AI Article Synopsis
- Eukaryotic genomes often have genes on opposite DNA strands, leading to the formation of cis-natural sense antisense transcripts (cis-NATs), which are linked to the creation of splice variants and small RNAs.
- In Arabidopsis, protein-coding cis-NATs show characteristics like high abundance and coexpression, suggesting a favorable chromatin environment that supports the close placement of these genes.
- The study indicates that while cis-NAT regions have unique histone modifications, the production of natural antisense small RNAs from these transcripts is limited, raising questions about the role of overlapping protein-coding genes in other eukaryotic species.
Article Abstract
Pairs of genes within eukaryotic genomes are often located on opposite DNA strands such that transcription generates cis-natural sense antisense transcripts (cis-NATs). This orientation of genes has been associated with the biogenesis of splice variants and natural antisense small RNAs. Here, in an analysis of currently available data, we report that within Arabidopsis (Arabidopsis thaliana), protein-coding cis-NATs are also characterized by high abundance, high coexpression, and broad expression. Our results suggest that a permissive chromatin environment may have led to the proximity of these genes. Compared with other genes, cis-NAT-encoding genes have enriched low-nucleosome-density regions, high levels of histone H3 lysine-9 acetylation, and low levels of H3 lysine-27 trimethylation. Promoters associated with broadly expressed genes are preferentially found in the 5' regulatory sequences of cis-NAT-encoding genes. Our results further suggest that natural antisense small RNA production from cis-NATs is limited. Small RNAs sequenced from natural antisense small RNA biogenesis mutants including dcl1, dcl2, dcl3, and rdr6 map to cis-NATs as frequently as small RNAs sequenced from wild-type plants. Future work will investigate if the positive transcriptional regulation of overlapping protein-coding genes contributes to the prevalence of these genes within other eukaryotic genomes.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613485 | PMC |
| http://dx.doi.org/10.1104/pp.112.212100 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Hybrid prodrug nanoassembly for hypoxia-triggered immunogenic chemotherapy and immune modulation.
J Control Release
January 2025
Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China; NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, China; State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, China. Electronic address:
Tumor hypoxia is a critical driver of cancer progression, metastasis, and therapy resistance, posing significant challenges in effective cancer treatment. Hypoxia-activable prodrugs offer a promising strategy to target tumors in low-oxygen conditions, but their efficacy is often hindered by intrinsic properties and extrinsic cues. In this study, we developed a dual-prodrug nanoassembly system (CPPA) composed of a hypoxia-triggerable camptothecin (CPT)-based dimeric prodrug (CP) and a lipid-conjugated STAT3 antisense oligonucleotide (ASO) prodrug (PA), aiming to enhance tumor-targeted chemotherapy and overcome the immune evasion within the tumor microenvironment.
View Article and Find Full Text PDFPhotochemical Stabilization of Self-Assembled Spherical Nucleic Acids.
Small
January 2025
Department of Chemistry, McGill University, 801, Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
Oligonucleotide therapeutics, including antisense oligonucleotides and small interfering RNA, offer promising avenues for modulating the expression of disease-associated proteins. However, challenges such as nuclease degradation, poor cellular uptake, and unspecific targeting hinder their application. To overcome these obstacles, spherical nucleic acids have emerged as versatile tools for nucleic acid delivery in biomedical applications.
View Article and Find Full Text PDFSequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides.
Int J Mol Sci
December 2024
Konan Laboratory for Oligonucleotide Therapeutics (KOLOT), 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.
2',4'-methylene bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA; LNA) is a modified nucleic acid that improves the function of antisense oligonucleotide therapeutics. In particular, LNA in the DNA strand increases its binding affinity for the target RNA. Predicting the binding affinities of LNA-containing antisense oligonucleotides and RNA duplexes is useful for designing antisense oligonucleotides.
View Article and Find Full Text PDFIdentification of Antisense RNA NRAS-AS and Its Preliminary Exploration of the Anticancer Regulatory Mechanism.
Genes (Basel)
November 2024
College of Animal Science and Technology, Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou 225001, China.
Objective: To explore the influence of NRAS-AS on the proliferation, apoptosis, cell cycle, migration, and invasion ability of HCC cells, as well as its underlying mechanisms.
Methods: A double-stranded cDNA library for liver cancer cells was constructed, and identified NRAS-AS through High-throughput sequencing, bioinformatics, chain-specific fluorescent quantitative PCR, and RACE. NRAS-AS's effects on HepG2 and SMMC-7721 cells and gene expression were evaluated.
Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves.
BMC Genomics
January 2025
The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!