF6 was frequently upregulated in CRC samples and associated with poor prognosis, which promoted proliferation and metastasis in vitro and in vivo. We identified SRSF6-regulated AS targets and discovered the SRSF6 binding motif. Particularly, SRSF6 regulates ZO-1 aberrant splicing to function as an oncogene by binding directly to its motif in the exon23. Based on the result that SRSF6 RRM2 domain plays key roles in regulating AS and biological function, indacaterol, a β2-adrenergic receptor agonist approved for chronic obstructive pulmonary disease treatment, is identified as the inhibitor of SRSF6 to suppress CRC tumourigenicity.ConclusionsSRSF6 functions the important roles in mediating CRC progression through regulating AS, and indacaterol is repositioned as an antitumour drug through targeting SRSF6.Accession numbersThe accession numbers for sequencing data are SRP111763 and SRP111797.

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