Intergenic region

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.[2] 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.[2]

As all scientific knowledge is ultimately tentative—and in principle subject to revision given better evidence—it is possible some well-characterized intergenic regions (but also intra-genic regions like introns) may hypothetically contain as yet unidentified functional elements, such as non-coding RNA genes or regulatory sequences.[3] Such discoveries occur from time to time, but the amount of functional DNA discovered usually constitute only a tiny fraction of the overall amount of intergenic/intronic DNA.[3]

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] Junk DNA sequences are not maintained by purifying selection but gain-of-function mutations with deleterious fitness effects can occur.[7]

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.[8]

See also

References
  1. Tropp BE (2008). Molecular Biology: Genes to Proteins. Jones & Bartlett Learning. ISBN 9780763709167.
  2. Alberts, Bruce (2014). Essential Cell Biology (4th ed.). Garland Pub. pp. 172–209. ISBN 978-0815345251.
  3. Pallazo AF, Lee ES (January 2015). "Non-coding RNA: what is functional and what is junk?". Frontiers in Genetics. 60 (2): e1004351. doi:10.3389/fgene.2015.00002. PMC 4306305. PMID 25674102.
  4. Francis WR, Wörheide G (June 2017). "Similar Ratios of Introns to Intergenic Sequence across Animal Genomes". Genome Biology and Evolution. 9 (6): 1582–1598. doi:10.1093/gbe/evx103. PMC 5534336. PMID 28633296.
  5. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, et al. (October 2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498–511. doi:10.1093/molbev/msj050. PMID 16280547.
  6. Lynch, Michael (February 2006). "The origins of eukaryotic gene structure". Molecular Biology and Evolution. 23 (2): 450–468. doi:10.1101/gr.275638.121. PMC 8647833. PMID 34810219. S2CID 233328735.
  7. Pallazo AF, Gregory TR (May 2014). "The Case for Junk DNA". PLOS Genetics. 10 (5): e1004351. doi:10.1371/journal.pgen.1004351. PMC 4014423. PMID 24809441.
  8. Papadopoulos C, Callebaut I, Gelly JC, Hatin I, Namy O, Renard M, Lespinet O, Lopes A (December 2021). "Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution". Genome Research. 31 (12): 2303–2315. doi:10.1101/gr.275638.121. PMC 8647833. PMID 34810219.
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