Ultraconserved element

An ultraconserved element (UCE) is a region of the genome that is shared between evolutionarily distant taxa and shows little or no variation between those taxa. These regions and regions adjacent to them (flanking DNA) are useful for tracing the evolutionary history of groups of organisms.^[1][2] Another term for ultraconserved element is ultraconserved region (UCR).

The term "ultraconserved element" was originally defined as a genome segment longer than 200 base pairs (bp) that is absolutely conserved, with no insertions or deletions and 100% identity, between orthologous regions of the human, rat, and mouse genomes.^[3][4] 481 of these segments have been identified in the human genome.^[3][4] If ribosomal DNA (rDNA regions) are excluded, these range in size from 200 bp to 781 bp.^[4] UCEs are found on all human chromosomes except for 21 and Y.^[5]

Since its creation, this term's usage has broadened to include more evolutionarily distant species or shorter segments, for example 100 bp instead of 200 bp.^[3][4] By some definitions, segments need not be syntenic between species.^[3] Human UCEs also show high conservation with more evolutionarily distant species, such as chicken and fugu.^[4] Out of 481 identified human UCEs, approximately 97% align with high identity to the chicken genome, though only 4% of the human genome can be reliably aligned to the chicken genome.^[4] Similarly, the same sequences in the fugu genome have 68% identity to human UCEs, despite the human genome only reliably aligning to 1.8% of the fugu genome.^[4] Despite often being noncoding DNA,^[6] some ultraconserved elements have been found to be transcriptionally active, producing non-coding RNA molecules.^[7]

Evolution

Researchers originally assumed that perfect conservation of these long stretches of DNA implied evolutionary importance, as these regions appear to have experienced strong negative (purifying) selection for 300-400 million years.^[4][6][8] More recently, this assumption has been replaced by two main hypotheses: that UCEs are created through a reduced negative selection rate, or through reduced mutation rates, also known as a "cold spot" of evolution.^[3][4] Many studies have examined the validity of each hypothesis. The probability of finding ultraconserved elements by chance (under neutral evolution) has been estimated at less than 10⁻²² in 2.9 billion bases.^[4] In support of the cold spot hypothesis, UCEs were found to be mutating 20 fold less than expected under conservative models for neutral mutation rates.^[4] This fold change difference in mutation rates was consistent between humans, chimpanzees, and chickens.^[4] Ultraconserved elements are not exempt from mutations, as exemplified by the presence of 29,983 polymorphisms in the UCE regions of the human genome assembly GRCh38.^[9] However, affected phenotypes were only caused by 112 of these polymorphisms, most of which were located in coding regions of the UCEs.^[9] A study performed in mice determined that deleting UCEs from the genome did not create obvious deleterious phenotypes, despite deletion of UCEs in proximity to promoters and protein coding genes.^[10] Affected mice were fertile and targeted screens of the nearby coding genes showed no altered phenotype.^[10] A separate mouse study demonstrated that ultraconserved enhancers were robust to mutagenesis, concluding that perfect conservation of UCE sequences is not required for their function, which would suggest another reason for the sequence consistency besides evolutionary importance.^[11] Computational analysis of human ultraconserved noncoding elements (UCNEs) found that the regions are enriched for A-T sequences and are generally GC poor.^[12] However, the UNCEs were found to be enriched for CpG, or highly methylated.^[12] This may indicate that there is some change to DNA structure in these regions favoring their precise retention, but this possibility has not been validated through testing.^[12]

Function

Often, ultraconserved elements are located near transcriptional regulators or developmental genes performing functions such as gene enhancing and splicing regulation.^[3][4][13] A study comparing ultraconserved elements between humans and the Japanese puffer fish Takifugu rubripes proposed an importance in vertebrate development.^[14] Double-knockouts of UCEs near the ARX gene in mice caused a shrunken hippocampus in the brain, though the effect was not lethal.^[15] Some UCEs are not transcribed, and are referred to as ultraconserved noncoding elements.^[12] However, many UCRs in humans are extensively transcribed.^[7] A small number of those which are transcribed, known as transcribed UCEs (T-UCEs), have been connected with human carcinomas and leukemias.^[7] For example, TUC338 is strongly upregulated in human hepatocellular carcinoma cells.^[16] Indeed, UCEs are often affected by copy number variation in cancer cells much more than in healthy contexts, suggesting that altering the copy number of T-UCEs may be deleterious.^[17][18][19]

Role in human disease

Research has demonstrated that T-UCRs have a tissue-specific expression, and a differential expression profile between tumors and other diseases.^[5] The tables below highlight transcripts and polymorphisms within UCRs that have been shown to contribute to human diseases.^[5][9] For example, UCRs tend to accumulate less mutations than flanking segments, in both neoplastic and non-neoplastic samples from persons with hereditary non-polyposis colorectal cancer.^[20]

Regulation mechanisms of disease related ultraconserved element transcripts

miR/methylation/transcript factor associated with T-UCRs	Disease	References
miR-24-1/uc.160	Leukemia	Calin et al., 2007 [7]
miR-130b/uc.63	Prostate CA	Sekino et al., 2017 [21]
miR-153/uc.416	Colorectal and renal CA	Goto et al., 2016;[22] Sekino et al., 2017[21]
miR-155/uc.160	Gastric CA	Calin et al., 2007;[7] Pang et al., 2018[23]
miR-155/uc346A	Leukemia	Calin et al., 2007 [7]
mir-195/uc.283	Bladder CA	Liz et al., 2014 [24]
miR-195, miR-4668/uc.372	Lipid metabolism	Guo et al., 2018 [25]
mir-195/uc.173	Gastrointestinal tract	Xiao et al., 2018[26]
miR-214/uc.276	Colorectal CA	Wojcik et al., 2010[27]
miR-291a-3p/uc.173	Nervous system	Nan et al., 2016 [28]
miR-29b/uc.173	Gastrointestinal tract	J. Y. Wang et al., 2018 [29]
miR-339-3p, miR-663b-3p, miR-95-5p/uc.339	Lung CA	Vannini et al., 2017[30]
miR-596/uc.8	Bladder CA	Olivieri et al., 2016 [31]
DNA methylation/uc.160, uc.283, and uc.346	Colorectal CA	Kottorou et al., 2018 [32]
DNA methylation/uc.158 + A, uc.160+, uc.241 + A, uc.283 + A, uc.346 + A	Gastric CA	Goto et al., 2016;[22] Lujambio et al., 2010 [21]
Transcription factor SP1/uc.138 (TRA2β4)	Colorectal CA	Kajita et al., 2016 [33]
Transcription factor YY1/uc.8	Bladder CA	Terreri et al., 2016 [34]

Phenotype-associated polymorphisms within ultraconserved elements

Polymorphism name	Associated phenotype description	Source
rs17105335	Amyotrophic lateral sclerosis	Cronin et al. (2008)[35]
rs2020906	Lynch syndrome	Hansen et al. (2014)[36]
rs10496382	Height	Chiang et al. (2012)[37]
rs13382811	Severe myopia	Khor et al. (2013)[38]
rs104893634	Vertical talus congenital	Dobbs et al. (2006);[39] Shrimpton et al. (2004)[39]
rs2307121	Central corneal thickness	Lu et al. (2013)[40]
rs587777277	Bosch-Boonstra-Schaaf optic atrophy syndrome	Bosch et al. (2014)[41]
rs587777275	Bosch-Boonstra-Schaaf optic atrophy syndrome	Bosch et al. (2014)[41]
rs587777274	Bosch-Boonstra-Schaaf optic atrophy syndrome	Bosch et al. (2014)[41]
rs387906239	Familial adenomatous polyposis 1 attenuated	Soravia et al. (1999)[42]
rs3797704	No association with breast cancer	Chang et al. (2016)[43]
rs387906232	Familial adenomatous polyposis 1	Fodde et al. (1992)[44]
rs387906237	Familial adenomatous polyposis 1 attenuated	Curia et al. (1998)[45]
rs121434591	Distal myopathy	Senderek et al. (2009)[13]
rs587777300	Amyotrophic lateral sclerosis 21	Johnson et al. (2014)[46]
rs863223403	Au-Kline syndrome	Au et al. (2015)[47]
rs121917900	Cockayne syndrome B	Mallery et al. (1998)[48]
rs75462234	Papillorenal syndrome	Schimmenti et al. (1999)[49]
rs77453353	Renal coloboma syndrome	Amiel et al. (2000)[50]
rs76675173	Papillorenal syndrome	Schimmenti et al. (1997)[51]
rs587777708	Focal segmental glomerulosclerosis 7	Barua et al. (2014)[52]
rs11190870	Adolescent idiopathic scoliosis, no association with breast cancer	Chettier et al. (2015);[53] Gao et al. (2013);[54] Grauers et al. (2015);[55] Jiang et al. (2013);[56] Londono et al. (2014);[57] Miyake et al. (2013);[58] Shen et al. (2011);[59] Takahashi et al. (2011)[60]
rs724159963	Peroxisomal fatty acyl-CoA reductase 1 disorder	Buchert et al. (2014)[61]
rs16932455	Capecitabine sensitivity	O'Donnell et al. (2012)[62]
rs997295	Motion sickness; BMI	De et al. (2015);[63] Guo et al. (2013);[64] Hromatka et al.[65]
rs587777373	Congenital heart defects multiple types 4	Al Turki et al. (2014)[66]
rs398123839	Duchenne muscular dystrophy	Hofstra et al. (2004);[67] Roberts et al. (1992)[68]
rs863224976	Becker muscular dystrophy	Tuffery-Giraud et al. (2005)[69]
rs132630295	Spastic paraplegia 2 X-linked	Gorman et al. (2007)[70]
rs132630287	Spastic paraplegia 2 X-linked	Saugier-Veber et al. (1994)[71]
rs132630292	Pelizaeus/Merzbacher disease atypical	Hodes et al. (1997)[72]
rs137852350	Mental retardation X-linked 94	Wu et al. (2007)[73]
rs122459149	Emery-Dreifuss muscular dystrophy 6 X-linked	Gueneau et al. (2009);[74] Knoblauch et al. (2010)[75]
rs122458141	Myopathy X-linked with postural muscle atrophy	Schoser et al. (2009);[76] Windpassinger et al. (2008)[77]
rs786200914	Myopathy X-linked with postural muscle atrophy	Schoser et al. (2009)[76]
rs267606811	Myopathy X-linked with postural muscle atrophy	Windpassinger et al. (2008)[77]
rs62621672	Rett syndrome (nonpathogenic variant)	Zahorakova et al. (2007)[78]

See also

• Human accelerated regions