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Theory that RNA plays an independent role in determining phenotype
RNA-based evolution is a theory that posits that RNA is not merely an intermediate between the Watson and Crick model of the DNA molecule and proteins
RNA-based_evolution
Hypothetical stage in the early evolutionary history of life on Earth
from RNA to DNA and the evolution of Bacteria, Archaea, and Eukaryota. He believes the last universal common ancestor was RNA-based and evolved RNA viruses
RNA_world
Family of large biological molecules
structure RNA virus DNA History of RNA biology List of RNA biologists RNA Society Macromolecule RNA-based evolution Aptamer RNA origami Transcriptome RNA world
RNA
Subclass of viruses
RNA virus is a virus characterized by a ribonucleic acid (RNA) based genome. The genome can be single-stranded RNA (ssRNA) or double-stranded (dsRNA)
RNA_virus
Scientific hypotheses on the origin and evolution of DNA
(acting as ribozymes). This ancient RNA world likely influenced the evolution of the current genetic code, which is based on four nucleotide bases. The limitation
Origin_of_DNA
Enzyme that synthesizes RNA from an RNA template
RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes
RNA-dependent_RNA_polymerase
Change in the heritable traits of populations
November 2020. Joyce, Gerald F. (11 July 2002). "The antiquity of RNA-based evolution". Nature. 418 (6894): 214–221. Bibcode:2002Natur.418..214J. doi:10
Evolution
Type of RNA molecules
contributed to the RNA world hypothesis, which suggests that RNA may have been important in the evolution of prebiotic self-replicating systems. The most common
Ribozyme
Records of Earth's development
(1): 23–31. PMID 15906258. Joyce, G.F. (2002). "The antiquity of RNA-based evolution". Nature. 418 (6894): 214–21. Bibcode:2002Natur.418..214J. doi:10
History_of_Earth
RNA that facilitates the addition of amino acids to a new protein
Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides
Transfer_RNA
Nitrogen-containing biological compounds that form nucleosides
chain has been formed. In DNA, the most common modified base is 5-methylcytosine (m5C). In RNA, there are many modified bases, including those contained
Nucleotide_base
Evolutionary origin and subsequent development of cells
According to this hypothesis, the ancient RNA world transitioned into the modern cellular world via the evolution of protein synthesis, followed by replacement
Evolution_of_cells
Theory that viruses predate cellular life
reflect evolution spanning from an early RNA world to the modern DNA/protein world. Viroids and ribozymes, as the simplest known self-replicating RNA elements
Virus_world_hypothesis
Class of viruses in the Baltimore classification
RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase
Positive-strand_RNA_virus
Molecule that carries genetic information
RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based
DNA
S2CID 16567006. Joyce, Gerald F. (July 11, 2002). "The antiquity of RNA-based evolution". Nature. 418 (6894): 214–221. Bibcode:2002Natur.418..214J. doi:10
History_of_life
Small non-coding ribonucleic acid molecule
and even some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRNAs base-pair to complementary sequences
MicroRNA
RNA component of the large subunit of the eukaryotic ribosome
28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components
28S_ribosomal_RNA
Enzyme that synthesizes RNA from DNA during Transcription
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that
RNA_polymerase
Possible earliest ancestor of the LUCA ancestral cell
self-replicating RNA with an RNA genome instead of the usual DNA genome. In Carl Woese's Darwinian threshold period of cellular evolution, progenotes are
First universal common ancestor
First_universal_common_ancestor
Overview of and topical guide to change in the heritable characteristics of organisms
function or fitness RNA-based evolution – Theory that RNA plays an independent role in determining phenotype Co-operation (evolution) – Groups of organisms
Outline_of_evolution
Subfield of evolutionary biology and virology concerned with the evolution of viruses
chance of mutations and evolution can change depending on the type of virus (e.g., double stranded DNA, double stranded RNA, or single stranded DNA)
Viral_evolution
Type of vaccine
An mRNA vaccine is a type of vaccine that uses a copy of a molecule called messenger RNA (mRNA) to produce an immune response. The vaccine delivers molecules
MRNA_vaccine
RNA component of the ribosome, essential for protein synthesis in all living organisms
transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in
Ribosomal_RNA
Medications based on ribonucleic acids
based on messenger RNA (mRNA), antisense RNA (asRNA), RNA interference (RNAi), RNA activation (RNAa) and RNA aptamers. Of the four types, mRNA-based therapy
RNA_therapeutics
Molecular process
properties of RNAs. RNA editing may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule. RNA editing is relatively
RNA_editing
RNA component
for it are referred to as 16S rRNA genes and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl
16S_ribosomal_RNA
Ancestor of all current life on Earth
to convert information from DNA to mRNA to proteins. A phylogenetic tree directly portrays the idea of evolution by descent from a single ancestor. An
Last universal common ancestor
Last_universal_common_ancestor
List of standard rules to translate DNA encoded information into proteins
as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence
DNA_and_RNA_codon_tables
Biological process of gene regulation
ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. Once mRNA is degraded,
RNA_interference
Biological entity within the hierarchy of biological organization
early unit of selection and evolution that would later transition into living cells. It is possible that RNA-based evolution is still taking place today
Unit_of_selection
conserved by evolution are far more likely to be the functional form. The methods below use this approach. Many ncRNAs function by binding to other RNAs. For
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Characteristic of a group of organisms with a common ancestor
course of evolution, this RNA world was replaced by the evolutionary emergence of the DNA world. A world of independently self-replicating RNA genomes apparently
Common_descent
Reaction that cleaves the RNA molecule
RNA hydrolysis is a reaction in which a phosphodiester bond in the sugar-phosphate backbone of RNA is broken, cleaving the RNA molecule. RNA is susceptible
RNA_hydrolysis
Hypothetical life before complete cells
hypothetical lipid-based structure, could have confined RNA in ancient times. This structure allowed the RNA to remain in close proximity with other RNA molecules
Pre-cell
Lab technique in cellular biology
mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq
RNA-Seq
RNA that is read by the ribosome to produce a protein
Messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in
Messenger_RNA
Biomolecule
RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded non-coding RNA molecules, typically 20–24 base pairs
Small_interfering_RNA
Life that has no cellular structure
evolution of life from inanimate matter (abiogenesis). In 2024, researchers announced the possible discovery of viroid-like, but distinct, RNA-based elements
Non-cellular_life
RNA molecule that specifies a target sequence
Guide RNA (gRNA) or single guide RNA (sgRNA) is a short sequence of RNA that guides a CRISPR-associated protein to its nucleic acid sequence target by
Guide_RNA
Family of DNA sequences found in prokaryotic organisms
2013). "CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes". RNA Biology. 10 (5): 679–686. doi:10.4161/rna.24022. PMC 3737325
CRISPR
Phylum of viruses
complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the
Negative-strand_RNA_virus
Small nuclear RNA component of the spliceosome
U6 snRNA is the non-coding small nuclear RNA (snRNA) component of U6 snRNP (small nuclear ribonucleoprotein), an RNA-protein complex that combines with
U6_spliceosomal_RNA
Sequence of DNA that determines traits in an organism
a typical gene were based on high-resolution genetic mapping and on the size of proteins and RNA molecules. A length of 1500 base pairs seemed reasonable
Gene
Non-protein coding transcripts longer than 200 nucleotides
ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs)
Long_non-coding_RNA
Protein engineering method
controlled, laboratory environment. Directed evolution has its origins in the 1960s with the evolution of RNA molecules in the "Spiegelman's Monster" experiment
Directed_evolution
Class of enzymes which synthesize nucleic acid chains or polymers
DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions
Polymerase
Study of changes in DNA and RNA over time
Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components
Molecular_evolution
Technique in molecular biology
precisely defined RNA molecules, run-off transcription remains one of the fundamental preparative steps in RNA-based directed evolution. Run-off transcription
Run-off_transcription
Life arising from non-living matter
polymers such as proteins and RNA. On the other side, the process after the LUCA is readily understood: biological evolution caused the development of a
Abiogenesis
DNA oligonucleotides that can perform a specific chemical reaction
other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA). However, in contrast to the abundance of protein enzymes in biological
Deoxyribozyme
Technique for the automated directed evolution of proteins
Phage-assisted continuous evolution (PACE) is a phage-based technique for the automated directed evolution of proteins. It relies on relating the desired
Phage-assisted continuous evolution
Phage-assisted_continuous_evolution
Type of synthetic ribozyme
The RNA Ligase ribozyme was the first of several types of synthetic ribozymes produced by in vitro evolution and selection techniques. They are an important
Ligase_ribozyme
Class of ribonucleic acid that is not translated into proteins
RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist, HOTAIR, and MALAT1
Non-coding_RNA
Type of virus according to Baltimore classification
template by the viral RNA dependent RNA polymerase (RdRp) to transcribe a positive-strand RNA functioning as messenger RNA (mRNA) for the host cell's ribosomes
Double-stranded_RNA_viruses
Process in genetics
is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase. The process occurs in three main steps: initiation
Bacterial_transcription
Genus of viruses
Greek λύσσα lyssa "rage, fury, rabies" and the Latin vīrus) is a genus of RNA viruses in the family Rhabdoviridae, order Mononegavirales. Mammals, including
Lyssavirus
Percentage of guanine and cytosine in DNA or RNA molecules
and with uracil (U) in RNA. Quantitatively, each GC base pair is held together by three hydrogen bonds, while AT and AU base pairs are held together
GC-content
Pathogenic small single-stranded circular RNA
steps through an RNA-based mechanism. They require RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which
Viroid
Rules by which information encoded within genetic material is translated into proteins
order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The
Genetic_code
tracking RNA rose as its roles in complex cellular functions has grown to not only include mRNA, rRNA, and tRNA, but also RNAi, siRNA, snoRNA, and lncRNA, among
Spinach_aptamer
Science of genes, heredity and variation
ribosomal RNA and transfer RNA). RNA can also have regulatory effects through hybridization interactions with other RNA molecules (such as microRNA). Although
Genetics
Organisms that live in salt water
(PDF) on 24 August 2015. Joyce GF (July 2002). "The antiquity of RNA-based evolution". Nature. 418 (6894): 214–21. Bibcode:2002Natur.418..214J. doi:10
Marine_life
Idea that ribosomal RNA was necessary for modern life
Carl Woese in 1977. It states that the evolution of ribosomal RNA was a necessary precursor to the evolution of modern life forms. This led to the advancement
Woese's_dogma
The timeline of human evolution outlines the major events in the evolutionary lineage of the modern human species, Homo sapiens, throughout the history
Timeline_of_human_evolution
(4 January 2016). "deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data"
List of long non-coding RNA databases
List_of_long_non-coding_RNA_databases
Chemical compound
etiology of RNA, TNA has become an important synthetic genetic polymer as a xeno nucleic acid (XNA) due to its ability to efficiently base pair with complementary
Threose_nucleic_acid
Set of genes all related by point mutations that have equivalent function or fitness
molecular evolution RNA world Nucleic acid secondary structure van Nimwegen, E; Crutchfield, JP; Huynen, M (Aug 17, 1999). "Neutral evolution of mutational
Neutral_network_(evolution)
Process of copying a segment of DNA into RNA
RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA)
Transcription_(biology)
Algorithm used in gene expression studies
The RNA integrity number (RIN) is an algorithm for assigning integrity values to RNA measurements. The integrity of RNA is a major concern for gene expression
RNA_integrity_number
Class of small RNA molecules
nucleolar RNAs (snoRNAs) are a class of non-coding small RNA molecules in the nucleolus that primarily guide chemical modifications of other RNAs, mainly
Small_nucleolar_RNA
Infectious agent that replicates in cells
studies of viral evolution have shown that recombination has been rampant in the species studied. Recombination is common to both RNA and DNA viruses.
Virus
Technique for producing oligonucleotides that specifically bind to a target
either single-stranded DNA or RNA that specifically bind to a target ligand or ligands. These single-stranded DNA or RNA are commonly referred to as aptamers
Systematic evolution of ligands by exponential enrichment
Systematic_evolution_of_ligands_by_exponential_enrichment
Short RNA molecule
microRNAs (nat-miRNAs) can base pair with their targets with high complementarity and regulate them through cleavage of the corresponding messenger RNAs.
MiR444 microRNA precursor family
MiR444_microRNA_precursor_family
RNA family
Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like
Transfer-messenger_RNA
Family of viruses
A retrovirus is a virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell.
Retrovirus
(2008). "The origin and evolution of tRNA inferred from phylogenetic analysis of structure". Journal of Molecular Evolution. 66 (1): 21–35. Bibcode:2008JMolE
Thermosynthesis
Molecular structure formed in DNA transcription
space for RNA polymerase (RNAP) to bind to the template strand and begin RNA synthesis. The transcription bubble size is usually 12 to 14 base pairs, which
Transcription_bubble
Hypothesis for classification of life
"Carl Woese's vision of cellular evolution and the domains of life". RNA Biology. 11 (3). RNA Biol.: 197–204. doi:10.4161/rna.27673. PMC 4008548. PMID 24572480
Three-domain_system
Transcription is heterocatalytic function of DNA
transcribes small non-coding RNAs, including tRNAs, 5S rRNA, U6 snRNA, SRP RNA, and other stable short RNAs such as ribonuclease P RNA. RNA Polymerases I, II, and
Eukaryotic_transcription
Gene editing method
system. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing
CRISPR_gene_editing
Kingdom of viruses
(RNA), including genes which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA)
Orthornavirae
Fragment of RNA or DNA able to be chemically labeled
DNA), digoxigenin, a non-radioactive, antibody-based marker, biotin or fluorescein. DNA sequences or RNA transcripts that have moderate to high sequence
Hybridization_probe
Three-dimensional shape of a nucleic acid polymer
Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures
Nucleic acid tertiary structure
Nucleic_acid_tertiary_structure
DNA sequences with no known biological function
Additionally, non-protein coding regions such as genes for ribosomal RNA and transfer RNA, regulatory sequences, origins of replication, centromeres, telomeres
Junk_DNA
Intergenic DNA sequence separating ribosomal RNA genes
small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript
Internal_transcribed_spacer
American evolutionary biologist
at Princeton University. She specializes in RNA-mediated epigenetic inheritance and molecular evolution. Landweber graduated summa cum laude with an
Laura_Landweber
Protein that plays a role in RNA silencing process
(siRNAs) and piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity (base pairing)
Argonaute
German molecular geneticist and evolutionary biologist
more RNAs are yet to be discovered. 2. Retroposition (conversion of RNA to DNA) is an ancient process, but has persisted throughout the evolution of most
Jürgen_Brosius
Ribosomal RNA Ribosome Ribosomes Ribozyme Risk communication RNA RNA editing RNA phage RNA polymerase RNA replicase RNA splicing Robertsonian fusion rRNA S (Svedberg
Index_of_genetics_articles
Theory of evolution by changes at the molecular level
Daniel (ed.). "Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases"
Neutral theory of molecular evolution
Neutral_theory_of_molecular_evolution
RNA structure
Especially Vibrionales RNA motif (PAGEV RNA motif) is a conserved RNA structure that was discovered by bioinformatics. PAGEV motif RNAs are found in Gammaproteobacteria
PAGEV_RNA_motif
Type of genetic component
suggesting their role in evolution. Like LTR retrotransposons, non-LTR retrotransposons contain genes for reverse transcriptase, RNA-binding protein, nuclease
Retrotransposon
Ribosomal component
RNA. 9 (2): 155–159. doi:10.1261/rna.2127103. PMC 1370378. PMID 12554855. Bokov K, Steinberg SV (February 2009). "A hierarchical model for evolution of
Peptidyl_transferase_center
Evolutionary process
Su, Bing (July 2008). "Molecular Evolution of a Primate-Specific microRNA Family". Molecular Biology and Evolution. 25 (7): 1493–1502. doi:10.1093/molbev/msn094
Human_evolution
Largest class of small non-coding RNA molecules in animals
Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through
Piwi-interacting_RNA
Macromolecular machine that synthesizes proteins in cells
messenger RNA (mRNA). During translation, the ribosome decodes successive codons in an mRNA molecule and, with the aid of transfer RNA (tRNA), links amino
Ribosome
RNA-like molecule
An L-ribonucleic acid aptamer (L-RNA aptamer, trade name Spiegelmer) is an RNA-like molecule built from L-ribose units. It is an artificial oligonucleotide
L-Ribonucleic_acid_aptamer
British chemist (1927–2007)
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
Leslie_Orgel
Laboratory technique
(PL), also known as proximity-based labeling, is a laboratory technique that labels biomolecules, usually proteins or RNA, proximal to a protein of interest
Proximity_labeling
RNA BASED-EVOLUTION
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