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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/
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
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. 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 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 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
ribotyping:
RESTRICTION FRAGMENT LENGTH POLYMORPHISM analysis of rRNA genes that is used for
differentiating between species or strains MeSH 2001 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 binding proteins: Protein categories 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 RNA folding:
the process by which a linear ribonucleic acid
(RNA) molecule acquires secondary structure through intra-molecular
interactions. The folded domains of RNA molecules are often the sites of
specific interactions with proteins in forming RNA�protein (ribonucleoprotein)
complexes. Nature RNA folding
https://www.nature.com/subjects/rna-folding
Since RNA is
single-stranded, it can fold upon itself and form structures that are
protein-like in both appearance and functionality. HHMI
Biointeractive
https://www.hhmi.org/biointeractive/rna-folding
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
RNA,
Mitochondrial: RNA molecules
encoded by the MITOCHONDRIAL GENOME. MeSH 2019
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 http://www.nigms.nih.gov/news/reports/single_molecules.html#examples
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 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.
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 http://en.wikipedia.org/wiki/Small_hairpin_RNA
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 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
(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
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.
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 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
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
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. See also Drug
targets for a different kind of target.
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 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 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 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
RNA resources IUPAC definitions are reprinted with the permission of
the International Union of Pure and Applied Chemistry.
RNA glossary & taxonomy
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Evolving Terminologies for Emerging Technologies
Comments? Questions?
Revisions?
Mary Chitty MSLS
mchitty@healthtech.com
Last revised
January 09, 2020
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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.
Wikipedia http://en.wikipedia.org/wiki/Long_non-coding_RNA
micro-RNA
miRNA:
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
nonsense codons: See under stop codons
Northern blotting: Microarrays
nucleic acids: DNA
or RNA
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
Wikipedia http://en.wikipedia.org/wiki/Ribosomal_RNA
ribosomics: -Omes
& -omics
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 amplification:
Amplification of messenger RNA (mRNA). Related terms:
amplified antisense RNA; Expression, genes &
beyond
RNA biochips, RNA chips: Microarrays
categories
RNA biomarkers: Biomarkers
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
Nature
Reviews Focus on RNAi
http://www.nature.com/focus/rnai/
RNA ligand: Any RNA used to modulate gene or
protein expression by protein binding.
Broader term: microRNAs See also under antisense cleavers &
blockers: Pharmaceutical biology Related terms: Functional
genomics
transcription factors:
Expression gene & protein
transcriptome, transcriptomics:
-Omes
& -omics
Wikipedia http://en.wikipedia.org/wiki/Transfer_RNA
DDBJ/ EMBL/ GenBank
Feature Table, Version 2017 http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Nature Reviews
Focus on RNAi http://www.nature.com/focus/rnai/
NCBI, DNA and RNA databases
https://www.ncbi.nlm.nih.gov/guide/dna-rna/
How
to look for other unfamiliar terms
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