Repeated sequence (DNA)

Repeated sequences (also known as repetitive elements, repeating units 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 re-association 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 humans.[1]

Repetitive elements found in genomes fall into different classes, depending on their structure and/or the mode of multiplication. 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 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]

Tandem repeats in human disease

Tandem repeat sequences, particularly trinucleotide repeats, underlie several human disease conditions. Trinucleotide repeats may expand in the germline over successive generations leading to increasingly severe manifestations of the disease. The disease conditions in which expansion occurs include Huntington’s disease, fragile X syndrome, several spinocerebellar ataxias, myotonic dystrophy and Friedrich ataxia.[7] Trinucleotide repeat expansions may occur through strand slippage during DNA replication or during DNA repair synthesis.[7]

Hexanucleotide GGGGCC repeat sequences in the C9orf72 gene are a common cause of amyotrophic lateral sclerosis and frontotemporal dementia.[8] CAG trinucleotide repeat sequences underlie several spinocerebellar ataxias (SCAs-SCA1; SCA2; SCA3; SCA6; SCA7; SCA12; SCA17).[8] Huntington’s disease results from an unstable expansion of repeated CAG sequences in exon 1 of the huntingtin gene (HTT). HTT encodes a scaffold protein that directly participates in repair of oxidative DNA damage.[9] It has been noted that genes containing pathogenic CAG repeats often encode proteins that themselves have a role in the DNA damage response and that repeat expansions may impair specific DNA repair pathways.[10] Faulty repair of DNA damages in repeat sequences may cause further expansion of these sequences, thus setting up a vicious cycle of pathology.[10]

Types

Main types

Major categories of repeated sequence or repeats:

  • Interspersed repeats (aka. interspersed nuclear elements). Transposable elements. DNA transposons.retrotransposons.LTR-retrotransposons (HERVs).non LTR-retrotransposons.SINEs (Short Interspersed Nuclear Elements).LINEs (Long Interspersed Nuclear Elements).SVAs

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.

Repeated sequences evolutionary derived from viral infection events.[11]

Other types

Note: The following are covered in detail in "Computing for Comparative Microbial Genomics".[12]

  • Direct repeats
    • Global direct repeat
    • Local direct simple repeats
    • Local direct repeats
    • Local direct repeats with spacer
  • Inverted repeats
    • Global inverted repeat
    • Local inverted repeat
    • Inverted repeat with spacer
    • Palindromic repeat
  • Mirror and everted repeats
gollark: <@356209633313947648> ```- Fortunes/Dwarf Fortress output/Chuck Norris jokes on boot (wait, IS this a feature?)- (other) viruses (how do you get them in the first place? running random files like this?) cannot do anything particularly awful to your computer - uninterceptable (except by crashing the keyboard shortcut daemon, I guess) keyboard shortcuts allow easy wiping of the non-potatOS data so you can get back to whatever nonsense you do fast- Skynet (rednet-ish stuff over websocket to my server) and Lolcrypt (encoding data as lols and punctuation) built in for easy access!- Convenient OS-y APIs - add keyboard shortcuts, spawn background processes & do "multithreading"-ish stuff.- Great features for other idio- OS designers, like passwords and fake loading (est potatOS.stupidity.loading [time], est potatOS.stupidity.password [password]).- Digits of Tau available via a convenient command ("tau")- Potatoplex and Loading built in ("potatoplex"/"loading") (potatoplex has many undocumented options)!- Stack traces (yes, I did steal them from MBS)- Backdoors- er, remote debugging access (it's secured, via ECC signing on disks and websocket-only access requiring a key for the other one)- All this useless random junk can autoupdate (this is probably a backdoor)!- EZCopy allows you to easily install potatOS on another device, just by sticking it in the disk drive of any potatOS device!- fs.load and fs.dump - probably helpful somehow.- Blocks bad programs (like the "Webicity" browser).- Fully-featured process manager.- Can run in "hidden mode" where it's at least not obvious at a glance that potatOS is installed.- Convenient, simple uninstall with the "uninstall" command.- Turns on any networked potatOS computers!- Edits connected signs to use as ad displays.- A recycle bin.- An exorcise command, which is like delete but better.- Support for a wide variety of Lorem Ipsum.```
gollark: Okay, that is... probably a better idea, yes.
gollark: Anyway, <@178948413851697152>, please do rewrite that query if you have *better* ideas.
gollark: Oh, probably, but this I can actually understand.
gollark: I have ended up writing this slightly ridiculous query: `SELECT * FROM pages WHERE updated = (SELECT MAX (updated) FROM pages WHERE name = ${req.params.name}) AND name = ${req.params.name}`(no SQL injection there, I use `sql-template-strings`)

See also

References
  1. de Koning, A. P. Jason; Gu, Wanjun; Castoe, Todd A.; Batzer, Mark A.; Pollock, David D.; Copenhaver, Gregory P. (1 December 2011). "Repetitive Elements May Comprise Over Two-Thirds of the Human Genome". PLOS Genetics. 7 (12): e1002384. doi:10.1371/journal.pgen.1002384. PMC 3228813. PMID 22144907.
  2. Ohno, S (1972). "So much 'junk' DNA in our genome". Brookhaven Symposia in Biology. 23: 366–70. PMID 5065367.
  3. Orgel, L.E.; Crick, F.H.C.; Sapienza, C. (December 1980). "Selfish DNA". Nature. 288 (5792): 645–646. doi:10.1038/288645a0. PMID 7453798.
  4. McClintock, Barbara (1 January 1956). "Controlling Elements and the Gene". Cold Spring Harbor Symposia on Quantitative Biology. 21: 197–216. doi:10.1101/SQB.1956.021.01.017. PMID 13433592.
  5. Shapiro, James A.; von Sternberg, Richard (May 2005). "Why repetitive DNA is essential to genome function". Biological Reviews. 80 (2): 227–250. doi:10.1017/S1464793104006657. PMID 15921050.
  6. Cournac, Axel; Koszul, Romain; Mozziconacci, Julien (8 January 2016). "The 3D folding of metazoan genomes correlates with the association of similar repetitive elements". Nucleic Acids Research. 44 (1): 245–255. doi:10.1093/nar/gkv1292. PMC 4705657. PMID 26609133.
  7. Usdin, Karen; House, Nealia C. M.; Freudenreich, Catherine H. (22 January 2015). "Repeat instability during DNA repair: Insights from model systems". Critical Reviews in Biochemistry and Molecular Biology. 50 (2): 142–167. doi:10.3109/10409238.2014.999192. PMC 4454471. PMID 25608779.
  8. Abugable, Arwa A.; Morris, Julia L.M.; Palminha, Nelma M.; Zaksauskaite, Ringaile; Ray, Swagat; El-Khamisy, Sherif F. (September 2019). "DNA repair and neurological disease: From molecular understanding to the development of diagnostics and model organisms". DNA Repair. 81: 102669. doi:10.1016/j.dnarep.2019.102669. PMID 31331820.
  9. Maiuri, Tamara; Mocle, Andrew J.; Hung, Claudia L.; Xia, Jianrun; van Roon-Mom, Willeke M. C.; Truant, Ray (25 December 2016). "Huntingtin is a scaffolding protein in the ATM oxidative DNA damage response complex". Human Molecular Genetics. 26 (2): 395–406. doi:10.1093/hmg/ddw395. PMID 28017939.
  10. Massey, Thomas H.; Jones, Lesley (30 January 2018). "The central role of DNA damage and repair in CAG repeat diseases". Disease Models & Mechanisms. 11 (1): dmm031930. doi:10.1242/dmm.031930. PMC 5818082. PMID 29419417.
  11. Villarreal, Luis P. (2005). Viruses and the Evolution of Life. ASM Press. ISBN 978-1-55581-309-3.
  12. Ussery, David W.; Wassenaar, Trudy M.; Borini, Stefano (2009). "Word Frequencies and Repeats". Computing for Comparative Microbial Genomics. Computational Biology. 8. pp. 137–150. doi:10.1007/978-1-84800-255-5_8. ISBN 978-1-84800-254-8.
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