Non-coding DNA


Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules. Other functional regions of the non-coding DNA fraction include regulatory sequences that control gene expression; scaffold attachment regions; origins of DNA replication; centromeres; and telomeres. Some non-coding regions appear to be mostly nonfunctional, such as introns, pseudogenes, intergenic DNA, and fragments of transposons and viruses. Regions that are completely nonfunctional are called junk DNA.

Fraction of non-coding genomic DNA

In bacteria, the coding regions typically take up 88% of the genome. The remaining 12% does not encode proteins, but much of it still has biological function through genes where the RNA transcript is functional and regulatory sequences, which means that almost all of the bacterial genome has a function. The amount of coding DNA in eukaryotes is usually a much smaller fraction of the genome because eukaryotic genomes contain large amounts of repetitive DNA not found in prokaryotes. The human genome contains somewhere between 1–2% coding DNA. The exact number is not known because there are disputes over the number of functional coding exons and over the total size of the human genome. This means that 98–99% of the human genome consists of non-coding DNA and this includes many functional elements such as non-coding genes and regulatory sequences.
Genome size in eukaryotes can vary over a wide range, even between closely related species. This puzzling observation was originally known as the C-value paradox where "C" refers to the haploid genome size. The paradox was resolved with the discovery that most of the differences were due to the expansion and contraction of repetitive DNA and not the number of genes. Some researchers speculated that this repetitive DNA was mostly junk DNA. The reasons for the changes in genome size are still being worked out and this problem is called the C-value Enigma.
This led to the observation that the number of genes does not seem to correlate with perceived notions of complexity because the number of genes seems to be relatively constant, an issue termed the G-value Paradox. For example, the genome of the unicellular Polychaos dubium has been reported to contain more than 200 times the amount of DNA in humans. The pufferfish Takifugu rubripes genome is only about one eighth the size of the human genome, yet seems to have a comparable number of genes. Genes take up about 30% of the pufferfish genome and the coding DNA is about 10%. The reduced size of the pufferfish genome is due to a reduction in the length of introns and less repetitive DNA.
Utricularia gibba, a bladderwort plant, has a very small nuclear genome compared to most plants. It likely evolved from an ancestral genome that was 1,500 Mb in size. The bladderwort genome has roughly the same number of genes as other plants but the total amount of coding DNA comes to about 30% of the genome.
The remainder of the genome consists of promoters and regulatory sequences that are shorter than those in other plant species. The genes contain introns but there are fewer of them and they are smaller than the introns in other plant genomes. There are noncoding genes, including many copies of ribosomal RNA genes. The genome also contains telomere sequences and centromeres as expected. Much of the repetitive DNA seen in other eukaryotes has been deleted from the bladderwort genome since that lineage split from those of other plants. About 59% of the bladderwort genome consists of transposon-related sequences but since the genome is so much smaller than other genomes, this represents a considerable reduction in the amount of this DNA. The authors of the original 2013 article note that claims of additional functional elements in the non-coding DNA of animals do not seem to apply to plant genomes.
According to a New York Times article, during the evolution of this species, "... genetic junk that didn't serve a purpose was expunged, and the necessary stuff was kept." According to Victor Albert of the University of Buffalo, the plant is able to expunge its so-called junk DNA and "have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed."

Types of non-coding DNA sequences

Noncoding genes

There are two types of genes: protein coding genes and noncoding genes. Noncoding genes are an important part of non-coding DNA and they include genes for transfer RNA and ribosomal RNA. These genes were discovered in the 1960s. Prokaryotic genomes contain genes for a number of other noncoding RNAs but noncoding RNA genes are much more common in eukaryotes.
Typical classes of noncoding genes in eukaryotes include genes for small nuclear RNAs, small nucleolar RNAs, microRNAs, short interfering RNAs, PIWI-interacting RNAs, and long noncoding RNAs. In addition, there are a number of unique RNA genes that produce catalytic RNAs.
Noncoding genes account for only a few percent of prokaryotic genomes but they can represent a vastly higher fraction in eukaryotic genomes. In humans, the noncoding genes take up at least 6% of the genome, largely because there are hundreds of copies of ribosomal RNA genes. Protein-coding genes occupy about 38% of the genome; a fraction that is much higher than the coding region because genes contain large introns.
The total number of noncoding genes in the human genome is controversial. Some scientists think that there are only about 5,000 noncoding genes while others believe that there may be more than 100,000. The difference is largely due to debate over the number of lncRNA genes.

Promoters and regulatory elements

Promoters are DNA segments near the 5' end of the gene where transcription begins. They are the sites where RNA polymerase binds to initiate RNA synthesis. Every gene has a noncoding promoter.
Regulatory elements are sites that control the transcription of a nearby gene. They are almost always sequences where transcription factors bind to DNA and these transcription factors can either activate transcription or repress transcription. Regulatory elements were discovered in the 1960s and their general characteristics were worked out in the 1970s by studying specific transcription factors in bacteria and bacteriophage.
Promoters and regulatory sequences represent an abundant class of noncoding DNA but they mostly consist of a collection of relatively short sequences so they do not take up a very large fraction of the genome. The exact amount of regulatory DNA in mammalian genome is unclear because it is difficult to distinguish between spurious transcription factor binding sites and those that are functional. The binding characteristics of typical DNA-binding proteins were characterized in the 1970s and the biochemical properties of transcription factors predict that in cells with large genomes, the majority of binding sites will not be biologically functional.
Many regulatory sequences occur near promoters, usually upstream of the transcription start site of the gene. Some occur within a gene and a few are located downstream of the transcription termination site. In eukaryotes, there are some regulatory sequences that are located at a considerable distance from the promoter region. Some regulatory sequences are called enhancers or silencers but there is no rigorous definition that distinguishes them from other transcription factor binding sites.

Introns

Introns are the parts of a gene that are transcribed into the precursor RNA sequence, but ultimately removed by RNA splicing during the processing to mature RNA. Introns are found in both types of genes: protein-coding genes and noncoding genes. They are present in prokaryotes but they are much more common in eukaryotic genomes.
Group I and group II introns take up only a small percentage of the genome when they are present. Spliceosomal introns are only found in eukaryotes and they can represent a substantial proportion of the genome. In humans, for example, introns in protein-coding genes cover 37% of the genome. Combining that with about 1% coding sequences means that protein-coding genes occupy about 38% of the human genome. The calculations for noncoding genes are more complicated because there is considerable dispute over the total number of noncoding genes but taking only the well-defined examples means that noncoding genes occupy at least 6% of the genome.

Untranslated regions

The standard biochemistry and molecular biology textbooks describe non-coding nucleotides in mRNA located between the 5' end of the gene and the translation initiation codon. These regions are called 5'-untranslated regions or 5'-UTRs. Similar regions called 3'-untranslated regions are found at the end of the gene. The 5'-UTRs and 3'UTRs are very short in bacteria but they can be several hundred nucleotides in length in eukaryotes. They contain short elements that control the initiation of translation and transcription termination as well as regulatory elements that may control mRNA stability, processing, and targeting to different regions of the cell.

Origins of replication

DNA synthesis begins at specific sites called origins of replication. These are regions of the genome where the DNA replication machinery is assembled and the DNA is unwound to begin DNA synthesis. In most cases, replication proceeds in both directions from the replication origin.
The main features of replication origins are sequences where specific initiation proteins are bound. A typical replication origin covers about 100-200 base pairs of DNA. Prokaryotes have one origin of replication per chromosome or plasmid but there are usually multiple origins in eukaryotic chromosomes. The human genome contains about 100,000 origins of replication representing about 0.3% of the genome.