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Biopharmaceutical RNA glossary & taxonomy
Evolving Terminologies for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty
Last revised January 12, 2015

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Biology term index:   Site Map  Related glossaries include 
Technologies Gene amplification & PCR   Genomic technologies  Microarrays   Informatics Genomic Informatics
Biology DNA, Expression, Gene definitions, Proteins, protein structures Sequences, DNA & beyond
  It seems that not until the technologies for working with nucleic acids and proteins are better integrated will their researchers be more connected than they are now. 

alternative RNA splicing: A biological process that is crucial for gene expression in most animal life, including humans. Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. More than half of all human genes are alternatively spliced, so it is expected that alternative pre- mRNA splicing will be responsible for the identification of more than 90 percent of all human proteins. Benoit Chabot, Université de Sherbrooke, Canada Research Chairs Profile, 2001

The inclusion or exclusion of different exons to form different mRNA transcripts.  See also under Proteomics proteomic diversity

alternative transcripts: Expression gene & protein

amplified antisense RNA aRNA: Researchers at Stanford University used such a method to produce amplified heterogeneous populations of RNA from limited quantities of cDNA. [Van Gelder RN, et al. "Amplified RNA synthesized from limited quantities of heterogeneous cDNA." Proceedings of the National Academy of Sciences, USA. 1990; 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. After second- strand cDNA synthesis, T7 RNA polymerase was used to generate aRNA. (aRNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.) The investigators reported that this approach achieved up to 80- fold molar amplification from nanogram quantities of cDNA. They also found that the amplicons were similar in size distribution to the parent cDNA and showed sequence heterogeneity. More recently, another group of researchers reported that they had developed a process for optimizing low- abundance RNA, by combining aRNA amplification with template- switching. They found that one round of amplification produced approximately 103 fold of the estimated amount of starting mRNA, and two rounds produced an approximately 105 fold increase. Wang E, et al. "High- fidelity mRNA amplification for gene profiling." Nature Biotechnology 18: 457- 459, 2000

The term amplified antisense RNA (aRNA) is also used as an alternative to cRNA. For our purposes, the distinction between these chemical forms is not important. 

antisense RNA:  RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.   MeSH, 1991

RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. More specifically, antisense oligonucleotides that are useful as reagents for target validation, or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. 

A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. Related terms:  Pharmaceutical biology antisense, antisense DNA, antisense oligonucleotides.

antisense technology: Oligonucleotides designed to bind target RNAs (e.g. mRNA, microRNA, etc.) based on sequence complementarity in order to block their natural function. Antisense technology can also  describe a general approach that includes RNAi and siRNAs. Alnylam Glossary

canonical siRNA: Two strands of RNA, each 21 nucleotides long with a central region of complementarity that is 19 base-pairs long for the formation of dsRNA and two nucleotide overhangs at each of the 3' ends. Alnylam Glossary

catalytic RNA: RNA which contains an intron sequence that has an enzyme- like catalytic activity. This intron sequence has been shown to fold up to form a complex surface that can function like an enzyme in reactions with other RNA molecules and thus synthesize new molecules even in the absence of protein.  MeSH, 1991

Ever since HHMI investigator Thomas Cech at the University of Colorado in Boulder uncovered the catalytic properties of RNA in 1982, researchers have been diligently studying these ribozymes. Scientists have since discovered more than 500 ribozymes in a diverse range of organisms and have found that they share many similarities with their more widespread protein cousins, enzymes. Howard Hughes Medical Institute News, Oct. 9, 1998  Related term: ribozymes

codon: The sequence of three consecutive nucleotides that occurs in mRNA which directs the incorporation of a specific amino acid into a protein or represents the starting or termination signals of  protein synthesis. IUPAC Biotech, IUPAC Medicinal Chemistry

A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE). MeSH, 1991

Coined by Sydney Brenner "for a triplet of bases that specifies an amino acid, introduced partly in satirical reference to Seymour Benzer's "cistron", "recon," and "muton", Brenner's "codon" is the one that survives in universal biological use. HJ Freeman Eighth Day of Creation, Cold Spring Harbor Laboratory Press, 1996 p. 469  Related terms: transcription, translation. Narrower terms initiator codon, start codon, stop codon, terminator codon.

complementary RNA cRNA: Synthetic RNA produced by transcription from a specific DNA single stranded template. Schwindlein

DNA-directed RNA polymerase: A group of enzymes that catalyzes DNA template- directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha- amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992) EC  MeSH, 1998  Related term: RNA polymerase RNAP

ds: Double-stranded (DNA or RNA)

eliRNA expressed long inhibitory dsRNA: 

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exon skipping: Gene definitions

Extracellular RNA (exRNA) is present in human body fluids, such as blood, saliva, urine, breast milk, amniotic fluid, cerebrospinal fluid, ascites and pleural effusions. The concept that secreted exRNA can alter target cell phenotypes is emerging as a universal and novel paradigm in intercellular signaling.  In view of this emerging paradigm, the NIH invites applications for projects that will develop novel therapies based on exRNA signaling.  The overall goal of this initiative is to develop and demonstrate the potential for clinical utility of exRNAs as therapeutic agents, and to develop tools and technologies to enable engineered RNAs to be packaged into extracellular vesicles or associated with RNA-binding proteins for use as extracellular delivery vehicles. These projects should include methods for the production, purification, and packaging of specific RNAs and methods to deliver them to target cells via extracellular space. Clinical Utility of Extracellular RNA for Therapy Development (UH2/UH3) RFA-RM-12-014

Recent observations demonstrate that exRNAs play an important role(s) in inter-cellular signaling and can have a profound impact on organismal physiology. Studies have shown, for example, that tumor-derived exRNAs can promote tumor growth and that endothelial cell-derived exRNAs can regulate gene expression in smooth muscle cells. In addition, there are new reports suggesting dietary derived exRNAs, found in human sera may play a role in modulating LDL levels. Microbes also secrete RNAs via extracellular vesicles and this may be a mechanism by which the microbiome influences host cell function from a distance. These observations suggest a mechanism of inter-kingdom information exchange through exRNAs. Hence an opportunity exists to investigate an entirely new paradigm of intercellular and inter-organismal communication by identifying fundamental principles of exRNA secretion, delivery, and the impact of RNAs secreted into the circulation or into other body fluids.  In addition to foundational biology, an opportunity exists to test the clinical utility of exRNAs as therapeutic molecules and/or diagnostic and prognostic indicators. Fundamental to this premise is the development of reference profiles of exRNAs in body fluids of the healthy population that will be supported through this research opportunity. A systematic analysis of circulating exRNA in body fluids of healthy individuals and environmentally derived exRNA, as applicable, would form the basis to facilitate novel strategies for diagnosis, intervention, and therapy for many diseases. Defining A Comprehensive Reference Profile of Circulating Human Extracellular RNA (U01) RFA-RM-13-014

hairpin ribozymes: Named for their conserved domains that form a hairpin- like shape, they are trans-cleaving molecules that tend to be 70 nucleotides in length. Like hammerhead ribozymes, they catalyze simple self- cleaving reactions of phosphodiester bonds and can be produced naturally or synthetically.  

hammerhead ribozymes: Small trans-cleaving ribozymes characterized by a hammerhead motif — three short helices flanking a central catalytic core of 15 conserved nucleotides. The best understood of the ribozymes. 

heteronuclear RNA hnRNA:  The fraction of nuclear RNA which contains primary transcripts of the DNA prior to processing to form messenger RNA.  Flesh and Bones Immunology Glossary   

initiator codon: A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon. MeSH, 1995  Related or identical term to: start codon?

lariat RNAs: Lariat RNAs are intermediates in RNA splicing as catalyzed by group II introns and the spliceosome. Efficient One-Step Synthesis of Biologically Related Lariat RNAs by a Deoxyribozyme** Yangming Wang and Scott K. Silverman* Angew Chem Int Ed Engl. Author manuscript; available in PMC 2006 July 24, doi: 10.1002/anie.200501643.

lincRNAs Long Intergenic Non Coding RNAs: Our research aims to understand the role of long intergenic non-coding RNAs (lincRNAs) in establishing the distinct epigenetic states of adult and embryonic cells and their misregulation in diseases such as cancer. To further explore how lincRNAs may define and or drive cell fate decisions we developed computational methods to provide initial hypothesis of their functions. Rinn Lab, Broad Institute  

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messenger RNA mRNA: An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes. mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation. IUPAC Biotech 

RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post- transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm. MeSH, 1965

Includes 5' untranslated region (5' UTR), coding sequences (CDS, exon) and 3' untranslated region (3' UTR)  [DDBJ/ EMBL/ GenBank Feature Table]

Messenger RNA, an intermediate between DNA sequences and the production of protein. The coding strand of DNA is transcribed as an mRNA (complementary to the coding strand), which is then translated by transfer RNA (tRNA) and building-block amino acids to produce a protein. Narrower terms:  UTR; Pharmaceutical biology: antisense RNA, sense RNA Broader term RNA Related term reverse transcription

micro-RNA miRNA:
microRNA as Biomarkers and Diagnostics March 17-18, 2014 • Boston, MA Program | Register | microRNA as Biomarkers and Diagnostics

With the first diagnostics set to debut within a year, the new research and development field of microRNAs is beginning to reveal its potential. This report establishes a baseline for observing microRNAs’ maturation, including assessments of: The science and analysis of first-generation microRNA commercial applications, The early adaptors and where they are heading with this emerging technology, Clinical applications, which will begin in oncology, followed by infectious diseases, neurology, metabolic disorders, and cardiovascular diseases, The youthfulness of the field of microRNA and more.  Insight Pharma Reports, microRNAs: Commercial Products on the horizon, 2008

A large class of 21- to 24- nucleotides noncoding RNAs ... We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development ... The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals. Nelson C. Lau et. al "An abundant class of tiny RNAs with probably regulatory roles in Caenorhabditis elegans" Science 294 (5543): 858- 862, 26 Oct. 2001  Narrower terms: siRNA, stRNA Broader term:  RNA interference RNAi  Equivalent term: non-protein coding genes?
microRNA, Nature Reviews 

non-coding RNA: RNA has traditionally been thought of as a molecule that imparts information, structure or catalytic activities. The role of a subset of RNA known as non-coding RNA (ncRNA) – including small non-coding RNAs (siRNAs, piRNAs, and miRNAs) and long non-coding RNAs (lncRNA) – has increasingly come under scientific scrutiny. Recent progress suggests that the involvement of ncRNAs in human diseases could be far more prevalent than previously appreciated. Multiple lines of evidence increasingly link mutations and dysregulations of ncRNAs to diverse human diseases, ranging from neurodegeneration to cancer. Targeting Non-Coding RNA  March 5-7, 2012 • San Diego, CA Program | Order CD

nonsense codons: See under stop codons
Northern blotting: Microarrays 
nucleic acids: DNA
or RNA

pRNA: Is this prohead, promoter and/or packaging RNA?

post-transcriptional RNA processing: Post- transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein. MeSH, 1983

precursor_RNA: Any RNA species that is not yet the mature RNA product;  may include 5' clipped region (5' clip), 5' untranslated region (5' UTR), coding sequences (CDS, exon), intervening sequences (intron), 3' untranslated region (3' UTR), and 3' clipped region (3' clip). ... used for RNA which may be the result of post- transcriptional processing. DDBJ/ EMBL/ GenBank Feature Table  Related term: RNA precursors Is this equivalent?

pre-mRNA splicing: The protein coding sequences of most eukaryotic messenger RNA precursors (pre- mRNAs) are interrupted by non- coding sequences called introns. Pre- mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre- mRNA splicing selectively joins different protein coding elements to form mRNAs that encode proteins with distinct functions, and is therefore an important source of protein diversity. TOM MANIATIS AND BOSILJKA TASIC, Alternative pre- mRNA splicing and proteome expansion in metazoans, Nature 418: 236 – 243, July 11, 2002; doi:10.1038/418236a  Broader term: splicing  Related terms: Pharmaceutical biology antisense, morpholinos

retroviruses: Retroviruses comprise a large and diverse family of enveloped RNA viruses defined by common taxonomic denominators that include structure, composition, and replicative properties (Coffin 1992ab, 1996). ... Retroviruses are broadly divided into two categories ---simple and complex ---distinguishable by the organization of their genomes (Fig. 2) (Coffin 1992a; Murphy et al. 1994).   ... The study of retroviruses has had a broad impact on diverse areas of biology and medicine, notably on molecular genetics, on the study of cellular growth control and carcinogenesis, and on biotechnology ( Varmus 1988; Temin 1992). The effect of retrovirology on our concept of genetic information, its molecular forms, transmission, and evolution has been nothing short of revolutionary.  John M Coffin et. al, Retroviruses, Cold Spring Harbor Laboratory Press, c1997 

reverse transcription: Gene amplification & PCR

ribonome: The population of RNA- coding regions of the genome. Mark Gerstein "What is Bioinformatics? Omes Table" 2001  Google = about 17 July 11, 2002; about 34 Aug 29, 2003; about 285 Nov 10, 2006  Related terms:  riboproteomics;  Cell biology ribosomes 

ribonomics: We have termed ribonomics the identification and analysis of linked mRNA subsets by using RNA- associated proteins. Ribonomics is distinct from transcriptomics, which is used to assess the total mRNA complement of the genome. The characterization of structurally and/ or functionally related subsets of mRNAs by using ribonomics or other partitioning methods may facilitate our understanding of gene products that are expressed simultaneously or sequentially for a specific outcome. [SA Tenenbaum, JD Keene, et. al "Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays" Proc. Natl. Acad. Sci. USA  97 (26) : 14085- 14090, Dec.  19, 2000

Our understanding of RNA in biology is currently limited in part by a lack of structural data, but perhaps more profoundly by limited knowledge of the cast of characters. It is not yet clear how many structured RNAs are expressed in different cell types, what biochemical pathways they participate in and what proteins they bind. Structural genomics of RNA will be most interesting when integrated with experimental and computational methods for identifying novel RNA genes and determining their biological relevance: an approach defined previously as 'ribonomics' [11]. Such an effort would have at least three essential goals: (i) to develop and implement methodologies for identifying and characterizing novel RNA genes; (ii) to develop techniques for high- throughput determination of RNA and RNA- protein structures; and (iii) to create and maintain a centralized database of RNA structures, sequences, functional data and modeling tools. Jennifer A. Doudna "Structural Genomics of RNA" Nature Structural Biology (7) 11 supp: 954- 956 November 2000

Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of  'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. V. Bourdeau "The distribution of RNA motifs in natural sequences" Nucleic Acids Research 27 (22): 4457- 4467, Nov. 15, 1999

Ribonomics, Inc. is a Systems Biology company focused on the development of innovative products for the diagnosis and treatment of human diseases. Employing proprietary technologies developed at Duke University Medical Center, the Company empirically connects biological pathways to human disease. This capability represents a powerful solution for accelerating drug discovery.  Ribonomics, Inc.  2002

In my laboratory, we pursue the functional consequences of mRNA binding by RNA- binding proteins, the determinants of RNA- binding specificity and the relationship among the proteins encoded by mRNAs in ribonomic clusters. There are many applications of these technologies to understanding growth, development and disease. The term was introduced by my colleagues and me in a series of articles from two Japanese symposia, and in a paper (Tenenbaum et al. PNAS 97 14085 (2000)) and in Keene, PNAS 98 7018 (2001). Jack Keene, Duke Univ. personal communication, Feb. 2002  Related terms:  riboproteomics; Cell biology ribosomes 

ribonucleic acid: See RNA

riboproteomics:  The systematic study of RNA and RNA-protein interactions as targets for developing small molecule drugs. Anadys, News Release, 2002 
Google = about 343 Aug 10, 2005; about 899 Nov 10, 2006

riboregulation: Riboregulation in E. coli: DsrA RNA acts by RNA: RNA interactions at multiple loci."  Richard A. Lease, Michael E. Cusick, and Marlene Belfort, Proceedings of the National Academy of Science U.S. PNAS 95 (21):  12456, October 13, 1998 

ribosomal frameshifting: A directed change in translational reading frame that allows the production of a single protein from two or more overlapping genes. The process is programmed by the nucleotide sequence of the mRNA and is sometimes also affected by the secondary or tertiary mRNA structure. It has been described mainly in viruses (especially retroviruses), retrotransposons, and bacterial insertion elements but also in some cellular genes. MeSH, 1996 

ribosomal proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits. MeSH 2003

ribosomal RNA rRNA: RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. IUPAC Biotech

Mature ribosomal RNA ; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins.  DDBJ/ EMBL/ GenBank Feature Table

ribosomal RNA rRNA genes: Gene categories

ribosomal self-splicing RNA:  Components of ribosomal RNA that undergo auto-catalyzed molecular rearrangements of their RNA sequence. MeSH 2004

ribosomes: Cell biology
ribosomics: -Omes & -omics

ribotyping: RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for differentiating between species or strains MeSH 2001

ribozymes: Naturally occurring RNAs with enzymatic activity that specifically bind to and cleave-  and therefore inactivate- mRNA molecules. Like the antisense approach, ribozymes provide a means of inhibiting a gene of interest for target validation studies. Ribozymes can be engineered to bind naturally to any RNA sequence, resulting in the cleavage and inactivation of mRNAs containing the target sequence. Narrower terms: hairpin ribozymes, hammerhead ribozymes Related term: catalytic RNA

RNA RiboNucleic Acid: Linear polymer molecules composed of a chain of ribose units linked between positions 3 and 5 by phosphodiester groups to which the bases adenine or guanine or uracil or cytosine, respectively are attached … The three most important types of RNAs in the cell are, c.f. mRNA, tRNA, rRna. IUPAC Biotech

A single stranded nucleic acid that contains the sugar ribose. There are several forms of RNA, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA [rRNA] (all involved in protein synthesis), as well as several small RNA’s whose functions are still being clarified. Certain viruses have RNA, instead of DNA, as their genetic material. [NIGMS]

A DNA like molecule. Different kinds of RNA exist that play specific roles in the process of gene expression.  NHLBI

An organic acid composed of repeating nucleotide units of adenine, guanine, cytosine, and uracil, whose ribose components are linked by phosphodiester bonds. Messenger RNA (mRNA) is the intermediate between the genetic message (DNA) and protein.  Narrower terms: miRNA, mRNA, hnRNA precursor RNA, rRNA, scRNA, siRNA, snRNA, snoRNA, stRNA,  tRNA Related terms: ribosomes, ribozymes, RNA polymerase, RNA splicing; Gene definitions: cDNA; Microarrays Northern blotting; Omes & omics ribonome, ribonomics  
RNA databases Databases & software directory
RNA World Institut fur Molekulare Biotechnologie, Jena, Germany

RNA amplification: Amplification of  messenger RNA (mRNA). Related terms:  amplified antisense RNA; Expression, genes & beyond  

RNA binding proteins: Protein categories
RNA biochips, RNA chips: Microarrays categories
RNA biomarkers: Biomarkers

RNA decoys. RNAs used to competitively bind pathogenic protein molecules in order to modulate their activity.  

RNA drug targets: Drug targets

RNA dynamics: Many recently discovered RNA functions rely on highly complex multistep conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA cotranscriptional folding, ligand sensing and signaling, site-specific catalysis in ribozymes, and the hierarchically ordered assembly of ribonucleoproteins. RNA dynamics are encoded by both the inherent properties of RNA structure, spanning many motional modes with a large range of amplitudes and timescales, and external trigger factors, ranging from proteins, nucleic acids, metal ions, metabolites, and vitamins to temperature and even directional RNA biosynthesis itself.  RNA dynamics: it is about time. Al-Hashimi HM, Walter NG. Curr Opin Struct Biol. 2008 Jun;18(3):321-9. Epub 2008 Jun 9.

RNA editing:  Kimball's Biology 
Wikipedia     Google = about 17,600 Jan. 15, 2004; about 361,000 Nov 10, 2006

RNA folding: While protein folding has garnered much attention over the last decade, RNA folding has received much less interest. From a theoretical point of view, one reason for this is the large molecular weight of RNA chains and role of electrostatics and counter ions in RNA folding. However, with recent techniques developed in protein folding, we have started to tackle the RNA problem. We are currently collaborating with several experimental groups at Stanford (Herschlag, Doniach, and Chu) to combine and compare our simulation results to experiment. This allows us to validate our simulations and allows one to refine the experimental data to yield more information about the structure and nature of folding. Vijay Pande, Pande Group Projects, Stanford Univ. US,

RNA genes, rRNA genes: Gene categories See also  RNA computational molecular archaeology

RNA genomics:  A few years ago, it became technically possible to detect the level of expression of large numbers of mRNAs in a sample at once, by hybridizing to surface immobilized arrays of nucleic acids. The first of these developed used arrays of photolithographically synthesized oligonucleotides (Lockhart et al., 1996). The use of these arrays to monitor gene expression got off to a slow start, largely because the technology was developed commercially and was expensive, which speeded the development of a number of non- array- based methods to survey mRNAs that are not widely used in research labs and that I will not review here. More recently, cheaper and nonproprietary means to produce arrays from PCR products were developed (DeRisi et al., 1997). Propagation of this later technology for making nucleotide arrays has greatly increased the speed at which gene expression monitoring methods are being adopted and producing important results.  Roger Brent "Genomic biology" modified version of his article in Cell 100: 169-183 Jan 2, 2000

RNA-Induced Silencing Complex: A multicomponent, ribonucleoprotein complex that cleaves specific mRNAs ( RNA, MESSENGER) which are targeted for degradation by homologous dsRNAs ( RNA, DOUBLE-STRANDED) during the process of RNA INTERFERENCE. It includes siRNA ( RNA, SMALL INTERFERING) that is generated from the specific dsRNA. MeSH 2003

RNAi RNA interference:  A gene silencing phenomenon whereby specific dsRNAs ( RNA, DOUBLE- STRANDED) trigger the degradation of homologous mRNA ( RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA- INDUCED SILENCING COMPLEX (RISC). DNA METHYLATION may also be triggered during this process. MeSH 2003
Nature Reviews Focus on RNAi 

Broader terms: gene expression regulation gene manipulation, gene silencing,  Post- transcriptional gene silencing PTGS; Narrower terms: miRNA, siRNA Related terms: gene disruption, knockout, RNA silencing

RNAi therapeutics: Interfering RNA (RNAi) offers tremendous therapeutic promise to silence genes that give rise to bad, proteins and, therefore, disease. RNAi Therapeutics: Challenges in Drug Development and Delivery thoroughly evaluates the field of RNAi therapeutics, with particular attention to the prospects and challenges faced in RNAi delivery. This report is a comprehensive blueprint for moving RNAi from the bench to the bedside.  Insight Pharma reports  RNAi Therapeutics, 2005

RNA ligand: Any RNA used to modulate gene or protein expression by protein binding. 

RNA polymerase:   The movement of RNA polymerase (RNAP) along DNA during transcription is a complex set of different activities, including initiation, elongation, pausing, backtracking, and arrest. A complete understanding of how this molecular machinery works requires characterization of the individual activities, when and why they occur, what structural components are required in each case, and what the biochemical parameters are. Since ensemble measurements will give only averages across a mixture of molecules engaged in a variety of these different behaviors, single molecule measurements may be the only way to examine the characteristics of each type of behavior independently NIGMS  "Single Molecule Detection and Manipulation Workshop" Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17- 18, 2000  Related terms: DNA-directed RNA polymerase; Ultrasensitivity single molecule

RNA precursors: RNA copies from DNA that exactly represent the genome sequence. This RNA cannot be used for producing protein until RNA splicing takes place. During this procedure the phosphodiester bonds at exon- intron boundaries are cleaved and the intron is excised. Consequently a new bond is formed between the ends of the exons. The resulting RNA is mature RNA which can be translated into protein. MeSH, 1988  Related/equivalent? term: precursor RNA

RNA probes:  RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus- sense RNA probes, minus- sense RNA probes, and antisense RNA probes. MeSH, 1989  Related terms: DNA probes

RNA processing vocabulary: Ulrich Melcher, 2004 about 50 terms l

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RNA splice sites:  Nucleotide sequences located at the ends of exons and recognized in pre- messenger RNA by the SPLICESOME. They are joined during the RNA SPLICING reaction, forming the junctions between exons.  MeSH, 2001

RNA splicing:  The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm. MeSH, 1982 Broader term: Sequences, DNA & beyond   splicing

RNA stability: The extent to which an RNA molecule retains its structural integrity and resists degradation under changing conditions in the cell or during isolation, purification, storage or other physical or chemical manipulations. MeSH 2000

RNAse H ribonuclease H: An endoribonuclease that specifically hydrolyzes the phosphodiester bonds of RNA hybridized to DNA. This enzyme does not digest single- or double-stranded DNA. 

RNAi target validation: Drug targets
RNA transcription:
 See Sequencing transcription

RNA transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms. MeSH 2003

RT-PCR: Gene amplification & PCR

short hairpin RNA shRNA: Wikipedia 

Small cytoplasmic RNA scRNA:  any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote.  DDBJ/ EMBL/ GenBank Feature Table

Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).  MeSH, 2000 

Small interfering RNA siRNA: Small ANTISENSE RNAs (20 -25 nucleotides) that are generated from specific dsRNAs ( RNA, DOUBLE- STRANDED) which trigger targeted mRNA ( RNA, MESSENGER) degradation ( RNA INTERFERENCE). They serve as guides for the cleavage of homologous mRNA in the RNA- INDUCED SILENCING COMPLEX. The same ribonuclease, Dicer, that is required for processing of the dsRNAs to siRNA is also involved in processing MICRORNAS (miRNAs) from their precursor RNAs. MeSH 2003

Synthetic short double-stranded RNA molecules that have been shown to inhibit gene expression in mammalian and other cells by several orders of magnitude. Broader term: microRNAs See also under antisense cleavers & blockers: Pharmaceutical biology  Related terms: Functional genomics   Genetic & Genomic Manipulation

small nuclear RNA snRNA: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors. MeSH, 1986 

Small nuclear RNA; any one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions. DDBJ/ EMBL/ GenBank Feature Table

Pronounced "snurps"  Related terms: Cell biology spliceosome   RNA interference RNAi

Small nucleolar RNA snoRNA: Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.  MeSH, 2000 

small temporal RNA stRNA:  Two ~ 21-nt RNAs regulate C. elegans temporal development, and we argue that one of these RNAs is likely to regulate developmental timing in bilaterian animals.  We propose that these types of RNAs be called small temporal RNA (stRNAs). Genome sequence comparisons and expression analyses among bilaterian animals may reveal additional stRNAs that regulate other developmental transitions. Amy E Pasquinelli et. al "Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA" Nature 6808: 86-89, 2 Nov. 2000  Broader term: microRNAs; Related term: RNA interference RNAi

SMaRT spliceosome- mediated RNA trans- splicing technology: A technique that can effectively reprogram the genetic message at the mRNA level by splicing out the mutated parts of a gene and replacing it with the normal message by spliceosome- mediated trans -splicing. Trademarked by Intronn LLC. 

spliced leader RNA: The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre- mRNAs by TRANS- SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).  MeSH, 1999

spliceosomes: Cell biology

start codon:  The set of three nucleotides in an mRNA molecule with which the ribosome starts the process of translation. The start codon sets the reading frame for translation. The most commonly used start codon is AUG, which is decoded as methionine in eukaryotes and as N-formylmethionine in prokaryotes. AUG appears to be the only start codon used by eukaryotes, while in bacteria, GUG (valine) may sometimes be employed. FAO  Related terms: initiation codon; initiator  

stop codon: Termination codon A set of three nucleotides for which there is no corresponding tRNA molecule to insert an amino acid into the polypeptide chain. Protein synthesis is hence terminated and the completed polypeptide released from the ribosome. Three stop codons are found: UAA (ochre), UAG (amber) and UGA (opal). Mutations which generate any of these three codons in a position which normally contains a codon specifying an amino acid are known as nonsense mutations. Stop codons can also be called nonsense codons. See chain terminator; nonsense mutation; suppressor. [FAO]

target:   The material -- DNA or RNA - that one exposes to the probes on a microarray so that hybridization can be measured subsequently. May also refer to molecules in the body that may be addressed by drugs to produce a therapeutic effect.  CHI High- Content Analysis Market Outlook report, 2004    See also Drug targets for a different kind of target.

target-specific siRNA: Drug targets

terminator codon: Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids MeSH, 1995

tiny RNAs: See micro-RNAs

trans-acting RNA: A Trans- Acting RNA as a Control Switch in Escherichia coli: DsrA Modulates Function by Forming Alternative Structures Richard A. Lease*,  Marlene Belfort, Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and School of Public Health, State University of New York at Albany, PNAS, 97 (18) 9919- 9924, August 29, 2000

trans-cleaving ribozyme: A ribozyme that acts by binding RNA molecules via base- pairing, cleaving the bound target RNA and releasing the cleavage products.

trans-splicing group I ribozyme. A ribozyme capable of recognizing and base- pairing with a target mutant RNA, cleaving the mutant sequence and ligating a wild- type sequence onto the normal cleavage fragment. Can also catalyze trans -splicing of downstream exons to free upstream exons.  

transcription: Sequences, DNA & beyond
transcription factors: Expression gene & protein
transcriptome, transcriptomics: -Omes & -omics

transfer RNA tRNA:  A single-stranded RNA molecule containing about 70- 90 nucleotides, folded by intrastand base pairing into a characteristic secondary (“cloverleaf”) structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis. IUPAC Biotech

The small RNA molecules, 73- 80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains. MeSH, 1972

Mature transfer RNA, a small RNA molecule (75 - 85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence DDBJ/ EMBL/ GenBank Feature Table

trans-splicing: The joining of RNA from two different genes. One type of trans- splicing is the "spliced leader" type (primarily found in protozoans such as trypanosomes and in lower invertebrates such as nematodes) which results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs. Another type of trans- splicing is the "discontinuous group II introns" type (found in plant/ algal chloroplasts and plant mitochondria) which results in the joining of two independently transcribed coding sequences. Both are mechanistically similar to conventional nuclear pre- mRNA cis- splicing. Mammalian cells are also capable of trans- splicing. MeSH, 1999

uracil: A nitrogenous base normally found in RNA but not DNA; uracil is capable of forming a base pair with adenine. DOE

Alnylam Glossary  30 plus terms defined
DDBJ/ EMBL/ GenBank Feature Table, Version 6.7, 2007, 100 + definition.
DOE, Human Genome Project Information, Oak Ridge National Laboratory, Dictionary of Genetic Terms. 2007, 100+ definitions.  
Insight Pharma Reports  RNAi Therapeutics, 2005
IUPAC  International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions
MeSH Medical Subject Headings, (PubMed Browser) National Library of Medicine, Revised annually.  250,000 entry terms, 19,000 main headings. 
Nature Reviews Focus on RNAi 
RNAi Gateway, BioMedCentral 

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IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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