Non-coding DNA

junk DNAnoncoding DNAnon-codingnoncodingfunctional noncoding RNAsnon-coding regionnon-coding regionsjunknon-protein-coding regionsnon-coding sequence
Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences.wikipedia
256 Related Articles

DNA

deoxyribonucleic aciddouble-stranded DNAdsDNA
Non-coding DNA sequences are components of an organism's DNA that do not encode protein sequences.
A large part of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences.

Human genome

genomehuman DNAhuman geneticist
For example, it was originally suggested that over 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA, while 20% of a typical prokaryote genome is non-coding.
Human genomes include both protein-coding DNA genes and noncoding DNA.

Cis-regulatory element

Cis-regRNA elementcis-acting
Cis-regulatory elements are sequences that control the transcription of a nearby gene.
Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes.

Genome size

genome reductionreducedgenome degradation
In eukaryotes, genome size, and by extension the amount of non-coding DNA, is not correlated to organism complexity, an observation known as the C-value enigma.
Some single-celled organisms have much more DNA than humans, for reasons that remain unclear (see non-coding DNA and C-value enigma).

Intergenic region

intergenicintergenic DNAintergenic sequences
For example, it was originally suggested that over 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA, while 20% of a typical prokaryote genome is non-coding.
Intergenic regions are a subset of noncoding DNA.

Utricularia gibba

bladderworthumped bladderwortThe Humped Bladderwort
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA.
The sequencing of its DNA revealed only 3% non-coding material.

Pseudogene

pseudogenespseudogenizationpseudo genes
Pseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell.
Although not fully functional, pseudogenes may be functional, similar to other kinds of noncoding DNA, which can perform regulatory functions.

ENCODE

modENCODEEncyclopedia of DNA ElementsENCODE Project
The international Encyclopedia of DNA Elements (ENCODE) project uncovered, by direct biochemical approaches, that at least 80% of human genomic DNA has biochemical activity.
The ENCODE project's claim that 80% of the human genome has biochemical function was rapidly picked up by the popular press who described the results of the project as leading to the death of junk DNA.

Takifugu

Japanese pufferfishJapanese and Chinese relativespuffer fish
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; approximately 90% of the Takifugu genome is non-coding DNA.
Apparently due to some unknown selection pressure, intronic and extragenic sequences have been drastically reduced within this family.

Untranslated region

UTRuntranslated regionsUTRs
Cis-elements may be located in 5' or 3' untranslated regions or within introns.
These often long sequences were once thought to be useless or junk mRNA that has simply accumulated over evolutionary time.

Exon

exonsexons.coding region
Studies of group I introns from Tetrahymena protozoans indicate that some introns appear to be selfish genetic elements, neutral to the host because they remove themselves from flanking exons during RNA processing and do not produce an expression bias between alleles with and without the intron.
Although unicellular eukaryotes such as yeast have either no introns or very few, metazoans and especially vertebrate genomes have a large fraction of non-coding DNA.

Mutation

mutationsgenetic mutationmutated
Pseudogenes arise from retrotransposition or genomic duplication of functional genes, and become "genomic fossils" that are nonfunctional due to mutations that prevent the transcription of the gene, such as within the gene promoter region, or fatally alter the translation of the gene, such as premature stop codons or frameshifts.
Other types of mutation occasionally create new genes from previously noncoding DNA.

Genome

genomesgenetic materialgenomic
Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "non-coding DNA" instead; "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage.
The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA.

Enhancer (genetics)

enhancerenhancersgene enhancer
Enhancer sequences may also exert very distant effects on the transcription levels of genes.
In the comparative genomics approach, sequence conservation of non-coding regions can be indicative of enhancers.

Gene

genesnumber of genesgene sequence
Pseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell.
This DNA has often been referred to as "junk DNA".

Retrovirus

retrovirusesRetroviridaeretroviral
Endogenous retrovirus sequences are the product of reverse transcription of retrovirus genomes into the genomes of germ cells.
Most insertions have no known function and are often referred to as "junk DNA".

Conserved non-coding sequence

Conserved non-coding DNA sequenceconserved noncoding sequencesconserved regions of non-coding DNA
This is indicated by comparative genomics studies that report highly conserved regions of non-coding DNA, sometimes on time-scales of hundreds of millions of years.
A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved.

Promoter (genetics)

promoterpromoterspromoter region
Promoters facilitate the transcription of a particular gene and are typically upstream of the coding region.
CpG islands also occur frequently in promoters for functional noncoding RNAs such as microRNAs.

C-value

C-value paradoxC-value enigma1C
In eukaryotes, genome size, and by extension the amount of non-coding DNA, is not correlated to organism complexity, an observation known as the C-value enigma.
This observation was deemed counterintuitive before the discovery of non-coding DNA.

Conserved sequence

sequence conservationconservedhighly conserved
Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "non-coding DNA" instead; "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage.
Conservation can occur in coding and non-coding nucleic acid sequences.

De novo gene birth

de novoDe novo'' gene birthde novo'' emergence
A study published in 2019 shows that new genes (termed de novo gene birth) can be fashioned from non-coding regions.
De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic.

RNA polymerase

DNA-dependent RNA polymeraseRNAPRNA polymerases
A repressor is a DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes.

Evidence of common descent

evidence for evolutionevidence of evolutionevidence for biological evolution
Shared sequences of apparently non-functional DNA are a major line of evidence of common descent.
Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, "dead" genes that steadily accumulate mutations.

T. Ryan Gregory

Dr. T. Ryan Gregory
According to T. Ryan Gregory, the nature of junk DNA was first discussed explicitly in 1972 by a genomic biologist, David Comings, who applied the term to all non-coding DNA.
His research focuses primarily on the issue of genome size evolution (the "C-value enigma") in animals and the origins and biological significance of "junk DNA".

Onion Test

The Onion Test is a way of assessing the validity of an argument for a functional role for non-coding DNA, sometimes called "junk DNA".