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]
^Zhang, Y. Miles; Williams, Jason L.; Lucky, Andrea (3 September 2019). "Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics". Insect Systematics and Diversity. 3 (5). doi:10.1093/isd/ixz016.
^ abcdReneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D (May 2012). "Long identical multispecies elements in plant and animal genomes". Proceedings of the National Academy of Sciences of the United States of America. 109 (19): E1183–E1191. doi:10.1073/pnas.1121356109. PMC 3358895. PMID 22496592.
^ abcdefgBejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (May 2004). "Ultraconserved elements in the human genome". Science. 304 (5675): 1321–1325. Bibcode:2004Sci...304.1321B. CiteSeerX 10.1.1.380.9305. doi:10.1126/science.1098119. PMID 15131266. S2CID 2790337.
^Cite error: The named reference Pereira Zambalde-2020 was invoked but never defined (see the help page).
^Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, et al. (August 2007). "Human genome ultraconserved elements are ultraselected". Science. 317 (5840): 915. Bibcode:2007Sci...317..915K. doi:10.1126/science.1142430. PMID 17702936. S2CID 35322654.
^Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, et al. (September 2007). "Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas". Cancer Cell. 12 (3): 215–229. doi:10.1016/j.ccr.2007.07.027. PMID 17785203.
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contains a long, highly evolutionarily conserved sequence known as an UltraconservedElement (UCE) that is within the retained intron and overlaps the alternative...
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Bejerano, Gill; Pheasant, Michael; Makunin, Igor; et al. (28 May 2004). "Ultraconserved Elements in the Human Genome" (PDF). Science. 304 (5675): 1321–1325...
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