All DNA is considered coding DNA

Transposons

Transposons are coding DNA sequences that can change their location within the DNA (so-called ’jumping genes’). Transposons are found in all organisms. They can contain one or more genes. The places where transposons are integrated into the genome are usually random. A large part of the natural mutations are caused by transposons. This means that these are also elements that increase the wealth of variants in nature.

This change of location, known as transposition, has not yet been fully clarified, but it is probably important because it can spread genetic information quickly and also promotes mutations. There are DNA transposons (class II transposons) and RNA transposons (class I transposons or retroelements). In both cases, the enzymes necessary for jumping are encoded by the sequence placed on the transposon itself. The transposon thus brings its own tool and is therefore often viewed as a kind of ’integrated virus’, since the procedure is similar to that of the retroviruses.

A distinction is made between transposons more conservative (Cutting out pieces of DNA) and more replicative (Copying via mRNA) transposition. DNA transposons are usually moved by conservative transposition. Characteristic of DNA transposons are special, repeating, non-coding sequences before and after the jumping gene, which serve as a recognition site for the transposase (so-called inverted repeats or IRs). In conservative transposition, a complete (i.e. double-stranded) DNA sequence is cut out and then reinserted elsewhere.

Such a jump, however, leaves traces (footprints). The transposon is often surrounded by non-coding sequences from the host DNA, so-called direct repeats (DRs). They arise from the fact that when the gap is opened by the transposase, the two DNA strands are not cut exactly "opposite", but rather something is offset. The resulting gap is therefore not identical on both DNA strands. After inserting the transposon, the remaining gaps are filled in again by normal DNA synthesis (incorporation or addition of the missing bases). Now there are two short, identical sequences before and after the cut that are tantamount to a duplication. When the transposon sequence is cut out again, these duplicates are often retained and are referred to as footprints. These duplications brought about in this way (depending on the sequence, insertions or inversions can also arise) are to be regarded as mutations, as this can result in a changed reading of information, among other things.

In replicative transposition (i.e. class I transposons), a section of DNA is copied into an mRNA copy, translated into what is known as cDNA (complementary DNA) using a reverse transcriptase (enzyme that builds the strand complementary to the mRNA) reincorporated into the DNA strand. The opposite strand that is still missing is then supplemented by a DNA polymerase. The result is a coding sequence that appears twice on the DNA: once in the starting position and once in the new position. Class I transposons often have adjacent repeat sequences (long terminal repeats, LTRs) and are then referred to as retrotransposons or LTR retrotransposons. If the LTRs are missing, the sequences are called retroposons (not to be confused with retrotransposons).