Junk DNA - What is Junk DNA?

In genetics, "junk DNA" or noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome si e is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding !ersus noncoding DNA !aries greatly bet"een species.#uch of this DNA has no kno"n biological function. $o"e!er, many types of noncoding DNA sequences do ha!e kno"n biological functions, including the transcriptional and translational regulation of protein%coding sequences. &ther noncoding sequences ha!e likely but as%yet undetermined function, an inference from high le!els of homology and conser!ation seen in sequences that do not encode proteins but appear to be under hea!y selecti!e pressure. Junk DNA Term 'unk DNA, a term that "as introduced in ()*+ by ,usumu &hno, is a pro!isional label for the portions of a genome sequence of a for "hich no discernible function has been identified. According to a ()-. re!ie" in ''Nature'' by /eslie &rgel and 0rancis 1rick, junk DNA has "little specificity and con!eys little or no selecti!e ad!antage to the organism". 2he term is currently, ho"e!er, a some"hat outdated concept, being used mainly in popular science and in a colloquial "ay in scientific publications, and may ha!e slo"ed research into the biological functions of noncoding DNA. ,e!eral lines of e!idence indicate that many "junk DNA" sequences ha!e likely but unidentified functional acti!ity, and other sequences may ha!e had functions in the past. ,till, a large amount of sequence in these genomes falls under no e3isting classification other than "junk". 0or e3ample, one e3periment remo!ed (4 of the mouse genome "ith no detectable effect on the phenotype. 2his result suggests that the remo!ed DNA "as largely nonfunctional. In addition, these sequences are enriched for the heterochromatic histone modification $56)me5.

but transcription does not necessarily imply function.NA. including most sequences "ithin introns and most intergenic DNA. 7hile o!erall genome si e. <nhancer sequences may e3ert !ery distant effects on the transcription le!els of genes. and by e3tension the amount of noncoding DNA.NA. Types of Junk DNA Sequences Noncoding functional NA Noncoding . =romoters facilitate the transcription of a particular gene and are typically upstream of the coding region. the genome of the unicellular ''Polychaos dubium'' 8formerly kno"n as ''Amoeba dubia''9 has been reported to contain more than +. cardio!ascular disease. and the proportion of coding and noncoding DNA "ithin these genomes !aries greatly as "ell. !!"is!!-regulatory elements 1is%regulatory elements are sequences that control the transcription of a gene.NA and micro. transfer .4 of the ''2akifugu'' genome is noncoding DNA.NA.. are correlated to organism comple3ity.4 of all protein%coding genes in mammals and may be !ital components in the progression or treatment of !arious diseases including cancer. #icro. #ore than )-4 of the human genome does not encode protein sequences. times the amount of DNA in humans.NA include ribosomal .NAs are functional . . yet seems to ha!e a comparable number of genes: appro3imately ).NA molecules that are not translated into protein. 1is%elements may be located in >' or 5' untranslated regions or "ithin introns. =i"i%interacting . there are many e3ceptions. and the immune system response to infection.DNA Fraction of Junk DNA 2he amount of total genomic DNA !aries "idely bet"een organisms. 0or e3ample. <3amples of noncoding .NAs are predicted to control the translational acti!ity of appro3imately 5. 2he pufferfish ''Takifugu rubripes'' genome is only about one eighth the si e of the human genome.About -.4 of the nucleotide bases in the human genome may be transcribed.

#utation "ithin these retro%transcribed sequences can inacti!ate the !iral genome.ome introns do appear to ha!e significant biological function. #any introns appear to be mobile genetic elements. account for a large proportion of the genomic sequences in many species. . <ndogenous retro!irus sequences are the product of re!erse transcription of retro!irus genomes into the genomes of germ cells. =seudogenes that are the of retrotransposition of an . the trn/%intron is found in all green plants and appears to ha!e been !ertically inherited for se!eral billions of years. and as much as +>4 is recogni ably formed of retrotransposons. "hich include long interspersed nuclear elements 8/IN<s9 and short interspersed nuclear elements 8. including more than a billion years "ithin chloroplasts and an additional +?5 billion prior in the cyanobacterial ancestors of chloroplasts.NA acti!ity as "ell as protein%coding gene e3pression.NA. . Appro3imately -4 of the human genome is made up of endogenous retro!irus sequences.IN<s9. e!ident in hosts that ha!e become dependent on such introns o!er long periods of time: for e3ample. epeat sequences$ transposons and %iral elements 2ransposons and retrotransposons are mobile genetic elements. . possibly through ribo yme functionality that may regulate t. transcribed to precursor m. but ultimately remo!ed by .ome e3amples ha!e been found of .IN<s e3erting transcriptional control of some protein%encoding genes. @enome si e !ariation in at least t"o kinds of plants is mostly the result of retrotransposon sequences.etrotransposon repeated sequences.NA. and a substantial number of pseudogenes are acti!ely transcribed. . are the most abundant mobile elements in the human genome.NA splicing during the processing to mature messenger .NA and r. Alu sequences.NA intermediate are kno"n as processed pseudogenes: pseudogenes that arise from the genomic remains of duplicated genes or residues of inacti!ated are nonprocessed pseudogenes. classified as a short interspersed nuclear element.#ntrons Introns are non%coding sections of a gene.

Functions of Junk DNA #any noncoding DNA sequences ha!e !ery important biological functions.ome specific sequences of noncoding DNA may be features essential to chromosome structure. but do regulate "hen and "here genes are e3pressed.ome noncoding DNA sequences are genetic "s"itches" that do not encode proteins. .ome noncoding DNA sequences determine ho" much of a particular protein gets generated. 1omparati!e genomics re!eals that some regions of noncoding DNA are highly conser!ed.. eukaryotes appear to require a minimum amount of non%coding DNA. in the genomes of humans and mice. . protein%coding DNA sequences account for only about +. 0or e3ample.Telomeres 2elomeres are regions of repetiti!e DNA at the end of a chromosome. =seudogene sequences appear to accumulate mutations more rapidly than coding sequences due to a loss of selecti!e pressure. eukaryotic genomes. In humans the predicted minimum is about >4 of the total genome. "hich pro!ide protection from chromosomal deterioration during DNA replication. . "hich di!erged from a common ancestor A>?*> million years ago. . 2his minimum amount can be predicted using a gro"th model for regulatory genetic net"orks. &ther sequences of noncoding DNA determine "here transcription factors attach. implying that it is required for regulatory purposes. implying that these noncoding regions are under strong e!olutionary pressure and positi!e selection. sometimes on time%scales representing hundreds of millions of years.4 of conser!ed DNA. According to a comparati!e study of o!er 5. centromere function and homolog recognition in meiosis. "ith the remaining majority of conser!ed DNA represented in noncoding regions. prokaryotic and o!er 5.

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