Instruct: Given a question, retrieve relevant documents that answer the question.
Query: When was the theory of RNA announced?
The Miller–Urey experiment in 1952, and others since, demonstrated the synthesis of organic compounds, such as amino acids, formaldehyde and sugars, from the original inorganic precursors the researchers presumed to have been present in the primordial soup (but is no longer considered likely). This experiment inspired many others. In 1961, Joan Oró found that the nucleotide base adenine could be made from hydrogen cyanide (HCN) and ammonia in a water solution.[6] Experiments conducted later showed that the other RNA and DNA nucleobases could be obtained through simulated prebiotic chemistry with a reducing atmosphere.[7]
On June 4, 2010, the university unveiled a new $12.5 million biomedical research center, The RNA Institute, whose mission would be to form an alliance of genetic scientists and biomedical investigators from New York's Capital Region to spur research and development into RNA and its implications for medicines, drug therapies and technologies, and curing disease. On Nov. 5, 2010, UAlbany announced The RNA Institute had received a $5.37 million grant from the National Institutes of Health/National Center for Research Resources (NIH/NCRR) and $2 million in matching funds from the State of New York to fund the design, engineering and construction of of research facilities on par with those of modern pharmaceutical companies. Comple On the same day, the institute announced the establishment of The RNA Institute MassSpec Center, dedicated to the development of mass spectrometry-based technologies for investigating the structure-function relationships of natural and synthetic RNA as tools for drug discovery.
The function of sbRNAs may therefore be similar to that of vertebrate Y RNAs, namely acting as part of the Ro-RNA particle to control RNA quality and playing a role in chromosomal replication. Deletion of sbRNA does not prevent chromosome replication in "C. elegans", but this may be a result of other sbRNAs substituting missing elements (as in human Y RNA). This theory also explains why RNAi studies failed to detect a phenotype for knocked out sbRNAs.
The IMES-2 RNA motif is a conserved RNA structure that was identified by a study based on metagenomics and bioinformatics, and the underlying RNA sequences were identified independently by a similar earlier study. These RNAs are present in environmental sequences, and when discovered were not known to be present in any cultivated species. However, an IMES-2 RNA has been detected in alphaproteobacterium HIMB114, which is classified in the SAR11 clade of marine bacteria. This finding fits with earlier predictions that species that use IMES-2 RNAs are most closely related to alphaproteobacteria. IMES-2 RNAs are exceptionally abundant, as twice as many IMES-2 RNAs were found as ribosomes in RNAs sampled from the Pacific Ocean. Only two bacterial RNAs are known (6S RNA and transfer RNA) to be more highly transcribed than ribosomes.
RNA-OUT is a non-coding RNA that is antisense to the RNA-IN non-coding RNA. Transposition of insertion sequence IS10 is regulated by an anti-sense RNA which inhibits transposase expression when IS10 is present in multiple copies per cell. IS10 antisense pairing is facilitated by the RNA-binding protein, Hfq. RNA-OUT consists of a stem-loop domain topped by a flexibly paired loop; the 5' end of the target molecule, RNA-IN, is complementary to the top of the loop, and complementarity extends for 35 nucleotides down one side of RNA-OUT.
At first, regulatory RNA was thought to be a eukaryotic phenomenon, a part of the explanation for why so much more transcription in higher organisms was seen than had been predicted. But as soon as researchers began to look for possible RNA regulators in bacteria, they turned up there as well.[41] Currently, the ubiquitous nature of systems of RNA regulation of genes has been discussed as support for the RNA World theory.[40][48] Bacterial small RNAs generally act via antisense pairing with mRNA to down-regulate its translation, either by affecting stability or affecting cis-binding ability.[40] Riboswitches have also been discovered. They are cis-acting regulatory RNA sequences acting allosterically. They change shape when they bind metabolites so that they gain or lose the ability to bind chromatin to regulate expression of genes.[49][50]
Diener's 1989 hypothesis had proposed that the unique properties of viroids make them more plausible macromolecules than introns, or other RNAs considered in the past as possible "living relics" of a hypothetical, pre-cellular RNA world. If so, viroids have assumed significance beyond plant virology for evolutionary theory, because their properties make them more plausible candidates than other RNAs to perform crucial steps in the evolution of life from inanimate matter (abiogenesis). Diener's hypothesis was mostly forgotten until 2014, when it was resurrected in a review article by Flores et al., in which the authors summarized Diener's evidence supporting his hypothesis as:
The small nuclear U2 RNA found in splicing complexes is thought to aid splicing by interacting with the lariat sequence. Complementary sequences for both the lariat sequence and the acceptor signal are present in a segment of only 15 nucleotides in U2 RNA. Further, the U1 RNA has been proposed to function as a guide in splicing to identify the precise donor splice junction by complementary base-pairing. The conserved regions of the U1 RNA thus include sequences complementary to the stop codons. These observations enabled Senapathy to predict that that stop codons had operated in the origin of not only the splice-junction signals and the lariat signal, but also some of the small nuclear RNAs.
RNA-based evolution is a theory that posits that RNA is not merely an intermediate between DNA and proteins, but rather a far more dynamic and independent role-player in determining phenotype. By regulating the transcription of DNA sequences, the stability of RNA, and the capability of messenger RNA to be translated, RNA processing events allow for a diverse array of proteins to be synthesized from a single gene. Since RNA processing is heritable, it is subject to natural selection and contributes to the evolution and diversity of most eukaryotic organisms.
The most extensively studied transcriptional termination factor is the Rho protein of "E. coli". The Rho protein recognizes a cytosine-rich region of the elongating mRNA, but the exact features of the recognized sequences remain unknown. Rho forms a ring-shaped hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5' to 3' with respect to the mRNA). When the Rho protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA. The structure, as well as the activity, of the Rho protein is similar to that of the F subunit of ATP synthase, supporting the theory that the two share an evolutionary link. The antibiotic bicyclomycin works by inhibiting Rho.
While often delegated to the field of astrobiology, attempts to understand how and when life arose are relevant to geobiology as well. The first major strides towards understanding the “how” came with the Miller-Urey experiment, when amino acids formed out of a simulated “primordial soup”. Another theory is that life originated in a system much like the hydrothermal vents at mid-oceanic spreading centers. In the Fischer-Tropsch synthesis, a variety of hydrocarbons form under vent-like conditions. Other ideas include the “RNA World” hypothesis, which postulates that the first biologic molecule was RNA and the idea that life originated elsewhere in the solar system and was brought to Earth, perhaps via a meteorite.
When the RNA is cleaved, polyadenylation starts, catalysed by polyadenylate polymerase. Polyadenylate polymerase builds the poly(A) tail by adding adenosine monophosphate units from adenosine triphosphate to the RNA, cleaving off pyrophosphate. Another protein, PAB2, binds to the new, short poly(A) tail and increases the affinity of polyadenylate polymerase for the RNA. When the poly(A) tail is approximately 250 nucleotides long the enzyme can no longer bind to CPSF and polyadenylation stops, thus determining the length of the poly(A) tail. CPSF is in contact with RNA polymerase II, allowing it to signal the polymerase to terminate transcription. When RNA polymerase II reaches a "termination sequence" (TTATTT on the DNA template and AAUAAA on the primary transcript), the end of transcription is signaled. The polyadenylation machinery is also physically linked to the spliceosome, a complex that removes introns from RNAs.
In the late 1960s, Orgel proposed that life was based on RNA before it was based on DNA or proteins. His theory included genes based on RNA and RNA enzymes. This view would be developed and shaped into the now widely-accepted RNA world hypothesis.
Genes of all organisms, except bacteria, consist of short protein-coding regions (exons) interrupted by long sequences that intervene the coding sequences (introns). When a gene is expressed, its DNA sequence is copied into a “primary RNA” sequence by the enzyme RNA polymerase. Then the “spliceosome” machinery physically removes the introns from the RNA copy of the gene by the process of splicing, leaving only a contiguously connected series of exons, which becomes the “messenger” RNA (mRNA). This mRNA is now “read” by another cellular machinery, called the “ribosome,” to produce the encoded protein. Thus, although introns are not physically removed from a gene, a gene's sequence is read as if introns never existed. 
RNA thermometers, along with riboswitches, are used as examples in support of the RNA world hypothesis. This theory proposes that RNA was once the sole nucleic acid present in cells, and was replaced by the current DNA → RNA → protein system.
There have been furious debates on whether the issue of RNA quality control does exist. However, with the concern of various lengths of half lives of diverse RNA species ranging from several minutes to hours, degradation of defective RNA can not easily be attributed to its transient character anymore. Indeed, reaction with ROS takes only few minutes, which is even shorter than the average life-span of the most unstable RNAs. Adding the fact that stable RNA take the lion’s share of total RNA, RNA error deleting becomes hypercritical and should not be neglected anymore. This theory is upheld by the fact that level of oxidized RNA decreases after removal of the oxidative challenge.
Some potential factors include ribonucleases, which are suspected to selectively degrade damaged RNAs under stresses. Also enzymes working at RNA precursor pool level, are known to control quality of RNA sequence by changing error precursor to the form that can't be included directly into nascent strand.
While in the Szostak lab, Bartel isolated the first ribozymes directly from random sequence, using "in vitro" evolution (among these, the Class I ligase). After he became independent at the Whitehead Institute, he further evolved this ribozyme to function as a RNA-dependent RNA polymerase to extend primers on external RNA templates, bolstering the "RNA world" theory.
IS605-orfB RNA motifs refer to conserved RNA or DNA structures that were discovered by bioinformatics.
Although such motifs were published as a RNA candidates, there is some reason to suspect that they might function as a single-stranded DNA. In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. If the motifs function as RNA, they likely are small RNAs, that are independently transcribed.
Noted molecular biologist and biophysicist Dr. Colin Blake from the Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, commented on Dr. Senapathy's theory that: "Recent work by Dr. Senapathy, when applied to RNA, comprehensively explains the origin of the segregated form of RNA into coding and non-coding regions. It also suggests why a splicing mechanism was developed at the start of primordial evolution. The presence of random sequence was therefore sufficient to create in the primordial ancestor the segregated form of RNA observed in the eukaryotic gene structure.”
Moreover, if this theory is correct, exons should be delimited by stop codons, especially at the 3’ ends of exons (that is, the 5’ end of introns). Actually they are precisely delimited more strongly at the 3’ ends of exons and less strongly at the 5’ ends in most known genes, as predicted. These stop codons are the most important functional parts of both splice junctions (the canonical bases GT:AG). The theory thus provides an explanation for the “conserved” splice junctions at the ends of exons and for the loss of these stop codons along with introns when they are spliced out. If this theory is correct, splice junctions should be randomly distributed in eukaryotic DNA sequences, and they are. The splice junctions present in transfer RNA genes and ribosomal RNA genes, which do not code for proteins and wherein stop codons have no functional meaning, should not contain stop codons, and again, this is observed. The lariat signal, another sequence involved in the splicing process, also contains stop codons. 
Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. However, the presence of these introns in eukaryotes and absence in prokaryotes created a debate about the time in which these introns appeared. Two theories arose: the "introns early" theory and the "introns late" theory. Supporters of the "introns early theory" believed that introns and RNA splicing were the relics of the RNA world and therefore both prokaryotes and eukaryotes had introns in the beginning. However, prokaryotes eliminated their introns in order to obtain a higher efficiency, while eukaryotes retained the introns and the genetic plasticity of the ancestors. On the other hand, supporters of the "introns late" theory believe that prokaryotic genes resemble the ancestral genes and introns were inserted later in the genes of eukaryotes. What is clear now is that the eukaryotic exon-intron structure is not static, introns are continually inserted and removed from genes and the evolution of introns evolves parallel to exon shuffling.
In prokaryotes, transcription is carried out by a single type of RNA polymerase, which needs a DNA sequence called a Pribnow box as well as a sigma factor (σ factor) to start transcription. In eukaryotes, transcription is performed by three types of RNA polymerases, each of which needs a special DNA sequence called the promoter and a set of DNA-binding proteins—transcription factors—to initiate the process. RNA polymerase I is responsible for transcription of ribosomal RNA (rRNA) genes. RNA polymerase II (Pol II) transcribes all protein-coding genes but also some non-coding RNAs (e.g., snRNAs, snoRNAs or long non-coding RNAs). Pol II includes a C-terminal domain (CTD) that is rich in serine residues. When these residues are phosphorylated, the CTD binds to various protein factors that promote transcript maturation and modification. RNA polymerase III transcribes 5S rRNA, transfer RNA (tRNA) genes, and some small non-coding RNAs (e.g., 7SK). Transcription ends when the polymerase encounters a sequence called the terminator.
As noted above, Colin Blake, the author of the Gilbert-Blake theory for the origin of introns and exons, states, “Recent work by Senapathy, when applied to RNA, comprehensively explains the origin of the segregated form of RNA into coding and noncoding regions. It also suggests why a splicing mechanism was developed at the start of primordial evolution.”
Baltimore extended this work and examined two RNA tumor viruses, Rauscher murine leukemia virus and Rous sarcoma virus. He went on to discover reverse transcriptase (RTase or RT) - the enzyme that polymerizes DNA from an RNA template. In doing so, he discovered a distinct class of viruses, later name retroviruses, that use an RNA template to catalyze synthesis of viral DNA. This overturned a "central dogma" of genetic theory, the belief that genetic information flowed unidirectionally from DNA to RNA (and thence to proteins). Reverse transcriptase is essential for the reproduction of retroviruses, allowing such viruses to turn viral RNA strands into viral DNA strands. The viruses that fall into this category include HIV.
An alternative — or complementary — theory of RNA origin is proposed in the PAH world hypothesis, whereby polycyclic aromatic hydrocarbons (PAHs) mediate the synthesis of RNA molecules.[84] PAHs are the most common and abundant of the known polyatomic molecules in the visible Universe, and are a likely constituent of the primordial sea.[85] PAHs and fullerenes (also implicated in the origin of life)[86] have been detected in nebulae.[87]