RNA, or ribonucleic acid, is a vital molecule involved in various cellular processes. Many factors can influence its structure, function, and stability.
Factors Affecting RNA
Several factors can affect RNA, impacting its integrity, expression, and ultimately, its function within a cell. These factors can be broadly categorized as:
1. Chemical Insults:
- Endogenous and Exogenous Agents: RNA is susceptible to damage from both internal (endogenous) and external (exogenous) sources. Reactive oxygen species (ROS) and alkylating chemicals are examples of noxious agents that can significantly alter RNA's chemical properties and thus its function. [Reference: Abstract]
2. RNA Degradation:
- Quality of RNA Samples: The quality of RNA samples used in experiments, such as RNA-sequencing (RNA-seq), greatly impacts results. Degraded RNA can lead to inaccurate transcript quantification and skewed conclusions. [Reference: RNA-seq: impact of RNA degradation on transcript quantification...]
3. Enzymatic Modification:
- Demethylases: Enzymes like ALKBH5 are RNA demethylases that can alter methylation patterns on RNA molecules. Changes in methylation can have significant consequences; for instance, ALKBH5 deficiency in mice leads to impaired fertility. [Reference: ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA...]
- RNA Editing Enzymes: Enzymes responsible for RNA editing alter the sequence of RNA, thereby affecting the encoded protein's function.
- Dicer-like enzymes: Specific enzymes like DCL2 (Dicer-like 2) are involved in the miRNA pathway which affects RNA virus susceptibility. [Reference: A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses.]
4. Genetic Factors:
- Nonsense Mutations: Premature stop codons (nonsense mutations) within genes can influence the abundance of the resulting mRNA molecule. The location of the termination codon within introns impacts how this effect plays out. [Reference: A rule for termination-codon position within intron-containing genes...]
5. RNA-Binding Proteins:
- FUS Protein: Proteins such as FUS (fused in sarcoma) are RNA-binding proteins involved in RNA processing and are linked to diseases like amyotrophic lateral sclerosis (ALS). Their activity can affect circular RNA (circRNA) expression. [Reference: FUS affects circular RNA expression in murine embryonic stem cell...]
6. Transcriptional Regulation:
- RNA Polymerases: Eukaryotic cells employ three distinct nuclear RNA polymerases that transcribe different gene classes. The activity and regulation of these polymerases directly impact RNA production. [Reference: Eukaryotic RNA Polymerases and General Transcription Factors...]
7. Other Factors:
- Circular RNAs (circRNAs): The expression levels of circRNAs, such as Cdr1as, which have unique roles in cellular processes, can be affected by various cellular mechanisms and influences. [Reference: Loss of a mammalian circular RNA locus causes miRNA...]
- Small RNAs: Small RNAs, including miRNAs, mediate regulatory processes impacting gene expression and other cellular processes. These processes can influence the immune response to lipopolysaccharides (LPS). [Reference: Small RNA mediated gradual control of lipopolysaccharide...]
- Batch Effects: In RNA-seq experiments, batch effects stemming from technical variations across different sample preparations can introduce bias and require correction methods like ComBat-seq. [Reference: ComBat-seq: batch effect adjustment for RNA-seq count data...]
