Instruct: Given a question, retrieve relevant passages that can help answer the question.
Query: Has RNA been proven?
The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.
Transport of sRNAs during infection is likely facilitated by extracellular vesicles (EVs) and multivesicular bodies (MVBs). The composition of RNA in plant EVs has not been fully evaluated, but it is likely that they are, in part, responsible for trafficking RNA. Plants can transport viral RNAs, mRNAs, microRNAs (miRNAs) and small interfering RNAs (siRNAs) systemically through the phloem. This process is thought to occur through the plasmodesmata and involves RNA-binding proteins that assist RNA localization in mesophyll cells. Although they have been identified in the phloem with mRNA, there is no determinate evidence that they mediate long-distant transport of RNAs. EVs may therefore contribute to an alternate pathway of RNA loading into the phloem, or could possibly transport RNA through the apoplast. There is also evidence that plant EVs can allow for interspecies transfer of sRNAs by RNA interference such as Host-Induced Gene Silencing (HIGS). The transport of RNA between plants and fungi seems to be bidirectional as sRNAs from the fungal pathogen "Botrytis cinerea" have been shown to target host defense genes in Arabidopsis and tomato.
The Latescibacteria, OD1, OP11, TM7 RNA motif (LOOT RNA motif) is a conserved RNA structure that was discovered by bioinformatics.
LOOT motif RNAs are found in multiple bacterial phyla that have only recently been discovered, and are currently not well understood: Latescibacteria, OD1/Parcubacteria, OP11 AND TM7. In some cases, no specific organism has been isolated in the relevant phylum, but the existence of the bacterial phylum is known only through analysis of metagenomic sequences. Curiously, the LOOT motif is not known in any phylum that has been studied for a long time.
The Ocean-V RNA motif is a conserved RNA structure discovered using bioinformatics. Only a few Ocean-V RNA sequences have been detected, all in sequences derived from DNA that was extracted from uncultivated bacteria found in ocean water. As of 2010, no Ocean-V RNA has been detected in any known, cultivated organism.
RIN has become a standard method of measuring integrity, even in meta-analyses such as "Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis", wherein the authors analyzed a number of different RNA extraction methods, using the resultant RIN as a measure of their efficiency at producing high-quality RNA. RIN has also been used to test the efficiency of other techniques, such as microdissections, on maintaining RNA integrity in human cells, so it has a wide variety of uses in testing the quality of new techniques. RIN has become an industry standard to test various methods for the quality of their produced RNA, and it is also used in a wide variety of non-meta analyses so that the scientists are able to ensure that the quality of their RNA is trustworthy and their results are thus sound, often with a benchmark minimal RIN being used as a standard to ensure all of their RNA is high enough quality to yield reliable findings.
The Termite-"flg" RNA motif (also called tg-flg) is a conserved RNA structure identified by bioinformatics. Genomic sequences corresponding to Termite-"flg" RNAs have been identified only in uncultivated bacteria present in the termite hindgut. As of 2010 it has not been identified in the DNA of any cultivated species, and is thus an example of RNAs present in environmental samples.
"Lone Star virus's" genome consist of negative, single-stranded RNA. It is in the "Bunyaviridae" family of viruses. Its genus is the "Phlebovirus" and its species name is "Lone Star virus". It has been proven to produce titers in human and monkey cells seventy-two hours after inoculation. Although it was discovered in 1967, it has never been genetically characterized.
The CyaR RNA (formerly known as RyeE RNA) non-coding RNA was identified in a large scale screen of "Escherichia coli" and was called candidate 14. The exact 5' and 3' ends of this RNA are uncertain. This gene lies between yegQ and orgK in "E. coli". This small RNA was shown to be bound by the Hfq protein. This RNA has been renamed as CyaR for (cyclic AMP-activated
RNA). It has been shown that the CyaR RNA acts as a repressor of the porin OmpX. It has also been shown that "cyaR" expression is tightly controlled by the cyclic AMP receptor protein, CRP.
This RNA modification databases are a compilation of databases and web portals and servers used for RNA modification. RNA modification occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs. More than 100 different types of RNA modifications have been characterized across all living organisms. It can affect the activity, localization as well as stability of RNAs, and has been linked with human cancer and diseases.
In the UV-C light spectrum (200-280 nm), the wavelength 254 nm has been proven to be the most efficient wavelength to inactivate micro-organisms by damaging the nucleic acids (DNA and RNA), which disrupts the organism's ability to replicate.
Please note that this refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.
RNA thermometers and riboswitches are thought to be evolutionarily ancient due to their wide-scale distribution in distantly-related organisms. It has been proposed that, in the RNA world, RNA thermosensors would have been responsible for temperature-dependent regulation of other RNA molecules. RNA thermometers in modern organisms may be molecular fossils which could hint at a previously more widespread importance in an RNA world.
As RNA integrity has long been known to be a problem in molecular biology studies, there are a few methods that have been used historically to determine the integrity of RNA. The most popular has long been agarose gel electrophoresis with ethidium bromide staining, allowing one to visualize the bands from the rRNA peaks. The height of the 28S and 18S bands can be compared to each other, with a 2:1 ratio indicating non-degraded RNA. While this method is very cheap and easy, there are several issues with this method, primarily its subjectivity, leading to inconsistent, non-standardized RNA quality assessments, and the large amounts of RNA that are needed to visualize it on an agarose gel, which can be problematic if there is not much RNA to work with. There are also a number of different problems that can arise from agarose gel electrophoresis, such as poor loading, uneven running, and uneven staining that lead to increased variability in the accuracy of using agarose gel electrophoresis to determine RNA integrity. Clearly, a standardized, repeatable, objective method of determining RNA integrity was needed.
Because it has been widely known that many viruses have RNA rather than DNA as their genetic material and go through at least one stage in their life cycle when they make double-stranded RNA, RNA interference has been considered to be a potentially evolutionarily ancient mechanism for protecting organisms from viruses. The small interfering RNAs produced by Dicer cause sequence specific, post-transcriptional gene silencing by guiding an endonuclease, the RNA-induced silencing complex (RISC), to mRNA. This process has been seen in a wide range of organisms, such as Neurospora fungus(in which it is known as quelling), plants(post-transcriptionl gene silencing) and mammalian cells(RNAi). If there is a complete or near complete sequence complementarity between the small RNA and the target, the Argonaute protein component of RISC mediates cleavage of the target transcript, the mechanism involves repression of translation predominantly.
RNAi has varying effects in different species of Lepidoptera (butterflies and moths). Possibly because their saliva and gut juice is better at breaking down RNA, the cotton bollworm, the beet armyworm and the Asiatic rice borer have so far not been proven susceptible to RNAi by feeding.
One issue with the RNA world hypothesis is that synthesis of RNA from simple inorganic precursors is more difficult than for other organic molecules. One reason for this is that RNA precursors are very stable and react with each other very slowly under ambient conditions, and it has also been proposed that living organisms consisted of other molecules before RNA. However, the successful synthesis of certain RNA molecules under the conditions that existed prior to life on Earth has been achieved by adding alternative precursors in a specified order with the precursor phosphate present throughout the reaction. This study makes the RNA world hypothesis more plausible.
The "Pyrobac"-1 RNA motif is a conserved RNA structure discovered by bioinformatics. RNAs conforming to this motif have been found only in "Pyrobaculum", a genus of archaea. Instances of the motif are hypothesized to function as non-coding RNAs. The motif has been shown to be part of sRNA202 and sRNA203 canonical and noncanonical pseudouridine guide RNAs (H/ACA RNA) in "Pyrobaculum."
Self-replication The ability to self-replicate, or synthesize other RNA molecules; relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165-bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189-bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11 nucleotide long RNA strand from primed template strands.[23] This 189 base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self replication, but is a potential lead for further investigation. The longest primer extension performed by a ribozyme polymerase was 20 bases.[24] In 2016, researchers reported the use of in vitro evolution to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. Each RNA polymerase ribozyme was engineered to remain linked to its new, synthesized RNA strand, this allowed the team to isolate successful polymerases. The isolated RNA polymerases were again used for another round of evolution. After several rounds of evolution, they obtained one RNA polymerase ribozyme called 24-3 that was able to copy almost any other RNA, from small catalysts to long RNA based enzymes. Particular RNAs were amplified up to 10,000 times, a first RNA version of the polymerase chain reaction (PCR). The RNA polymerase is not yet able to make copies of itself.[25] Catalysis The ability to catalyze simple chemical reactions—which would enhance creation of molecules that are building blocks of RNA molecules (i.e., a strand of RNA that would make creating more strands of RNA easier). Relatively short RNA molecules with such abilities have been artificially formed in the lab.[26][27] A recent study showed that almost any nucleic acid can evolve into a catalytic sequence under appropriate selection. For instance, an arbitrarily chosen 50-nucleotide DNA fragment encoding for the Bos taurus (cattle) albumin mRNA was subjected to test-tube evolution to derive a catalytic DNA (Deoxyribozyme, also called DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity had evolved.[28] In general, DNA is much more chemically inert than RNA and hence much more resistant to obtaining catalytic properties. If in vitro evolution works for DNA it will happen much more easily with RNA. Amino acid-RNA ligation The ability to conjugate an amino acid to the 3'-end of an RNA in order to use its chemical groups or provide a long-branched aliphatic side-chain.[29] Peptide bond formation The ability to catalyse the formation of peptide bonds between amino acids to produce short peptides or longer proteins. This is done in modern cells by ribosomes, a complex of several RNA molecules known as rRNA together with many proteins. The rRNA molecules are thought responsible for its enzymatic activity, as no amino acid molecules lie within 18Å of the enzyme's active site,[14] and, when the majority of the amino acids in the ribosome were stringently removed, the resulting ribosome retained its full peptidyl transferase activity, fully able to catalyze the formation of peptide bonds between amino acids.[30] A much shorter RNA molecule has been synthesized in the laboratory with the ability to form peptide bonds, and it has been suggested that rRNA has evolved from a similar molecule.[31] It has also been suggested that amino acids may have initially been involved with RNA molecules as cofactors enhancing or diversifying their enzymatic capabilities, before evolving to more complex peptides. Similarly, tRNA is suggested to have evolved from RNA molecules that began to catalyze amino acid transfer.[32]
Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, mature mRNA consists exclusively of exons and has all introns removed. 
Two functions have been described for Y RNAs in the literature: As a repressor of Ro60, and as an initiation factor for DNA replication. Mutant human Y RNAs lacking the conserved binding site for Ro60 protein still support DNA replication, indicating that binding to Ro protein and promoting DNA replication are two separable functions of Y RNAs. Although Y RNA-derived small RNAs are similar in size to microRNAs, it has been shown that these Y RNA fragments are not involved in the microRNA pathway.
A small marker height is desired, indicating only small amounts of RNA have been degraded and proceeded to the smallest lengths, indicated by the short marker. If a large number is found here, that indicates that large amounts of the rRNAs have been degraded to small pieces that would be found closer to this marker. This situation can be seen in the 'poor quality' RNA electropherogram found in figure 2, where the height of the peak over the marker (far left) is very large, so the RNA has been greatly degraded.
In prokaryotic samples, the algorithm is somewhat different, but the Agilent 2100 Bioanalyzer Expert software is able to calculate RIN for prokaryotic samples now as well. The difference likely arises from the fact that, while mammalian samples have 28S and 18S ribosomal RNAs as their predominant species, prokaryotic RNAs have the sizes shifted slightly smaller, to 23S and 16S, so the algorithm must be shifted to accommodate that. Another crucial fact about calculating prokaryotic RNA integrity numbers is that RIN has not been validated to the extent that it has for eukaryotic RNA. It has been shown that higher RIN values correlate with better downstream results in eukaryotes, but this hasn't been done as extensively for prokaryotes, so it may mean less in prokaryotes.
It has been shown that vault non-coding RNAs contain multiple cytosine residues that have been methylated by the NSUN2 protein. In NSUN2 deficient cells, the loss of cytosine-5 methylation causes incorrect processing into small RNA fragments that end up functioning similar to micro RNAs. As a result, it has been suggested that impaired vault RNA processing may contribute to the symptoms that are manifested in NSUN2 deficiency diseases.
The scientific community has been quick to harness RNA silencing as a research tool. The strategic targeting of mRNA can provide a large amount of information about gene function and its ability to be turned on and off. Induced RNA silencing can serve as a controlled method for suppressing gene expression. Since the machinery is conserved across most eukaryotes, these experiments scale well to a range of model organisms. In practice, expressing synthetic short hairpin RNAs can be used to reach stable knock-down. If promoters can be made to express these designer short hairpin RNAs, the result is often potent, stable, and controlled gene knock-down in both in vitro and in vivo contexts. Short hairpin RNA vector systems can be seen as roughly analogous in scope to using cDNA overexpression systems. Overall, synthetic and natural small RNAs have proven to be an important tool for studying gene function in cells as well as animals.
The LTR retrotransponsons require an RNA intermediate in their transposition cycle mechanism. Retrotransponsons synthesize a cDNA copy based on the RNA strand using a reverse transcriptase related to retroviral RT. The cDNA copy is then inserted into new genomic positions to form a retrogene. This mechanism has been proven to be important in gene evolution of rice and other grass species through exon shuffling.
The integrity of RNA is a major concern for gene expression studies and traditionally has been evaluated using the 28S to 18S rRNA ratio, a method that has been shown to be inconsistent. This inconsistency arises because subjective, human interpretation is necessary to compare the 28S and 18S gel images. The RIN algorithm was devised to overcome this issue. The RIN algorithm is applied to electrophoretic RNA measurements, typically obtained using capillary gel electrophoresis, and based on a combination of different features that contribute information about the RNA integrity to provide a more universal measure. RIN has been demonstrated to be robust and reproducible in studies comparing it to other RNA integrity calculation algorithms, cementing its position as a preferred method of determining the quality of RNA to be analyzed.