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 http://www.chairs.gc.ca/english/profile/viewprofile.cfm?ID=709

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: presents an opportunity to manipulate gene expression within the cells to treat various diseases, and acts as a powerful tool for studying gene function utilizing antisense agents to manage the diseases by regulating the expression of the specific factor that actually causes the particular disease. Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message.  Gitanjali Kher, ... Ambikanandan Misra, in Challenges in Delivery of Therapeutic Genomics and Proteomics, 2011 https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/antisense-technology

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  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 2.7.7.6.  MeSH, 1998  Related term: RNA polymerase RNAP

ds: Double-stranded (DNA or RNA)

eliRNA expressed long inhibitory dsRNA:   http://nar.oxfordjournals.org/cgi/reprint/34/13/3803.pdf 

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 http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-12-014.html

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 http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-13-014.html

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. 

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 http://www.rinnlab.com/  
Wikipedia http://en.wikipedia.org/wiki/Long_non-coding_RNA 

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  http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

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: 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 http://www.nature.com/reviews/focus/microrna/index.html 

non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xistand HOTAIR. The number of non-coding RNAs within the  human genome is unknown; however, recent transcriptomic  and  bioinformatic studies suggest that there are thousands of them.^{[1][2][3][4][5][6]} Many of the newly identified ncRNAs have not been validated for their function.^[7] It is also likely that many ncRNAs are non functional (sometimes referred to as junk RNA), and are the product of spurious transcription.^[8][9]  Wikipedia accessed 2018 Nov 10 https://en.wikipedia.org/wiki/Non-coding_RNA  

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 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html  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 1992a,  b, 1996). ... Retroviruses are broadly divided into two categoriessimple and complexdistinguishable 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, 1997  https://www.ncbi.nlm.nih.gov/pubmed/21433340

reverse transcription: Gene amplification & PCR

ribonome: The population of RNA- coding regions of the genome. Mark Gerstein "What is Bioinformatics? Omes Table" 2001  http://bioinfo.mbb.yale.edu/what-is-it/omes/omes.html   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 http://www.pnas.org/cgi/content/full/97/26/14085

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 https://www.nature.com/articles/nsb1100_954

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. was a Systems Biology company  

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:  Characterizing protein-protein and protein-RNA interaction networks is a fundamental step to understanding the function of an RNA-binding protein. In many cases, these interactions are transient and highly dynamic. Therefore, capturing stable as well as transient interactions in living cells for the identification of protein-binding partners and the mapping of RNA-binding sequences is key to a successful establishment of the molecular interaction network. Yeh HS., Chang JW., Yong J. (2016) Ribo-Proteomics Approach to Profile RNA–Protein and Protein–Protein Interaction Networks. In: Lin RJ. (eds) RNA-Protein Complexes and Interactions. Methods in Molecular Biology, vol 1421. Humana Press, New York, NY https://www.ncbi.nlm.nih.gov/pubmed/26965265

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 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Wikipedia http://en.wikipedia.org/wiki/Ribosomal_RNA  

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 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.  Ute Schepers RNA interference in practice, Wiley VCH GmbH 2005 https://books.google.com/books?id=0370VYwf6y8C&printsec=frontcover#v=onepage&q&f=false

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:  Wikipedia http://en.wikipedia.org/wiki/RNA_editing   Kimball's Biology Pages http://www.biology-pages.info/R/RNA_Editing.html