Biology · DNA, Replication & Repair

Genome sizes, mobile elements and noncoding sequences

Two organisms can differ greatly in DNA amount without differing by the same factor in protein-coding sequence or gene number. A genome is not just a long list of protein instructions. Its size, organisation, repeated material and evolutionary history all matter when interpreting a comparison.

Use the earlier ideas of nucleotides, complementary molecules, enzymes, inheritance and mutation. A nucleotide is a building block of a nucleic acid. A template is an existing sequence that guides construction of a complementary sequence. The symbols 5′ and 3′ are read five prime and three prime; they identify chemically different strand ends. Every short sequence and numerical example here is constructed for explanation unless identified as historical evidence.

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By the end, you can

Compare genome measurements without equating DNA amount with complexity, and recognise that coding, function and mobility describe different properties.

State which DNA is being counted

A genome is the genetic material of an organism or biological entity. For cellular organisms, it is DNA. In eukaryotes, nuclear and organelle genomes may be distinguished. When comparing sizes, specify whether the measurement concerns one chromosome set, all nuclear DNA in a cell or another defined collection. A cell's DNA amount also changes when its chromosomes are replicated.

Haploid means one chromosome set. A haploid nuclear-genome size is not automatically the amount of DNA in every cell of that organism. Cells can carry multiple sets or replicated chromosomes, and particular specialised cells can differ further. Comparing unlike definitions can create an apparent genome difference that is really a difference in what was counted.

Base pairs are a length measure for double-stranded DNA. Gene number is a different measure, as is the amount of protein-coding sequence. Genes can differ in length, include noncoding regions and produce products that are functional RNA. A bigger genome therefore does not establish a proportionately larger number of proteins or a greater level of organismal complexity.

Noncoding describes a coding property, not one shared function

Here, protein-coding sequence means sequence specifying amino acids in a protein. Noncoding DNA does not specify protein amino acids. Some noncoding sequences participate in gene regulation, encode functional RNA or contribute to chromosome organisation. Other regions have no established function, or may persist mainly through their history of replication and transmission.

Finding biochemical activity in a region does not by itself establish that the activity is important for an organism in every setting. Equally, failing to detect function with one test does not prove there is none. Functional claims need a stated meaning of function and appropriate evidence, such as what changes when the region is altered under relevant conditions.

The bars compare two invented haploid nuclear genomes using the same length scale. They divide total sequence only into protein-coding and other sequence. This is a simplified accounting definition, not an annotation of real organisms. Categories such as regulatory, repeated and mobile-element-derived DNA can overlap, so those labels should not be added as separate pieces of the same total without checking their definitions.

More coding DNA can occupy a smaller fraction

Constructed, nonoverlapping coding/other bins are defined only for this calculation. Regulatory, repeated or mobile-element-derived labels can overlap those bins and must not be added as extra stacked totals. Bars must share their scale.

Read the diagram in words

Two stacked horizontal bars use a common zero-to-32 scale measured in millions of base pairs. Genome A consists of 2 coding and 6 other million base pairs; B consists of 3 coding and 29 other million base pairs. Both segments are labelled directly as well as shown with distinct patterns. Totals are 8 and 32, with coding proportions 25% and 9.375%, the latter optionally displayed as about 9.4%.

Haploid nuclear DNA length (million base pairs): 0–32

0 · 8 · 16 · 24 · 32

More coding DNA can occupy a smaller fraction
Constructed genome	Protein-coding sequence	Other sequence	Haploid nuclear DNA length (million base pairs)
Constructed genome A	2	6	8
Constructed genome B	3	29	32

Constructed genome A · Protein-coding sequence: 2/8 = 25%
Constructed genome B · Protein-coding sequence: 3/32 = 9.375%

B total length is 4 × A

B coding length is 1.5 × A

9.375% ≈ 9.4%

These counts do not establish gene numbers or organismal complexity

Some sequences can change genomic location

Transposable elements are genetic elements capable of moving or generating a new insertion at another genomic location. Barbara McClintock's maize research connected changes in chromosome position with changes in genetic behaviour. Later molecular work identified different mechanisms; a single jumping-sequence cartoon cannot represent them all.

DNA transposons move through mechanisms involving DNA. Some are excised and inserted elsewhere, while other mechanisms are replicative. Retrotransposons instead use an RNA intermediate that is copied back into DNA, allowing a new DNA insertion. The paired diagram compares a selected cut-and-paste example with an RNA-mediated copying example; it does not assign one mechanism to every element.

Insertions can disrupt sequences, change regulation or provide material later used in a new function. Repeated copies and inactive remnants can remain in genomes. An element-derived region is not necessarily moving today, and a mobile element can itself contain protein-coding sequence. Coding status, mobility, current activity and evolutionary origin answer different questions.

Movement and copying can use different intermediates

Original schematic comparing selected mechanisms. DNA transposition also has replicative mechanisms. Not all element-derived sequences remain active, and a mobile element can contain protein-coding DNA. No real insertion site, activity rate or experimental procedure is supplied.

Read the diagram in words

One panel shows a selected DNA cut-and-paste element as a marked block removed from a donor DNA line and inserted into a different position of a target DNA line. The second shows a retrotransposon DNA block remaining at its original location, an RNA intermediate copied from it, a new DNA copy made from that RNA and a new target-site insertion. Arrows distinguish movement from transcription and reverse transcription; donor and target are schematic sites, not necessarily different chromosomes.

Selected DNA cut-and-paste mechanism

DNA donor site with element: Selected cut-and-paste example.
Excised DNA element: The element is removed from this donor site.
New DNA insertion site: Element joins target DNA; donor-site repair is omitted.

Selected DNA cut-and-paste mechanism
From	To	Relationship
DNA donor site with element	Excised DNA element	Excise DNA
Excised DNA element	New DNA insertion site	Insert DNA

RNA-mediated copying mechanism

Original retrotransposon DNA: Original DNA copy remains at its location.
RNA intermediate: RNA is made using the element's DNA information.
New DNA copy: Reverse transcription copies RNA into DNA.
Additional DNA insertion: A new copy is inserted at another site.

RNA-mediated copying mechanism
From	To	Relationship
Original retrotransposon DNA	RNA intermediate	Transcription
RNA intermediate	New DNA copy	Reverse transcription
New DNA copy	Additional DNA insertion	Insert DNA copy

Processing enzymes and donor-site repair omitted

Worked example

Compare size and proportion separately

In the constructed bars, genome A totals 8 million base pairs, including 2 million defined as protein-coding. Genome B totals 32 million base pairs, including 3 million protein-coding. B has four times the total length, but only 3 ÷ 2 = 1.5 times the coding length.

The coding proportions are 2 ÷ 8 = 25% for A and 3 ÷ 32 = 9.375% for B, shown as about 9.4% when rounded. B contains more coding DNA in absolute amount but a smaller coding fraction. These numbers establish neither gene counts nor relative complexity, because neither was measured.

Check your understanding

Does a genome with four times as many base pairs necessarily have four times as many genes?
Show reasoning
No. Genes differ in length and genome composition varies. DNA length alone does not determine gene number.
Does the label noncoding mean that a sequence has no biological function?
Show reasoning
No. It describes failure to encode protein amino acids under the definition used here. Some noncoding regions have established roles; others have uncertain or no demonstrated function.
Can protein-coding sequence and mobile-element-derived sequence always be added as nonoverlapping genome categories?
Show reasoning
No. A mobile element can contain protein-coding sequence. The categories concern different properties and may overlap.

What to carry forward

Keep genome length, coding amount, demonstrated function and element history separate; no one of those measurements supplies all the others.

References

Resources supporting this lesson’s explanations and examples.