Glossary

Alternate Reading Frame (ARF): The transcription of a coding sequence can start at different nucleotides of the first or later codon, resulting in two polypeptides with no sequence similarity.

Alternative cis-splicing: Several different mature mRNAs can be processed from the same pre-mRNA molecule via different exon selection.

Alternative trans-splicing: Several different mature mRNAs can be processed from the same two or more pre-mRNA molecules via different exon selection.

Anti-parallel strand: DNA is formed of two strands, the positive strands starts from the 5’end and runs to the 3’ end, while the negative, anti-sense, or anti-parallel strand starts from 3’ towards the 5’ end. The DNA strand serving as a template must be traversed in a 3’ to 5’ direction. The direction of the RNA polymerase movement, determined by the direction of the promotor where transcription begins, determines which strand serves as a template. Therefore coding sequences, and even exons involved in producing together one product, can be encoded on both DNA strands.

Bicistronic/multicistronic mRNA molecules: A transcript with the potential to code for two/more than one final product.

Chimeric transcripts: An mRNA transcript containing sequence elements from at least two separate ORFs, or an ORF and a sequence element downstream from the stop codon of the first ORF.

Cis: Latin: ‘on this or the near side of’. With respect to the mechanism of mRNA splicing, ‘cis’ has changed its traditional meaning derived from the cis-trans test and now denotes that the mature RNA is synthesized from one pre-mRNA molecule or transcript. All exons, even if derived from two different, adjacent genes, are in cis-position, meaning they are transcribed to ONE pre-mRNA molecule

Cistron: The section of a chromosome that controls a single function. Formally defined by the cis-trans test.

Cis-trans test: A test to define a unit of genetic function, based on whether two mutations of the same character occur in the same gene or in two genes on the same chromosome. Mutations in two different genes complement one another when each occurs on a different member of a pair of homologous chromosomes (the traditional meaning of trans position), resulting in restoration of the wild-type character.

Co-transcription/co-transcriptional splicing: Two ORFs (meaning both have their own start and stop codons) are transcribed into one pre-mRNA and processed into a fusion mRNA containing elements from both sequences.

C-terminal: The end of a protein (either the polymerases involved in the process of transcription or the polypeptide product of the DNA) corresponding to the 3’end of the coding sequence for that protein.

Downstream: Sequence elements that lie closer to the 3’ end of the chromosome strand and are therefore transcribed or read later than the upstream sequence.

Exon: Exons can be defined either as those elements of the DNA that correspond to parts of the mature mRNA or as those elements that correspond to parts of the sequence of the final product (protein or functional RNA). The difference between these two definitions is significant in some cases of trans-splicing.
Frameshift: see alternative Reading frame.

Group II introns: Possibly originating in eubacteria, these self-splicing introns systems are now typical components of contemporary organelle genomes in plants, algae, fungi, and protists. Fragmentation of the characteristic group II secondary structure for trans-splicing may have led to the separate small nuclear RNAs (snRNA) in the nuclear spliceosome that interacts with the intron sequences in nuclear DNA. Fragments of the group II introns are sometimes called transoms to describe such discontinuous gene-associated sequences.

Heterotypic trans-splicing: Synthesis of mature mRNA from two different, discontinuously transcribed pre-mRNA transcripts.

Homotypic trans-splicing: Synthesis of mature mRNA from two identical but discontinuously transcribed pre-mRNA transcripts

In-Frame splicing: Splicing of sequence elements of the pre-mRNA (which can be introns, exons, or parts of an exon) such that the elements retain the original reading frame, or the reading frame of an alternative mRNA processed from the same pre-mRNA.

Intein: Inteins are ‘selfish’ DNA elements inserted in-frame and translated together with their host proteins. Protein splicing is defined as the excision of an intervening protein sequence (the intein) from a protein precursor and the concomitant ligation of the flanking protein fragments (the exteins) to form a mature extein host protein and the free intein. Protein splicing was shown to occur in heterologous organisms, in different in-vitro systems and with various natural and engineered host flanks. Hence, protein splicing is probably independent of specific host cell factors.

Intermolecular splicing: Also called discontinuous mRNA synthesis. The exons derive, and/or the introns are spliced out, from two (or more) separate pre-mRNA molecules or transcription units. See Trans-splicing.

Intramolecular splicing: Also called continuous mRNA synthesis. The exons derive from, and/or the introns are spliced out from, one pre-mRNA molecule. See Cis-splicing.

Mature mRNA: mRNAs act as intermediary (messenger) molecules to direct the synthesis of the final product of a DNA sequence. Many kinds of processing are now known which turn the immediate products of DNA transcriptions (see Pre mRNA) into mature mRNA.

N-terminal: The end of a protein (either the RNA polymerases involved in the process of transcription or the polypeptide product of the DNA) corresponding to the 5’end of the coding sequence.

ORF: Open reading frame: A DNA sequence starting with a start codon and ending with a stop codon, and therefore potentially signals a coding sequence that is translated into a functional product RNA or polypeptide.

Out-of-Frame splicing: Splicing of sequence elements of the pre-mRNA (can be introns, exons, or parts of an exon) which results in a shift of the reading frame when compared to an alternative mature mRNA processed from the same pre-mRNA.

Pre-mRNA: The immediate product of the transcription of one strand of the original DNA sequence. Many kinds of processing are now known which turn the immediate products of DNA transcriptions into Mature mRNA.

Pre-mRNA splicing: The cutting out of the intervening sequences, called introns, between the exons that code for the functional parts of the protein, to process the mature mRNA. In the nucleus, small nuclear ribonucleoprotein particles (snRNPs) containing U1, U2. U4, U5 and U6 RNAs are essential to the splicing process. Consensus sequences at the 3’ and 5’splice sites are recognized by the U2 and U1 snRNPs respectively, while the other three RNAs assemble as a tri-sn-RNP complex to form the spliceosome.

RNA editing: This process involves mainly C-to-U alterations of the mature RNA molecule before the translation into the final product. Most frequently altered are first and second codon positions, in some cases resulting in the creation of either AUG initiation codons (as in the Wheat nad1 RNA) or termination codons (e.g. UGA).

Spliceosome: see Pre-mRNA splicing

Splicing: see pre-messenger splicing, cis-splicing, intermolecular and intramolecular splicing, and trans-splicing.

snRNP: small nuclear ribonucleoproteins, involved in the process of RNA splicing in the nucleus (see Pre-mRNA splicing).

Trans: Latin: ‘across, beyond, crossing, on the other side’. With respect to the mechanism of pre-mRNA splicingtrans’ has changed its original meaning derived from the cis-trans test and now denotes that the mature RNA is synthesized from at least two pre-mRNA molecules. ‘Trans’ in this context does not indicate the position of the exons on the chromosome; they might be adjacent or far apart on the same chromosome, on the same or the anti-parallel strand of the same chromosome, or on different chromosomes.

Trans-splicing: An intermolecular reaction whereby two discrete mRNA molecules are precisely linked to form a mature species that contains the separately transcribed exons but lacks part of each precursor (fragmented intronic sequences such as split group II introns).

Upstream: Sequence elements that are lying closer to the 5’ end of the chromosome strand and are therefore transcribed or read earlier than the denoted sequence.