The Dictionary of Genomics, Transcriptomics and Proteomics

By Guenter Kahl

Now in its fifth edition and for the first time available as an electronic product with all entries cross-linked.

This very successful long-seller has once again been thoroughly updated and greatly expanded. It now contains over 13,000 entries, and comprehensively covering genomics, transcriptomics, and proteomics. Each entry contains an extensive explanation, including a comprehensive listing of synonyms and acronyms, and all formulas have been redrawn to create a uniform style, while most of the figures are custom designed for this dictionary.
The ultimate reference for all terms in the -omics fields.

• Language: English
• Publisher: Wiley
• Release date: Jun 17, 2015
• ISBN: 9783527678662

Book preview

Preface

The precursors of the present

have been on the market for about 19 years, starting out with a single slim book entitled Dictionary of Gene Technology, that tried to tackle the then-immense masses of 4,000 terms of this more technical branch of Molecular Biology. Ever since then and in 4–5 year intervals, the amount of knowledge roughly doubled, finally leading to three volumes in 2009, each of them out-sizing the first book by volume and numbers of terms. Around 12,000 technical terms of the omics era accumulated by then, and this development is by no means over. As a result, in the present four volumes of the Dictionary, again bigger in size and volume, another 3,000 terms have been added, amassing around 15,000 terms, to cope with the racy development of genomics, transcriptomics and proteomics. To keep pace with the expected future growth of knowledge and to respect the current tendency towards electronic media, the present four-volume edition will be the last printed version, and from now on only be electronically available.

Notwithstanding this adaptive change, the author nevertheless felt that the share of proteomics had to be increased, with all those newly discovered chromatin proteins, components of many nuclear multi-protein complexes, RNA-binding proteins, generally nuclear proteins with all their variants and modifications in mind. Additionally, the growing importance of RNAs had to be appreciated (with an immense repertoire of novel non-coding RNAs, small RNAs, regulatory RNAs, or generally, RNAs transcribed from the non-coding genome). As explained in prefaces of previous editions, new terms will soon be created, new techniques will be introduced, and this dictionary inevitably will have omissions. Though I have striven to avoid errors, ambiguities and misinterpretations, certain inadequacies will be discovered, and I apologize for them at this point. It only remains to ask Confucius for a good closing word:

(Kongzi, Confucius, 551-479 BC, Chinese philosopher and reformer)

Seligenstadt am Main, February 2015

Günter Kahl

A cautionary note to readers

Is the comprehensive Dictionary in your hands worth its price, and is it appropriate in the 21st century to carry a 5–6 kg heavy tome around with you? Well, every single bit of information in this tome is also deposited somewhere in the internet, and mostly for free! Yes, somewhere! However, in science, it is not an issue, that something is somewhere freely available, but the something must be accessible rapidly, and it must be trustworthy. So, speed and credibility are issues. And everybody, who spent an intolerable lot of her/his precious time to dig out a special term or a method in the swamp of internet, still can't be sure of which of the many variants contributed by mostly anonymous people she or he can really trust. At this point it is best to close your browser and consult

and the index of all four volumes. And instead of meandering around and believing in the credibility of an anonymous contributor to an online discussion forum, you are better off trusting Kahl's Dictionary. In contrast to many risky internet sources, which demand time-wasting efforts to finally find an inadequate or even faulty description of your something, the present Dictionary provides a reliable authority. Now, why then should you otherwise sell your limited time and resources down the river?

Instructions for Users

All the entries are arranged in strict alphabetical order, letter by letter. For example, mismatched primer precedes "mismatch gene synthesis, and this is followed by mismatch repair. Or, photo-digoxygenin precedes photo-footprinting, which in turn precedes photo-reactivation". In case an entry starts with, or contains a Roman, Greek or Arabic numeral, it has first to be translated into Latin script. A few examples illustrate the translation:

For help, the user may consult the Greek alphabet and the Roman numerals below.

The main entry title, printed in bold type, is followed by synonyms in parentheses. Italicized letters in titles (and text) of entries indicate use of these letters for abbreviations.

Cross referencing is either indicated by an arrow, or the words see, see also, and compare.

By using the cross-references as a road map between definitions, the reader will gain an appreciation of molecular biology as an integrated whole rather than a collection of fragments of isolated information.

Organismal name: The formal Latin binomial names of organisms are italicized, whereas common names and derivatives of the Latin names are not.

Etymology of the terms: Most biological terms originate from Greek or Latin language. Only the most common word roots are defined in this dictionary.

Greek Alphabet and Roman Numerals

Greek alphabet

Roman numerals

Abbreviations and Symbols

Acronyms

Many scientists and editors, but also innocent readers lament the proliferation of acronyms in the scientific and technical literature, especially their luxurious use and misuse in the description of technologies. This author is fully aware of the impertinence for layman and expert alike to be exposed to the millions of existing acronyms, and the millions to come. Although many acronyms are simply annoying, many of them confusing and superfluous, the technical all-day language makes use of others, that I consider valuable.

Now, how to discriminate useful from unnecessary, and good from bad acronyms? A useful (good) acronym for a technique should be unique, pronounceable with normal linguistic capabilities, memorably short and easily recognized, should not be fantastic, but best include the first letters of each word in the full name of the technique. Given all these attributes are present, a useful acronym doubtless simplifies communication and eases daily laboratory language. But this useful acronym will be trivialized, if a myriad of minimal variations of the original technique will be labeled by new unrelated terms: a disaster for communication. One of the reasons for the avalanche of acronyms, especially in the area of Genomics, Transcriptomics and Proteomics is the publication of a particular method by two (or more) different researchers, who introduce their own, but differing acronyms for identical things. The resulting confusions are persisting, unless a committee clarifies the situation. Normally, one such acronym will survive, the others will die out. The worst is a co-existence of two different acronyms for identical technologies.

Unnecessary (bad) acronyms are creations, that, for example, describe a series of combined individual techniques in a workflow, each of which was already labeled with a specific acronym. Also, if one expects that a particular novel technique will only be used once, namely by the inventor, then any acronym will be obsolete. Additionally, the use of an acronym must be avoided, if this acronym already exists in other scientific fields or is in popular use. Unfortunately, a bewildering diversity exists for this category of bad acronyms. However, since acronyms will be necessary components of scientific language in future, the scientist creating a new acronym should at least be sure that it does not already exist. Disappointingly, in too many cases the same acronym is misused for totally different techniques or items (exemplified with PAP, look there). Simply consult Nature Methods 8: 521 (2011) with a comment on NUAPs (no unnecessary acronyms, please).

In the four volumes of this Dictionary, all available acronyms are mentioned and the underlying meaning shortly explained. The author leaves it to the reader to decide whether an acronym belongs to one or the other category. However, the author would very much welcome a diffidence to create ever increasing numbers of acronyms and thereby to add to the Babylonian confusion in Genomics, Transcriptomics and Proteomics.

A

A

Abbreviation for adenine (6-aminopurine, Ade), a → purine base characteristic for DNA and RNA.

Single-letter code for alanine, an → amino acid.

AA-aRNA

See → aminoallyl-aRNA.

AAD

See → arbitrarily amplified DNA.

A-allele

Any → single nucleotide polymorphism that is caused by the exchange of either a cytidine, a guanine or a thymidine for an adenine. See → C-allele, → G-allele, → T-allele.

AATAAA sequence

See → poly(A) addition signal.

Ab

See → antibody.

Abasic site

Any gap in a nucleic acid sequence that originates from the loss of a → base. See → AP endonuclease, → AP site.

ABC-LAMP

See → alternately binding quenching probe competitive loop-mediated isothermal amplification.

ABC-PCR

See → alternately binding probe competitive polymerase chain reaction.

ABC technique

A method for the localization of histologically significant → antigens and other markers in tissue sections. In short, the section is first incubated with primary antiserum raised against the antigen of interest (e.g. containing a rabbit antibody against a tumor-associated antigen). Then a biotin-labeled secondary antibody is added (in this case: biotinylated anti-rabbit IgG). Subsequently a pre-formed avidin-biotinylated enzyme complex (ABC), probably a three-dimensional array of many biotinylated enzyme molecules crosslinked by avidin binds to the biotinylated secondary antibody, which is detected by an incubation of the section with the substrate of the enzyme (that is converted to a colored product).

ABC transporter

See → ATP binding cassette transporter.

Aberrant RNA

Aberrant RNA (aRNA): Any (usually small) RNA, that appears after DNA damage (by e.g. EMS), and is recognized by → RNA-dependent RNA polymerase, that catalyzes the formation of → double-stranded RNA from the aRNA template, and thereby induces the → RNA interference pathway.

Aberrant RNA (abRNA): A hypothetical RNA molecule, produced directly from a → transgene, being double-stranded (aberrant) and serving as template for the synthesis of short complementary RNA molecules (cRNA) by specialized cellular RNA-dependent RNA polymerases (RdRPs). These cRNAs in turn could pair with transgene → messenger RNAs to form double-stranded RNAs (e.g. catalyzed by cellular RNA-dependent RNA polymerases), the substrates for mRNA degradation. See → RNA interference.

Aberrant splicing

See → alternative splicing.

ABF

See → abscisic acid-responsive element-binding factor.

ab initio gene prediction

The identification of genes in a DNA sequence by specific computer programs, that predict individual gene features such as e.g. → consensus sequences located in the → promoter, the → exon-intron or → intron-exon boundaries, the → 3'-untranslated region, the → poly(A) addition sequence, or others, also located far away from a gene as e.g. → enhancers. Latin ab initio means from the start.

A-block

Any stretch in either one or both DNA → strands of → core promoters in Caenorhabditis elegans, consisting of three to five → adenines (As), that disfavors nucleosome occupancy (i.e. prevents normal → nucleosome positioning). The number of such A-blocks is therefore inversely correlated with the activity of the adjacent gene. See → T-block.

ABM paper

See → aminobenzyloxymethylcellulose paper.

Abortive expression

The defective expression of a foreign gene in a transgenic environment (e.g. the constitutive expression of a transferred gene in the receiving organism that was inducible in the organism of origin). Abortive expression usually reflects the different complement of → transcription factors, but may also be due to so-called → position effects in the new → chromatin microenvironment.

Abortive infection (non-productive infection; incomplete infection)

The infection of a bacterium by → bacteriophages, which does not lead to the production of infective virus though some or all virus components are synthesized in the host cell. Consequently neither → lysis nor → lysogenization occur.

Abortive initiation

The interruption of → transcription of a gene, after about 9-11 nucleotides have been polymerized by → DNA-dependent RNA polymerase II. The RNA polymerase does not move on the → promoter during this process, but melts a longer region of the underlying DNA and pulls a short section of the → downstream DNA towards its core. Abortive initiation leads to the dissociation of the → messenger RNA fragment from the → template, so that the → initiation process can be repeated. See → internal initiation.

Abortive splicing

Any → splicing process that uses → cryptic splice sites or does not lead to the correct ligation of → exons. Thus the final splice product is a non-functional mRNA.

Abortive transcription

The blockage of the → DNA-dependent RNA polymerase II-catalyzed → elongation of a 6-10 nucleotide RNA in statu nascendi, that leads to a cessation of RNA synthesis and a release of a truncated (and non-functional) → messenger RNA.

Abortive transduction (abortive transformation)

A process whereby transduced DNA molecules persist in the cytoplasm of the recipient cell as nonreplicating but stable (circular) entities.

Abortive transfection (transient transfection)

The uptake of foreign DNA into cultured animal or human cells, mediated by → direct gene transfer techniques that does not result in its stable integration into the host cell's genome.

Abortive transformation

See → abortive transduction.

A-box

The consensus sequence 5′-TGGCNNAGTGG-3′ in → transfer RNA and 5S ribosomal RNA genes that functions as internal control sequence for → DNA-dependent RNA polymerase III.

ABPP

See → activity-based protein profiling.

ABRE

See → abscisic acid-responsive element.

abRNA

See → aberrant RNA.

Abscisic acid-responsive element (ABA-responsive element, ABRE)

A conserved cis-regulatory sequence element (consensus sequence: 5′-C/TACGTGGC-3′; Arabidopsis thaliana: 5′-CACGTGG/TC-3′; Medicago truncatula: 5′-CAC/TGTGG/TC/G-3′) in the → promoters of more than 100 abscisic acid-responsive plant genes (e.g. genes encoding myo-inositol-1-phosphate synthase, calcium-lipid-binding protein, trehalose phosphatase, dehydrin, basic leucine zipper T7, phosphoribosylanthranilate transferase, Rab proteins, and others). ABREs are associated with more degenerate → coupling elements, and both are necessary and sufficient for abscisic acid-induced gene activation that is mediated by → ABA-responsive element-binding factors. These proteins recognize and bind to the ABREs.

Abscisic acid-responsive element-binding factor (ABF)

Any one of a class of → basic leucine zipper proteins (bZIPs) that specifically recognize and bind socalled → abscisic acid (ABA)-responsive elements (ABREs) in the → promoter of ABA-responsive plant genes. The expression of ABFs is induced by ABA and a variety of different stresses (e.g. salt and drought, generally desiccation stresses) and activate more than 100 ABA- or stress-responsive genes in plants.

Absolute targeting frequency (ATF)

The number of cells, in which recombinations occurred between a transferred foreign gene and the recipient genome divided by the total number of transformed cells.

Abundance

The average number of molecules of a specific → messenger RNA (mRNA) or a specific protein (also mRNA or protein classes) in a given cell at a given time. For example, in a typical cell, 5-10 species of superabundant → cDNAs comprise at least 20% of the mass of messenger RNA, 500-2,000 intermediately expressed mRNAs comprise 40-60% of the mRNA mass, and 10,000-20,000 rare messages account for 20-40% of the total mRNAs. This average distribution varies tremendously between different cells, or cells in different stages, different tissues, organs and organisms.

Abundant RNA

See → high abundancy messenger RNA.

Abzyme (antibody enzyme; catalytic monoclonal antibody, catmab)

An →antibody with enzymatic function(s).

ACB-PCR

See → allele-specific competitive blocker polymerase chain reaction.

Acceptor (recipient)

Any cell that receives genetic information (DNA or RNA) from a → donor, e.g. in bacterial → conjugation.

Acceptor end

The trinucleotide CCA at the 3′ end of → transfer RNA molecules. The terminal A becomes esterified to the amino acid via the 2′ – or 3′ position. See → acceptor stem.

Acceptor junction

See → acceptor splicing site.

Acceptor region

See → H-DNA.

Acceptor splice junction (acceptor splicing site, acceptor junction, acceptor splice signal, 3′-splice site, 3′-SS, right splicing junction, splice acceptor site)

The junction between an → exon and an → intron at the 3′ end of the intron in eukaryotic → split genes with the → consensus sequence AG: G. The colon indicates the splice point. Compare → donor splice junction, → GT-AG rule. See → splice junction.

Acceptor splicing site

See → acceptor splice junction.

Acceptor stem

The double-stranded extension of → tRNA molecules that carries a 3′- CCA -5′ to which amino acids are attached.

Accession

The record for a specific DNA sequence (or → clone) deposited in a public database (e.g. → GenBank, EMBL, or → DDBJ). See → accessioned clone, → accession number.

Accessioned clone

Any → clone whose sequence has been submitted to a public database and been assigned an → accession number.

Accession number

GenBank accession number: A unique identifier assigned to the entire sequence submitted to GenBank, that consists of a combination of letters and numbers, usually in the format of one letter followed by five digits (e.g., M12345) or two letters followed by six digits (e.g., AC123456). A GenBank accession number is a unique identifier for a complete sequence record, while a Sequence Identifier (e.g. Version, GI, or ProteinID) is an identification number assigned just to the sequence data.

RefSeq accession number: A unique identification number for a complete RefSeq sequence record, that consists of two letters followed by an underscore and six digits (e.g., NT_123456). The first two letters of the RefSeq accession number describe the type of sequence in the record: NT_1…(constructed genomic → contigs), NM_1…(the → cDNA sequences constructed from → messenger RNA), NP_1…(proteins), and NC_1…(chromosomes).

Accessory genome

A part of a bacterial → genome (or genome of any other organism), that is specific for a particular species, and therefore variable from species to species. Accessory genomes comprise from 200 to more than 1.500 specific genes, that code for socalled additional functions not absolutely needed for survival (e.g. donor properties, rare metabolic pathways, resistances towards toxins, or symbiotic or pathogenic peculiarities). For example, the genome of Pseudomonas aeruginosa is composed of a socalled → conserved nuclear genome and the accessory genome, consisting of sequences from → phages or → transposons, and frequently encoding transporter proteins or proteins catalyzing steps in degradation pathways for secondary metabolites or toxic compounds as e.g. antibiotics, terpenes or halogenated carbohydrates. Many regions of accessory genomes can be mobilized, i.e. excised from the genome, circularized, and transferred across species boundaries.

Accuracy

The average number of → nucleotides incorporated into a new DNA → strand, complementary to a → template strand, before an error (i. e. the incorporation of a wrong base) occurs. Compare → fidelity. See → error rate.

In general terms, accuracy describes how close a measured or calculated value (generally, parameter) is to the true value.

Ac-Ds system

See → activator-dissociation system.

ACE

See → affinity capture electrophoresis.

See → affinity coelectrophoresis.

See → amplification control element.

Acentric fragment

A → chromosome fragment that is the result of a chromosome breakage. Since it does not contain a → centromere, it is lost during mitosis.

ACES

See → artificial chromosome expression system.

Acetabularia

A large unicellular green alga of the order Dasycladaceae, used for grafting experiments, which demonstrated the nuclear control of cytoplasmic differentiation.

Acetylation

A → post-translational modification of proteins, i.e. the introduction of an acetyl residue (e.g. → histones are acetylated and consequently bind less strongly to DNA in → nucleosomes).

Acetylation island

Any genomic region, that is enriched in acetylated → histone H3 (H3Ac) and H4 (H4Ac) and histone H3 dimethylated on lysine 4 (H3K4me2), and usually maps to active → promoters, but also around → transcription start sites (TSSs) and downstream coding sequences. For example, the latent membrane protein 2A (LMP2A) promoter of the Epstein-Barr virus (EBV) genome in lymphoid cells is located on such an acetylation island, that also comprises a region between LMP2A and LMP1 promoters.

Acetylation mapping

The estimation of the number and precise location of acetyl groups in various → histones of → chromatin of a nucleus at a given time, probed with e.g. → chromatin immunoprecipitation.

Acetyl-CoA:histone acetyltransferase

See → histone acetyltransferase.

Acetylome

The entirety of acetylated proteins of a cell at a given time. Acetylated proteins can be detected by → mass spectrometry.

ACF1

See → ATP-dependent chromatin assembly factor.

AcGFP

See → Aequorea coerulescens green fluorescent protein.

ACGM

See → amplified consensus gene marker.

Achilles's heel cleavage

A comprehensive term for several techniques to cleave DNA at a single or small set of → restriction endonuclease → recognition sites in spite of the presence of more such sites. For example, a particular restriction site in a target DNA could be masked by the binding of a → transcription factor (or other → DNA-binding proteins as e.g. → lac repressor, → lex A protein, viral proteins), leaving all other sites accessible for a restriction methylase. This enzyme transfers a methyl group onto the C5 of a cytosyl residue of the recognition sequence. This methylation prevents cleavage of the site by the conjugate restriction endonuclease. After removal of the protein the target DNA can be restricted at the deprotected site(s). Instead of proteins, → triplexes can be used to mask a restriction site.

AchrDNA

See → Agrobacterium chromosomal DNA.

Acid amino acid

Any → amino acid that contains only one amino-, but two carboxy goups (example: aspartic acid). See → basic amino acid.

Acidic patch

A cluster of acidic amino acid residues in → histone H2A and → histone H2B, that is involved in → nucleosome-nucleosome interaction(s) and promotes nucleosome-nucleosome packing and the formation of the 30 nm fibre and thereby chromatin folding. The neutralization of just three acidic residues within this acidic patch on the nucleosome inhibits inter-nucleosome interactions. Additionally, the amino-terminal tail of → histone H4 from an adjacent nucleosome interacts with the acidic patch to mediate nucleosome-nucleosome interactions, which is, however, disrupted by the acetylation of H4K16 (i.e. inhibits chromatin compaction). The H4 tail can also interact with the acidic patch on its own nucleosome, and this interaction indirectly stabilizes the wrapping of DNA at the entry and exit points into and out of the nucleosome.

Acidic patch

Nucleosome structure and the acidic patch: a common interaction interface for many nucleosome-interacting proteins - The structure of the nucleosome (Protein Data Bank code 1AOI) is viewed down the superhelical axis of the DNA. Histones H3, H4, H2A and H2B are shown in light blue, green, yellow and red, respectively. The figure indicates the amino-terminal α-helix of H3 (H3αN), which organizes the penultimate 10 bp of the DNA, and the carboxy-terminal end of the H2A docking domain. Acidic residues on H2A and H2B (the ‘acidic patch’) that are involved in the interaction with the H4 tail and with nucleosome-interacting proteins (such as the latency-associated nuclear antigen (LANA) peptide, interleukin-33 (IL-33), regulator of chromosome condensation 1 (RCC1), silent information regulator 3 (Sir3) and high mobility group nucleosome-binding domain-containing protein 2 (HMGN2)) are indicated in bright red; additional residues that are implicated in the interaction interfaces with the proteins are shown in dark blue. The number of total histone residues implicated in all these protein-protein interfaces is relatively small, and all cluster in a contained region on the surface of the histone octamer. In the absence of these factors, the interaction of the H4 tail from a neighbouring particle with the acidic patch mediates nucleosome-nucleosome interactions, thereby promoting chromatin folding.

ACM-FISH

See → alpha, classical and midi satellite fluorescent in situ hybridization.

Acoustic droplet ejection (ADE)

A technique for the transfer of small volume droplets from a multi-well source plate (e.g. a → microtiter plate) onto an assay plate that is based on a focused pulse of acoustic waves applied to the bottom of the source plate. The acoustic impulse forces a droplet of precise volume to move. ADE eliminates all physical contact between the transducer instrument, the source plate, and the receiving multi-well microplate. ADE is employed for the transfer of small liquid volumes, the serial dilution of an original volume, and the transfer of volumes onto a microarray (e.g. a glass slide, or → nitrocellulose membrane).

Acoustic gene transfer

A method for the → direct gene transfer into plants which employs ultrasonic shock waves, generated by a laboratory sonifier, to induce microscopic cracks in the cell walls and permeability changes in the plasma membrane of the target cells (e.g. → protoplasts). Ultrasonically transferred genes are efficiently expressed and → transformation frequencies increased.

Acoustic microstreaming (micromixing)

A technique for the sensitive detection of low-abundance → cDNAs, that works with continuous acoustic mixing of the reaction mixture in → qPCR tubes at audio frequencies (150 Hz). Micromixing improves cDNA yields from → reverse transcription (RT) reactions of single-cell quantities of RNA (0.1–1 pg/µl) about 100fold, through reducing the number of cycles by 9 to 15, respectively.

ACP

See → architectural chromatin protein.

ACP (acyl carrier protein) tag: An 8 kDa (77 amino acids) → protein tag, that can be covalently fused to a target protein and specifically be labeled on the cell surface with coenzyme A (CoA) derivatives producing a covalent ester bond, a reaction catalyzed by ACP synthase (AcpS) of E. coli. In the labeling reaction, the substituted phosphopantetheine group of CoA is covalently attached to a conserved serine residue of the ACP-tag by a phosphopantetheinyl transferase (SFP synthase). The ACP tag itself can be covalently bound to a → fluorochrome, that can then be excited by laser light and detected by its emission light. Since the substrates of the ACP tag do not permeate the cell membrane, the tag itself is only suited to selectively label extra-cellular proteins, or extra-cellular portions of membrane proteins, or proteins bound to the cell surface as e.g. receptors. See → CLIP tag, → MCP tag, → protein tagging, → SNAP tag, also → protein fusion and purification technique, → expression vector (→ fusion vector).

ac-pre-miRNA

See → AGO2-mediated cleavage of the pre-miRNA.

ACP-PCR

See → annealing control primer polymerase chain reaction.

Acridine dye

Any one of a series of mutagenic heterocyclic compounds, including acridine and its derivatives. At low concentrations, aminoacridines (e.g. quinacrine) intercalate between the two strands of double-stranded DNA (dsDNA). Higher concentrations cause the binding of acridines to the outside of dsDNA, ssDNA, and ssRNA. Acridines interfere with DNA and RNA synthesis, cause frameshift mutations, and addition or deletion of bases. See → acridine orange, → acriflavine.

Acridine orange (3,6-bis-[dimethylamino]-acridinium chloride, euchrysine)

A basic acridine dye that binds to double-stranded nucleic acids by → intercalation, or to single and double-stranded nucleic acid by electrostatic interaction with the phosphate back-bone. Ultraviolet irradiation absorbed at 260 nm by a dye-dsDNA complex can be reemitted as fluorescence at 530 nm (green) or by single-stranded DNA or RNA at 640 nm (red). Acridine orange also functions as → mutagen. Sublethal concentrations of the dye are used for curing plasmids.

Acriflavine (euflavine, 3,6-diamino-10-methylacridinium chloride)

An → acridine dye producing → reading frame shift mutations.

Acrydite gel hybridization assay

A technique for the detection of specific DNA or RNA sequences and mutations in these sequences that is based on capture → oligonucleotides immobilized in a → polyacrylamide gel, through which the sample DNAs or RNAs are electrophoresed. If a sample DNA or RNA will find its complementary sequence in the gel, it will be captured (immobilized) and can be detected with either radioactive, luminescent or fluorescent label attached to it. In short, capture oligonucleotides are first synthesized and contain phosphoramidite (acrydite) groups at their 5′ termini. Then these modified oligonucleotides are mixed with acrylamide solution. Since acrydite is capable of free-radial copolymerization with acrylamide, the capture oligonucleotides are fixed in the gel. A complete gel usually has three zones: two zones without capture oligonucleotides flank a central zone with capture oligonucleotides. Now labeled single-stranded target DNAs or RNAs are electrophoresed through the gel. As complementary targets move into the capture zone, they are hybridized to the bound probes and thereby immobilized. Non-complementary targets will not hybridize and move through the capture layer. The acrydite gel hybridization assay can be used to purify specific nucleic acid sequences from complex and also crude DNA or RNA samples, and to detect even → single nucleotide polymorphisms (if the running temperature is increased in the presence of denaturants in the electrophoresis buffer).

Acrylamide

See → polyacrylamide gel.

Acrylamide-DNA

See → polyacrylamide-oligonucleotide conjugate.

Acrylamide gel electrophoresis

An infelicitous term for → polyacrylamide gel electrophoresis.

Acrylamide-HypNA

See → polyacrylamide-oligonucleotide conjugate.

Acrylamide-PNA

See → polyacrylamide-oligonucleotide conjugate.

Acrylamide-pPNA

See → polyacrylamide-oligonucleotide conjugate.

ACS

See → ARS consensus sequence.

Actidione

See → cycloheximide.

Actin

Any one of a series of highly conserved proteins that are involved in various types of cell motility, and maintenance of the cytoskeleton. Vertebrate cells contain three main groups of actin isoforms, coined α, β and γ, of which the α actins are major constituents of the contractile apparatus in muscle tissues. The β and γ actins co-exist in most cell types as components of the cytoskeleton and mediators of internal cell motility. Since actins are expressed at the same level in all cells nearly all the time, actin genes may serve as internal control in → gene expression experiments (as e.g. → Northern or → microarray analyses).

Actinomycetales

Gram-positive spore-forming soil bacteria that are responsible for the breakdown of complex substances such as cellulose, chitin and keratin. Producers of clinically important antibiotics (e.g. → streptomycin). Some Actinomycetales (Streptomycetes) are in use as a host-vector system for cloning. See also → actinomycin D.

Actinomycin C1

See → actinomycin D.

Actinomycin D (actinomycin C1, dactinomycin)

A polypeptide lactone antibiotic from Streptomyces chrysomallus, S. parvullus and S. antibioticus that intercalates with its chromophore between 5′-GpC-3′ of a DNA duplex molecule, its peptide side chains lying in the minor groove of the DNA double helix. The complex is stabilized by hydrogen bonds between the guanine base and the amino acid side chains of the antibiotic, by stacking forces between the chromophore ring and the guanosine sine base ring, and by numerous hydrophobic interactions between the peptide chains and the surface atoms of the minor groove of the DNA helix. Actinomycin D prevents gene expression by bacterial → RNA polymerase and eukaryotic RNA polymerases I and II.

Actin-related protein (ARP)

Any one of a series of cytoplasmic and nuclear proteins, that are functional and integral components of several → ATP-dependent chromatin remodeling complexes and → histone acetyltransferase complexes. Within a remodeling complex, ARPs (also monomeric actin) are organized in defined sub-assemblies. Some ARPs have specific functions. For example, within the INO80 complex, ARP8 serves as a → nucleosome recognition module, whereas ARP4 prefers free (H3-H4)2 over nucleosomes, and assists remodelers through binding to assembly or disassembly intermediates. In addition, nuclear ARPs assist in the spatial arrangement and dynamics of → chromatin within the nucleus (i.e. the organization of the nucleus), an activity that is independent of ARP function in the complexes.

Activated calf thymus DNA

DNA prepared from calf thymus that has been nicked and gapped by → DNase I, and serves as substrate for many → DNA polymerases.

Activating domain

See → activation domain.

Activation

The generation of reactive sites (functional groups) on the surface of relatively inert polymers (e.g. polyethylene, polypropylene, polystyrene, polycarbonate, polyamide or polytetrafluoroethylene) by a treatment with either electrical discharges (low-pressure plasma), UV irradiation and H2O2, or sulphuric acid in combination with oxidation mediators. Activation is a prerequisite for the efficient coupling of molecules such as oligonucletides, peptides or proteins to the polymer's surface. For example, if a polyolefine is activated with an oxygen plasma, the generated hydroxy (−OH), carbonyl- (C–O) or carboxy groups (−COOH) can be used to link socalled spacers, which expose functional groups (e.g. amino groups [−NH2], carboxyl groups [−COOH], epoxides or aldehydes [−HC–O]) for the coupling of peptides, → antibodies, enzymes, generally proteins, oligonucleotides, or DNAs.

Activation domain (AD; activating domain; C-terminal activation domain, CTAD, transcriptional activation domain)

A specific → 30–100 amino acid domain of → transcription factors, located at the C-terminus and rich in acidic amino acids that can form amphipathic α-helical structures and is necessary for the transcriptional activation of the target gene. For example, the yeast transcription factor GAL4 harbors such an activation domain, which can be discriminated into two regions (I: residues 148–236; II: residues 768–881), either of which activates transcription when fused to the → DNA-binding domain (residues 1–147). The activity of region I is directly proportional to its content of acidic residues. Principally, three different features of ADs can be discriminated: an acidic, negatively charged domain (e.g. in GAL4, GCN4), a glutamine-rich domain (e.g. in HAP1, HAP2, GAL11, OCT-1, OCT-2, Jun, AP-2, SRF, Sp1), and a proline-rich domain (e.g. in CTF/NF-1, AP-2, Jun, OCT-2, SRF). All these regions establish contacts to other proteins. Compare → DNA-binding domain.

Activation domain type

Any one of two differentially functional → activation domains of an → activator protein (definition a). Type I activation domains predominantly activates the → initiation of → transcription of the adjacent gene (examples: Sp1 or CTF), type IIA the → elongation (e.g. HIV1-Tat), and type IIB both initiation and elongation (e.g. VP16, p53, E2F1).

Activation-induced cytidine deaminase (AID)

A nuclear enzyme catalyzing the deamination of → cytidine to → uracil in single-, but not double-stranded DNA (or RNA) in vivo and in vitro. AID cooperates with the single-stranded DNA-binding protein replication protein A (RPA) and binds to → hot spots in the immunoglobulin variable region during → transcription, leading to cytosine deamination. According to the DNA deamination model of → antibody gene diversification, AID generates uracil within transcribed antibody gene DNA. The → uracil-N-glycosylase (UNG) normally removes uracil, creating an → abasic site. However, low-fidelity → DNA polymerases replicating such sites produce → transversion mutations. If UNG is inhibited, high-fidelity DNA polymerases will instead replicate across the uracil and generate a → transition mutation, reading uracil as thymine. Immunoglobin → gene conversions, → class switch recombinations and → somatic hypermutations require AID.

Activation tagging

See → activation T-DNA tagging.

Activation tagging vector (AT-vector)

Any → vector that allows to identify a plant target gene that has been tagged by → T-DNA. Tagged regions are cloned into such a vector containing an → origin of vegetative replication, → ampicillin and → hygromycin → selectable marker genes and a quadruplet of transcriptional → enhancers (e.g. from the → cauliflower mosaic virus 35S promoter) in between the → left and → right borders of the T-DNA. The enhancers drive the cloned nearby promoter, activation leads to expression of the cloned gene, and – in favorite cases – also to the expression of the hygromycin resistance gene, so that → selection of transformants is easily possible. After its construction the vector is transformed into → Agrobacterium tumefaciens, which is then used to transform wounded plant cells. If insertion of the T-DNA occurs close to an endogenous plant gene that is normally silent, its transcription is enhanced by the 35S enhancer package.

Activation T-DNA tagging (activation tagging)

The detection of plant genes with very low intrinsic activity by the use of an → activation tagging vector that is able to deregulate (and overexpress) genes close to its insertion site in the target plant genome by the action of the 35S enhancer quadruplet.

Activator

A protein (trans-activating protein) or RNA (see → activator RNA) molecule, which activates a gene after binding to → upstream regulatory sequences (e.g. → promoters). This binding either stabilizes the active state of the promoter, or destabilizes its inactive state. For example, the nuclear activator protein, that consists of distinct DNA-binding and activation domains, recognizes and binds to → enhancer sequences and thereby activates the → transcription of cognate genes. The DNA-binding domain specifically interacts with the enhancer, the affinity and specificity of binding being modulated by accessory proteins bound to adjacent DNA sites, thereby forming the so called → enhanceosome. The → activation domain contacts components of the transcription machinery and influences the → initiation of the transcription process. The signal transducer and activator of transcription (STAT) proteins, for example, are such activators, that transduce signals from growth factor and cytokine receptors, are phosphorylated by receptor tyrosine kinases or receptor-associated Janus kinases (JAKs), dimerize, enter the nucleus and activate transcription of target genes. See → co-activator, → transcription factor.

Any small molecule which alters the conformation of an enzyme after binding to specific sites, thereby increasing its catalytic activity.

See → activator-dissociation system.

A morphogenetically active substance which stimulates and regulates the development of a specific embryonic tissue or organ.

Activator-dissociation system (Ac-Ds system)

A group of the two interacting transposable elements Ac and Ds in maize (Zea mays). Ac is a 4.6 kb autonomous element, carrying a transposase gene, whose encoded protein binds to the terminal inverted repeat ends of both the Ac and the Ds elements, catalyzing their transposition to new locations in the genome. Ds is most often a derivative of Ac that does no longer produce a functional transposase and therefore is unable to transpose by itself. Ds is consequently non-autonomous. Upon Ac-mediated activation, however, Ds may change the expression rate of flanking genes, the timing of gene expression, and may also cause chromosome breakage. Ac determines the time period during morphogenesis when Ds acts. Ac/Ds loci are recognized and mapped by their action on neighboring genes.

Activator protein (AP)

Any one of a series of nuclear → transcription factors that regulate the activity of various genes. See → AP 1, → AP 2, → AP 3. Compare → AP endonuclease, → AP lyase.

Activator RNA

The hypothetical transcript of an → integrator gene that binds to a → receptor gene and activates one or several specific sets of genes (Britten-Davidson model).

Active chromatin

Any, mostly euchromatic region of the nucleus that supports transcription of the underlying genes. See also → active chromatin hub.

Active chromatin hub (ACH)

A three-dimensional structure of → chromatin, where several distant regulatory elements and → promoters of genes actively expressed under the control of these regulatory elements are assembled, thereby looping out the intervening chromatin. Such active chromatin hubs are efficiently facilitating → transcription in vivo, and can be detected by → chromosome conformation capture (3C) techniques. See → chromatin hub.

Active gene

Any→gene that is transcribed into a → ribosomal RNA, → transfer RNA, or → messenger RNA. Compare → cryptic gene.

Active gene signature

The specific → histone code of actively transcribed genes. For example, high levels of the → histone H3 modifications H3K4me1, H3K4me2, H3K4me3, H3K9me1, and H2A.Z surrounding the → transcription start site (TSS) as well as elevated levels of H2BK5me1, H3K36me3, H3K27me1 and H4K20me1 → downstream of the TSS and throughout the body of the corresponding gene are marks for active genes. See → inactive gene signature.

Active promoter cluster

Anyone of probably thousands of genomic regions, in which active → promoters prevail that are co-ordinately regulated such that the adjacent genes are transcribed simultaneously. Active promoter clusters can be identified by cross-linking the → RNA polymerase II preinitiation complex (PIC) proteins to the → chromatin with formaldehyde, shearing the chromatin into large fragments, precipitating the PIC-bound proteins with → monoclonal antibodies raised against e.g. → TATA-box-binding associated factor 1 (TAF 1), amplifying and fluorescently labeling the underlying DNA, and hybridizing the resulting fragments to millions of 50 mer → oligonucleotides representing e.g. the complete non-repeat part of e.g. the human genome at a 100 bp resolution.

Active repression

The specific silencing of a gene or a group of genes in the presence of activators. Active repression, for example, can be exerted by the modulation of the local acetylation state of → histones, the formation of specialized → chromatin structures, a direct or indirect interference with the activators, or an interference with the transcription machinery (see → global repressor, → repression, → Ssn6-Tup1 complex, → transcriptosome).

Active strand

A laboratory slang term for the strand in a double-stranded → microRNA or → siRNA that is incorporated into the → RISC complex. See → off-strand.

Active transcription factor (active TF)

Any → transcription factor that is posttranslationally modified (e.g. phosphorylated) and undergoes a conformational change such that it recognizes its → binding motif in → promoter regions, binds there, and activates the → transcription of the adjacent gene. It is yet unknown, what percentage of the total number of transcription factors are active at a given time in the nucleus of a eukaryotic cell.

Activity-based probe (ABP)

Any small molecule that covalently binds to residues in a → domain of a protein (e.g. an enzyme) necessary for its function (e.g. substrate binding and/or turnover) and blocks this function. ABPs generally consist of three elements, a reactive functional group (called warhead) able to covalently bind to the catalytic site of the protein, a tag permitting identification and purification of the target protein, and a linker connecting both elements, providing selective binding interactions and preventing steric congestion. For example, a potent warhead, diisopropyl fluorophosphate that inhibits serine proteases, can be linked via an FP-alkyl spacer to → biotin as the tag. After binding to the target proteases, the protease-ABP complex is e.g. electrophoresed in a denaturing → SDS polyacrylamide gel and detected by fluorescently labelled → streptavidin. Biotinylated ABPs also facilitate the purification of the target proteins. See → activity-based protein profiling.

Activity-based protein profiling (ABPP)

A technique for the detection of activity signatures of multiple enzymes in the → proteome of different cells, tissues or organs of an individual. The technique relies on socalled → activity-based probes (ABPs) directed towards the active centres of specific classes of enzymes. For example, fluorophosphonate (FP) ABPP probes that are tagged with a → fluorochrome (e.g. → rhodamine, Rh) target the active centres of serine hydrolases. Such probes are mixed with tissue homogenates, and the enzyme-probe adduct analyzed by → denaturing polyacrylamide gel electrophoresis with subsequent → fluorescence detection. Instead of rhodamine, biotinylated FP-ABPP probes can be used for the detection of enzyme classes in homogenates. The probe-labeled proteins are enriched by capture on → avidin-conjugated beads. After on-bead trypsin digestion of the captured proteins, the resulting peptide mixture can be analyzed by multi-dimensional liquid chromatography (LC)-mass spectrometry (MS).

Acute phase response

A reaction of mammalian cells to the presence of low levels of viral double-stranded RNA (dsRNA) that consists in the release of interferon and the activation of a dsRNA-responsive protein kinase (PKR). This enzyme phosphorylates and inactivates translation factor EIF2a, leading to the activation of 2′, 5′oligoadenylate synthase, finally resulting in RNase L activation. This in turn suppresses translation of any messenger RNA globally, which triggers apoptosis.

Acycloterminator

An acyclic functional analogue of a → 2′, 3′-dideoxynucleotide-5′-triphosphate that is accepted by → DNA polymerases, is incorporated into a growing DNA chain, and terminates the reaction, because it lacks a 3′OH group. Acycloterminators can be loaded with → fluorochromes (e.g. → TAMRA) to facilitate detection of their incorporation.

AD

See → activation domain.

ADAM

See → array-based discovery of adaptive mutations.

Adaptamer

Any chimeric oligonucleotide complementary to two different DNA sequences. Do not confuse with → aptamer.

Adaptation

Any change of the structure and/or function of an organism that enables it to better cope with changing environmental conditions.

Adapter primer (AP)

A synthetic → oligodeoxynucleotide that functions as a → primer for e.g. → reverse transcriptase or as → amplimer in the → polymerase chain reaction, and additionally carries one or several → restriction endonuclease sites. Adapter primers are used for e.g. → rapid amplification of cDNA ends.

Adapter-tagged competitive polymerase chain reaction (ATAC-PCR)

A variant of the conventional → quantitative competitive PCR for the high-throughput expression analysis of single genes. In short, → total RNA is first isolated, then → poly(A)+ messenger RNA (mRNA) extracted, and double-stranded → cDNA prepared with a biotinylated oligo(dT) primer and conventional → reverse transcriptase PCR. The resulting cDNA is then restricted with e.g. MboI, TaqI, HapII or NlmIII producing → overhangs. Cohesive end → adapters are then ligated to the termini of the restriction fragments using → T4 DNA ligase. The adapters carry a common end sequence, yet differ from each other by → spacer regions of varying lengths. Equal quantities of each adaptered cDNA sample are then mixed, the cDNA recovered with → strepavidin-coated → magnetic beads, and amplified with a → primer complementary to the common region of the adapter and a → gene-specific primer. The amplification products are then separated by → denaturing polyacrylamide gel electrophoresis on the basis of their variable spacer lengths. The ratio of the amplified products then allows to deduce the relative expression levels of the original mRNA samples. For scale-up experiments, several to many different adapters can be used in a single tube, i.e. a single PCR reaction. ATAC-PCR is relatively insensitive to RNA degradation, because only the 3′-end of mRNA is used. See → enzymatic degrading subtraction, → gene expression fingerprinting, → gene expression screen, → linker capture subtraction, → module-shuffling primer PCR, → preferential amplification of coding sequences, → quantitative PCR, → targeted display, → two-dimensional gene expression fingerprinting. Compare → cDNA expression microarray, → massively parallel signature sequencing, → microarray, → serial analysis of gene expression.

Adaptive gene

Any gene that allows the adaptation of an organism to a specific environment. Adaptive genes are non-essential for the survival of the organism (i.e. → null alleles are non-lethal), but contribute to the fitness of the carrier. Their sequences evolve very rapidly, and their expression patterns vary greatly between otherwise identical organisms living in different habitats. See → fast evolving gene, → orphan gene.

Adaptive genic evolution

The rearrangement of genomic (more specifically genic) sequences into novel combinations as a response to environmental factors (e.g. stress). For example, BARE-1 → retrotransposons are activated in Hordeum spontaneum, the wild ancestor of cultivated barley (Hordeum vulgare) by a dry environment coupled to greater exposure to sunlight. This leads to an increase in copy number of the retroelement. In contrast, lower aridity and less exposure to sunlight reduce both BARE-1 activity and copy number in otherwise identical plants.

Adaptive mutation (stress-inducible mutation, stationary-phase mutation)

Any → spontaneous mutation or also genome-wide hypermutation that occur in bacteria (e.g. E. coli cells) after a prolonged period of incubation (3–7 days or longer) on non-lethal selective medium, while the cells are starving and not dividing, or are dividing very slowly. Under these stress conditions, the cells activate the stress protein sigma-38 (σ38) that in turn activates the expression of the DNA polymerase IV (pol IV) gene. As a consequence, pol IV expression is quadrupled (from about 250 copies to 1,000 pol IV copies per cell). This error-prone enzyme introduces mutations into replicating DNA. In addition, the SOS response leads to increased levels of RecA and RecF′ that also are needed for adaptive mutation, which is under control of the SOS-controlled PsiB inhibitor, and the stress-response sigma factor, RpoS. Adaptive mutation then is a response to a stressful environment.

Adaptive mutation detection technique

See → array-based discovery of adaptive mutations.

Adaptive radiation

The evolution of new gene functions by rapid, punctuated bursts of amplifications of the best adapted genes in the genome of the organism that encounters a new biochemical niche, followed by competition among the gene copies present throughout the population starting to live in the niche. For example, the recognition of a new compound in the new environment by a pre-adapted membrane receptor protein that previously recognized a similar chemical, would be a case of adaptive radiation. See → competitive evolution.

Adaptive trait locus (ATL)

Any phenotypic character controlled by → adaptive genes.

Adaptive transcriptome

The complete set of → transcripts (see → transcriptome) temporarily present in a cell in response to internal (e.g. hormones) or environmental stimuli (e.g. light, viruses). The adaptive transcriptome contains transcripts from genes, whose → promoters are induced under the specific conditions. Once the induction ends, the transcripts are turned over such that finally the → constitutive transcriptome prevails.

Adaptor (adapter, oligonucleotide adaptor, splint)

A short synthetic → oligonucleotide with a preformed cohesive terminus. Such adaptor molecules are used to join one DNA duplex with → blunt ends to another DNA duplex with → cohesive ends. In short, the adaptor possesses one blunt end with a 5′ phosphate group and a cohesive end which is not phosphorylated (to prevent → self-ligation). The adaptor is ligated to the blunt-ended DNA target fragment and the construct phosphorylated at the 5′ termini with → polynucleotide kinase. Then the hybrid molecule is ligated into a corresponding → restriction site of the second DNA molecule (usually a vector). See for example → EcoRI adaptor ligation.

Adaptor RNA: See → transfer RNA.

See → adaptor hypothesis.

See → mediator.

Adaptor hypothesis

The theoretical requirement of a mediator (adaptor) between the information-carrying → messenger RNA molecule and the protein it codes for. This adaptor should be able to recognize both kinds of molecules. The adaptor hypothesis was verified by the discovery of → transfer RNA (tRNA) and the corresponding → aminoacyl-tRNA synthetases.

Adaptor long-range polymerase chain reaction (ALR-PCR)

A variant of the conventional → polymerase chain reaction (PCR) designed for the detection of genomic rearrangements and the localization of → deletions, → duplications, → insertions, or → inversions in closely related genomes. In short, → genomic DNA is first restricted with a suitable → restriction endonuclease (e.g. SphI, generating → cohesive ends, or NsiI, PciI, or FseI). Then the → adaptors are generated by annealing a 12- and a 24-mer → oligonucleotide → primer by heating a mixture of both to 50 °C, and then cooling it down to 10 °C. The 12-mer primer consists of 4 bases of the restriction endonuclease → recognition site (e.g. for SphI), and 8 bases complementary to the 24-mer primer to ensure the correct polarity of ligation with the cohesive ends of the genomic DNA fragments. The 24-mer universal → reverse primer in turn harbors 4 nucleotides complementary to the corresponding restriction site (e.g. for SphI; serves to increase PCR specificity) at its 3′-end. The resulting recessed restriction fragments are then ligated to the adaptors by → T4 DNA ligase, and the ligase inactivated by heat. Subsequently a → long-range two-step PCR with the same → annealing and → extension temperature is run to obtain amplification products of at least 10 kb, in which the formerly recessed ends are now filled in by dNTPs and DNA polymerase. It employs primers complementary to the the adaptor sequences. The PCR products are then directly sequenced. More than one product indicates multiple gene copies present in the test DNA. Finally the sequences from control and test samples are aligned, and genomic differences detected.