Intergenic region explained

An intergenic region is a stretch of DNA sequences located between genes.^[1] Intergenic regions may contain functional elements and junk DNA.

Properties and functions

Intergenic regions may contain a number of functional DNA sequences such as promoters and regulatory elements, enhancers, spacers, and (in eukaryotes) centromeres.^[2] They may also contain origins of replication, scaffold attachment regions, and transposons and viruses.

Non-functional DNA elements such as pseudogenes and repetitive DNA, both of which are types of junk DNA, can also be found in intergenic regions—although they may also be located within genes in introns. It is possible that these regions contain as of yet unidentified functional elements, such as non-coding genes or regulatory sequences.^[3] This indeed occurs occasionally, but the amount of functional DNA discovered usually constitute only a tiny fraction of the overall amount of intergenic or intronic DNA.

Intergenic regions in different organisms

In humans, intergenic regions comprise about 50% of the genome, whereas this number is much less in bacteria (15%) and yeast (30%).^[4]

As with most other non-coding DNA, the GC-content of intergenic regions vary considerably among species. For example in Plasmodium falciparum, many intergenic regions have an AT content of 90%.^[5]

Molecular evolution of intergenic regions

Functional elements in intergenic regions will evolve slowly because their sequence is maintained by negative selection. In species with very large genomes, a large percentage of intergenic regions is probably junk DNA and it will evolve at the neutral rate of evolution.^{[6] [7]} Junk DNA sequences are not maintained by purifying selection but gain-of-function mutations with deleterious fitness effects can occur.^[8]

Phylostratigraphic inference and bioinformatics methods have shown that intergenic regions can—on geological timescales—transiently evolve into open reading frame sequences that mimic those of protein coding genes, and can therefore lead to the evolution of novel protein-coding genes in a process known as de novo gene birth.^[9]

See also

• Exon
• Promoter (biology)
• ENCODE
• Heterochromatin
• Noncoding DNA
• Repetitive DNA
• Regulator gene
• Whole genome sequencing

External links

• ENCODE threads Explorer Characterization of intergenic regions and gene definition. Nature (journal)

Notes and References

1. Book: Jones & Bartlett Learning. 9780763709167. Tropp BE . Molecular Biology: Genes to Proteins. 2008.
2. Book: Alberts . Bruce . Essential Cell Biology. . 2014 . Garland Pub . 978-0815345251 . 172–209 . 4th.
3. Palazzo AF, Lee ES . Non-coding RNA: what is functional and what is junk? . Frontiers in Genetics . 60 . 2 . e1004351 . January 2015 . 25674102 . 4306305 . 10.3389/fgene.2015.00002 . free .
4. Francis WR, Wörheide G . Similar Ratios of Introns to Intergenic Sequence across Animal Genomes . Genome Biology and Evolution . 9 . 6 . 1582–1598 . June 2017 . 28633296 . 5534336 . 10.1093/gbe/evx103 .
5. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B . 6 . Genome sequence of the human malaria parasite Plasmodium falciparum . Nature . 419 . 6906 . 498–511 . October 2002 . 16280547 . 10.1093/molbev/msj050 . free .
6. Lynch . Michael . The Origins of Eukaryotic Gene Structure . Molecular Biology and Evolution . 23 . 2 . 2006-02-01 . 1537-1719 . 10.1093/molbev/msj050 . 450–468. free. 16280547 .
7. Papadopoulos . Chris . Callebaut . Isabelle . Gelly . Jean-Christophe . Hatin . Isabelle . Namy . Olivier . Renard . Maxime . Lespinet . Olivier . Lopes . Anne . Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution . Genome Research . 31 . 12 . 2021 . 1088-9051 . 34810219 . 8647833 . 10.1101/gr.275638.121 . 2303–2315.
8. Palazzo AF, Gregory TR . The Case for Junk DNA . PLOS Genetics . 10 . 5 . e1004351 . May 2014 . 24809441 . 4014423 . 10.1371/journal.pgen.1004351 . free .
9. Papadopoulos C, Callebaut I, Gelly JC, Hatin I, Namy O, Renard M, Lespinet O, Lopes A . Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution . Genome Research . 31 . 12 . 2303–2315 . December 2021 . 34810219 . 8647833 . 10.1101/gr.275638.121 .