Repeated sequence (DNA)

Repeated sequences (aka. repetitive elements, or repeats) are patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. Repetitive DNA was first detected because of its rapid reassociation kinetics.

In many organisms, a significant fraction of the genomic DNA is highly repetitive, with over two-thirds of the sequence consisting of repetitive elements in human.[1]

Repetitive elements found in eukaryotic genomes fall into different classes, depending on their mode of multiplication and/or structure. The disposition of repetitive elements consists either in arrays of tandemly repeated sequences, or in repeats dispersed throughout the genome (see below).

Functions

Debates regarding the potential in vivo functions of these elements have been long standing. Controversial references to ‘junk’ or ‘selfish’ DNA were put forward early on, implying that repetitive DNA segments are remainders from past evolution or autonomous self-replicating sequences hacking the cell machinery to proliferate.[2][3] Originally discovered by Barbara McClintock,[4] dispersed repeats have been increasingly recognized as a potential source of genetic variation and regulation. Together with these regulatory roles, a structural role of repeated DNA in shaping the 3D folding of genomes has also been proposed.[5] This hypothesis is only supported by a limited set of experimental evidence. For instance in human, mouse and fly, several classes of repetitive elements present a high tendency for co-localization within the nuclear space, suggesting that DNA repeats positions can be used by the cell as a genome folding map.[6]


Types

Main types

There are 3 major categories of repeated sequence or repeats:

In primates, the majority of LINEs are LINE-1 and the majority of SINEs are Alu's. SVAs are hominoid specific.

In prokaryotes, CRISPR are arrays of alternating repeats and spacers.

Other types

Note: The following are covered in detail in "Computing for Comparative Microbial Genomics".[7]

See also

References

  1. de Koning, AP Jason, et al. "Repetitive elements may comprise over two-thirds of the human genome." PLoS Genet 7.12 (2011): e1002384.
  2. Ohno, Susumu. "So much “junk” DNA in our genome." Brookhaven Symp Biol. Vol. 23. 1972.
  3. Orgel, Leslie E., F. H. C. Crick, and C. Sapienza. "Selfish dna." (1980): 645-646.
  4. McClintock B.Controlling element and the gene. Cold Spring Harb. Symp. Quant. Biol. 1956;21:197-216.
  5. Shapiro J.A., von Sternberg R.Why repetitive DNA is essential to genome function. Biol. Rev. 2005;80:227-250.
  6. The 3D folding of metazoan genomes correlates with the association of similar repetitive elementsA Cournac, R Koszul, J Mozziconacci - Nucleic acids research, 2016
  7. Ussery, David W.; Wassenaar, Trudy; Borini, Stefano (2008-12-22). "Word Frequencies, Repeats, and Repeat-related Structures in Bacterial Genomes". Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists. Computational Biology. 8 (1 ed.). Springer. pp. 133–144. ISBN 978-1-84800-254-8.

External links

This article is issued from Wikipedia - version of the 11/3/2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.