Structured RNAs play

Ebook "Frontiers in computational and systems biology" consists of 19 chapters and covers a wide spectrum of topics. Described applications of an RNA structure sampling algorithm to the rational design of short interfering RNAs for gene silencing by RNA interference and to target identification for microRNAs that play important roles in posttranscriptional gene regulation.

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Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers.

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Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder

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Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo.

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Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes.

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Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences.

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RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs have been reported through the RNAcompete compendium, structure specificities are known for only a small fraction. The main limitation lies in the design of the RNAcompete technology, which tests RBP binding against unstructured RNA probes, making it difficult to infer structural preferences from these data.

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G-quadurplex (G4) formation plays a role in many biological processes such as replication, transcription, translation, and telomeric maintenance. Stabilization of G4 structure by peptide has recently emerged as a potential approach in the regulation of protein expression. In this study, we reported on regulation of cyan fluorescent protein (CFP) expression by the interaction of G4 and RNA helicase associated with AU-rich elements (RHAU) peptide in E. coli.

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RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in the structure, as in the case of riboswitches, and thus the analysis of RNA folding kinetics is crucial for their study.

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RNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it’s important to identify RNA-binding residues in proteins.

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MicroRNAs (miRNAs) are a family of non-coding RNAs approximately 21 nucleotides in length that play pivotal roles at the post-transcriptional level in animals, plants and viruses. These molecules silence their target genes by degrading transcription or suppressing translation.

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RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been done to align two known RNA secondary structures with pseudoknots taking into account both sequence and structure information of the two RNAs.

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RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA.

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RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex.

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RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs.

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RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particular, RNA secondary structures, is critical for elucidating biological functions.

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Movement protein is a non-structural protein encoded by plant viruses to allow their movement from infected cell to neighbouring one. It defined as plant viruses- encoded factors that interact with plasmodesmata to mediate the intracellular spread of virus infection. viruses subvert an intracellular communication network that supports the trafficking of wide spectrum of endogenous protein and ribonucleo protein complexes that play non-cell autonomous roles in development and physiological processes.

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Sesame (Sesamum indicum L.), a member of the Pedaliaceae family, is one of the oldest oilseed crops. For its high oil content, it is known as the “queen of oilseeds”. MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation.

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Chapter 19 - Ribosomes and Transfer RNA. In chapter 3 we examined a few aspects of translation. We learned that ribosomes are the cell’s protein factories and that transfer RNA plays a crucial adapter role, binding an amino acid at one end and an mRNA codon at the other. Chapters 17 and 18 expanded on the mechanisms of translation initiation, elongation, and termination, without dealing in depth with ribosomes and tRNA. In this chapter, let us continue discussion of translation with a closer look at these two essential agents.

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In chapter 3 we examined a few aspects of translation. We learned that ribosomes are the cell’s protein factories and that transfer RNA plays a crucial adapter role, binding an amino acid at one end and an mRNA codon at the other. Chapters 17 and 18 expanded on the mechanisms of translation initiation, elongation, and termination, without dealing in depth with ribosomes and tRNA. In this chapter, let us continue discussion of translation with a closer look at these two essential agents.

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