Dataset Information

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.

ABSTRACT: Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: "Natural antisense" (208), artificial antisense used in "Genetic Engineering" (797), or "Natural antisense and Genetic Engineering"-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.

SUBMITTER: Santini L

PROVIDER: S-EPMC9569758 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.

Santini Luciane L Yoshida Leonardo L de Oliveira Kaique Dias KD Lembke Carolina Gimiliani CG Diniz Augusto Lima AL Cantelli Geraldo Cesar GC Nishiyama-Junior Milton Yutaka MY Souza Glaucia Mendes GM

International journal of molecular sciences 20221001 19

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to conte ...[more]

PMID: 36232906

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Project description:Antisense transcription has been extensively recognized as a regulatory mechanism for gene expression across all kingdoms of life. Despite the broad importance and extensive experimental determination of cis-antisense transcription, relatively little is known about its role in controlling cellular switching responses. Growing evidence suggests the presence of non-coding cis-antisense RNAs that regulate gene expression via antisense interaction. Recent studies also indicate the role of transcriptional interference in regulating expression of neighboring genes due to traffic of RNA polymerases from adjacent promoter regions. Previous models investigate these mechanisms independently, however, little is understood about how cells utilize coupling of these mechanisms in advantageous ways that could also be used to design novel synthetic genetic devices. Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation. We demonstrate the tunability of transcriptional interference through various parameters, and that coupling of transcriptional interference with cis-antisense RNA interaction gives rise to hypersensitive switches in expression of both antisense genes. When implementing additional positive and negative feed-back loops from proteins encoded by these genes, the system response acquires a bistable behavior. Our model shows that combining these multiple-levels of regulation allows fine-tuning of system parameters to give rise to a highly tunable output, ranging from a simple-first order response to biologically complex higher-order response such as tunable bistable switch. We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription. This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

Project description:Overuse of medical care is an increasingly recognized problem in clinical medicine.To identify and highlight original research articles published in 2015 that are most likely to reduce overuse of medical care, organized into 3 categories: overuse of testing, overtreatment, and questionable use of services. The articles were reviewed and interpreted for their importance to clinical medicine.A structured review of English-language articles on PubMed published in 2015 and review of tables of contents of relevant journals to identify potential articles that related to medical overuse in adults.Between January 1, 2015, and December 31, 2015, we reviewed 1445 articles, of which 821 addressed overuse of medical care. Of these, 112 were deemed most relevant based on their originality, methodologic quality, and number of patients potentially affected. The 10 most influential articles were selected by consensus using the same criteria. Findings included a doubling of specialty referrals and advanced imaging for simple headache (from 6.7% in 2000 to 13.9% in 2010); unnecessary hospital admission for low-risk syncope, often leading to adverse events; and overly frequent colonoscopy screening for 34% of patients. Overtreatment was common in the following areas: 1 in 4 patients with atrial fibrillation at low risk for thromboembolism received anticoagulation; 94% of testosterone replacement therapy was administered off guideline recommendations; 91% of patients resumed taking opioids after overdose; and 61% of patients with diabetes were treated to potentially harmfully low hemoglobin A1c levels (<7%). Findings also identified medical practices to question, including questionable use of treatment of acute low-back pain with cyclobenzaprine and oxycodone/acetaminophen; of testing for Clostridium difficile with molecular assays; and serial follow-up of benign thyroid nodules.The number of articles on overuse of medical care nearly doubled from 2014 to 2015. The present review promotes reflection on the top 10 articles and may lead to questioning other non-evidence-based practices.

Dataset Information

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.

Publications

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.

Similar Datasets

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