132:. Sialic acid is known to play a crucial part in cell signaling pathways and interaction processes. The loss of this gene is evident in the undetectable levels of sialic acid in humans but highly present in mouse, pig, chimpanzee and other mammal tissues and may provide more insight into the historic background of human evolution.
639:
Green, R. E.; Krause, J.; Briggs, A. W.; Maricic, T.; Stenzel, U.; Kircher, M.; Patterson, N.; Li, H.; Zhai, W.; Fritz, M. H. Y.; Hansen, N. F.; Durand, E. Y.; Malaspinas, A. S.; Jensen, J. D.; Marques-Bonet, T.; Alkan, C.; Prüfer, K.; Meyer, M.; Burbano, H. A.; Good, J. M.; Schultz, R.; Aximu-Petri,
80:
hCONDELs in humans cover approximately 0.14% of chimpanzee genome. The number of hCONDELs currently identified is 583 using the genome-wide comparison method; however, validation of these predicated regions of deletions through polymerase chain reaction methods produces 510 hCONDELs. The remainder of
85:
genome. hCONDELs, on average, remove about 95 base pairs (bp) of highly conserved sequences from the human genome. The median size of these 510 validated CONDELs is about 2,804 bp, thus showing a diverse range in length of the characteristic deletions. Another noticeable characteristic of hCONDELs
62:
genomes. Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, mouse and chicken sequences with BLASTZ followed by multiple alignment of the pairwise alignments done with MULTIZ. The highly conserved chimpanzee sequences were
491:
Gibbs, R. A.; Gibbs, J.; Rogers, M. G.; Katze, R.; Bumgarner, G. M.; Weinstock, E. R.; Mardis, K. A.; Remington, R. L.; Strausberg, J. C.; Venter, R. K.; Wilson, M. A.; Batzer, C. D.; Bustamante, E. E.; Eichler, M. W.; Hahn, R. C.; Hardison, K. D.; Makova, W.; Miller, A.; Milosavljevic, R. E.;
135:
The mechanisms and time of occurrence of hCONDELs are not entirely understood but given that conserved non-coding sequences play a major developmental role through regulation of genes, their loss in regions of deletions, it is expected that their loss in hCONDELs will result in developmental
39:
The group of CONDELs of a specific organism is specified by prefixing the CONDELs with the first letter of the organism. For instance, hCONDELs refer to the group of CONDELs found in humans whereas mCONDELs and cCONDELs refer to mouse and chimpanzee CONDELs respectively.
204:(SVZ) of the septum. The loss of this SVZ enhancer region in an hCONDEL may provide further insights into the role of DNA sequence changes that may have resulted in evolution of the human brain and may provide a better understanding of the evolution of humans.
67:
to identify conserved regions not present in humans. This identified 583 regions of deletions that were then referred to as hCONDELs. 510 of these identified hCONDELs were then validated computationally with 39 of these being validated by
224:
Woolfe, A.; Goodson, M.; Goode, D. K.; Snell, P.; McEwen, G. K.; Vavouri, T.; Smith, S. F.; North, P.; Callaway, H.; Kelly, K.; Walter, K.; Abnizova, I.; Gilks, W.; Edwards, Y. J. K.; Cooke, J. E.; Elgar, G. (2005).
115:
Of the 510 identified hCONDELs, only one of these deletions has been shown to remove a 92 bp sequence that is part of a protein-coding region in the human sequence. The deletion that affects the protein
168:
in humans compared to its close relatives, including chimpanzees. The 60.7kb hCONDEL which is located near the AR locus has been found to be responsible for removing a 5 kb sequence that codes for an
336:
McLean, C. Y.; Reno, P. L.; Pollen, A. A.; Bassan, A. I.; Capellini, T. D.; Guenther, C.; Indjeian, V. B.; Lim, X.; Menke, D. B.; Schaar, B. T.; Wenger, A. M.; Bejerano, G.; Kingsley, D. M. (2011).
128:
gene which codes for the cytidine monophosphate-N-acetylneurminic acid hydroxylase-like protein, an enzyme involved in the production of N-glycolylneuraminic acid, one type of
590:
Blanchette, M.; Kent, W. J.; Riemer, C.; Elnitski, L.; Smit, A. F.; Roskin, K. M.; Baertsch, R.; Rosenbloom, K.; Clawson, H.; Green, E. D.; Haussler, D.; Miller, W. (2004).
54:
article by McLean et al. in whole-genome comparison analysis. This involved firstly identifying a subset of 37,251 human deletions (hDELs) through pairwise comparisons of
81:
these hCONDELs are either false-positives or non-existent genes. hCONDELs have been confirmed through PCR with 88 percent of these shown to have been lost from the draft
492:
Palermo, A.; Siepel, J. M.; Sikela, T.; Attaway, S.; Bell, K. E.; Bernard, C. J.; Buhay, M. N.; Chandrabose, M.; Dao, C.; Davis, K. D.; et al. (2007).
31:
and may have played an important role in the development of specific traits and behavior that distinguish closely related organisms from each other.
27:
among closely related relatives. Almost all of these deletions fall within regions that perform non-coding functions. These represent a new class of
90:
regions. Simulations show that hCONDELs are enriched near genes involved in hormone receptor signaling and neural function, and near genes encoding
828:
Chou, H. -H.; Takematsu, H.; Diaz, S.; Iber, J.; Nickerson, E.; Wright, K. L.; Muchmore, E. A.; Nelson, D. L.; Warren, S. T.; Varki, A. (1998).
200:
enhancer binding site. The removal of this region, known to function as a suppressor, specifically increases the proliferation of the
86:(and other groups of identified CONDELs such as those from mouse and chimpanzee) is that they tend to be specifically skewed towards
172:
for the AR locus. Using the mouse construct with LacZ expression showed localization of this hCONDEL region (AR enhancer) to the
197:
91:
888:
640:
A.; Butthof, A.; Höber, B.; Höffner, B.; Siegemund, M.; Weihmann, A.; Nusbaum, C.; Lander, E. S.; Russ, C. (2010).
69:
541:
Schwartz, S.; Kent, W. J.; Smit, A.; Zhang, Z.; Baertsch, R.; Hardison, R. C.; Haussler, D.; Miller, W. (2003).
1048:
939:"Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers"
276:
Dermitzakis, E. T.; Reymond, A.; Scamuffa, N.; Ucla, C.; Kirkness, E.; Rossier, C.; Antonarakis, S. E. (2003).
1043:
887:
Poulin, F.; Nobrega, M. A.; Plajzer-Frick, I.; Holt, A.; Afzal, V.; Rubin, E. M.; Pennacchio, L. A. (2005).
137:
64:
995:
841:
653:
505:
455:
349:
289:
28:
781:"Exploration for Functional Nucleotide Sequence Candidates within Coding Regions of Mammalian Genes"
201:
169:
121:
24:
20:
1019:
937:
Gotea, V.; Visel, A.; Westlund, J. M.; Nobrega, M. A.; Pennacchio, L. A.; Ovcharenko, I. (2010).
919:
315:
1011:
968:
911:
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621:
572:
523:
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307:
258:
161:
145:
55:
140:
experiments done by Mclean et al. by fusion of mouse constructs fused to basal promoter with
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365:
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248:
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50:
196:. A 3,181 bp hCONDEL which is located near the GADD45G gene removes a forebrain-specific
999:
845:
830:"A mutation in human CMP-sialic acid hydroxylase occurred after the Homo-Pan divergence"
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509:
459:
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226:
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864:
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165:
117:
923:
715:
699:"Compositional constraints in the extremely GC-poor genome of Plasmodium falciparum"
698:
319:
1023:
986:
Hill, R. S.; Walsh, C. A. (2005). "Molecular insights into human brain evolution".
193:
338:"Human-specific loss of regulatory DNA and the evolution of human-specific traits"
227:"Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development"
243:
907:
152:) locus suggest a role in deletions that affect regulatory sequences in humans.
148:(AR) locus and the growth arrest and DNA-damage-inducible protein GADD45 gamma (
129:
82:
278:"Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs)"
444:"Human-Specific Changes of Genome Structure Detected by Genomic Triangulation"
173:
854:
796:
665:
518:
493:
468:
443:
302:
277:
177:
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915:
814:
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740:"Enrichment of regulatory signals in conserved non-coding genomic sequence"
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527:
477:
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379:
311:
262:
954:
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724:
181:
1007:
592:"Aligning Multiple Genomic Sequences with the Threaded Blockset Aligner"
361:
607:
149:
87:
59:
558:
410:
494:"Evolutionary and Biomedical Insights from the Rhesus Macaque Genome"
395:"Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome"
889:"In vivo characterization of a vertebrate ultraconserved enhancer"
697:
Musto, H.; Cacciò, S.; Rodríguez-Maseda, H.; Bernardi, G. (1997).
192:
Many hCONDELs are located around genes expressed during cortical
141:
125:
95:
393:
Chen, R.; Bouck, J. B.; Weinstock, G. M.; Gibbs, R. A. (2001).
23:
within the human genome containing sequences that are highly
136:
consequences that can be observed in human-specific traits.
164:(AR) gene may be responsible for the loss of whiskers and
442:
Harris, R. A.; Rogers, J.; Milosavljevic, A. (2007).
834:Proceedings of the National Academy of Sciences
738:Levy, S.; Hannenhalli, S.; Workman, C. (2001).
8:
331:
329:
219:
217:
48:The term hCONDEL was first used in the 2011
642:"A Draft Sequence of the Neandertal Genome"
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863:
853:
804:
755:
714:
673:
615:
566:
517:
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418:
369:
301:
252:
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160:An hCONDEL located near the locus of the
63:searched against the human genome using
213:
7:
543:"Human–Mouse Alignments with BLASTZ"
703:Memórias do Instituto Oswaldo Cruz
14:
156:Loss of whiskers and penile spine
144:expression for hCONDELs near the
757:10.1093/bioinformatics/17.10.871
779:Suzuki, R.; Saitou, N. (2011).
716:10.1590/S0074-02761997000600020
1:
244:10.1371/journal.pbio.0030007
908:10.1016/j.ygeno.2005.03.003
1065:
70:polymerase chain reaction
44:Identification of CONDELs
855:10.1073/pnas.95.20.11751
184:cells of penile organs.
666:10.1126/science.1188021
519:10.1126/science.1139247
469:10.1126/science.1139477
303:10.1126/science.1087047
188:Expansion of brain size
120:in humans results in a
955:10.1101/gr.104471.109
797:10.1093/dnares/dsr010
138:In situ hybridization
92:fibronectin-type-III
29:regulatory sequences
19:refer to regions of
1008:10.1038/nature04103
1000:2005Natur.437...64H
846:1998PNAS...9511751C
840:(20): 11751–11756.
658:2010Sci...328..710G
510:2007Sci...316..222.
460:2007Sci...316..235H
362:10.1038/nature09774
354:2011Natur.471..216M
294:2003Sci...302.1033D
288:(5647): 1033–1035.
202:subventricular zone
122:frameshift mutation
608:10.1101/gr.1933104
180:follicles and the
652:(5979): 710–722.
559:10.1101/gr.809403
504:(5822): 222–234.
454:(5822): 235–237.
411:10.1101/gr.203601
405:(11): 1807–1816.
162:androgen receptor
146:androgen receptor
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111:Sialic acid loss
106:Impact in humans
102:C2-set domains.
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1049:Human evolution
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744:Bioinformatics
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100:immunoglobulin
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194:neurogenesis
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79:
49:
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35:Nomenclature
16:
15:
130:sialic acid
83:Neanderthal
1038:Categories
208:References
174:mesenchyme
56:chimpanzee
237:(1): e7.
178:vibrissae
25:conserved
21:deletions
1016:16136130
973:20363979
924:21888183
916:15885503
896:Genomics
815:21586532
766:11673231
684:20448178
626:15060014
577:12529312
528:17431167
478:17431168
429:11691844
380:21390129
320:35299360
312:14526086
263:15630479
182:mesoderm
170:enhancer
17:hCONDELs
1024:4406401
996:Bibcode
964:2860159
874:9751737
842:Bibcode
806:3111233
725:9566216
675:5100745
654:Bibcode
646:Science
506:Bibcode
498:Science
456:Bibcode
448:Science
371:3071156
350:Bibcode
290:Bibcode
282:Science
150:GADD45G
124:in the
88:GC poor
72:(PCR).
60:macaque
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98:-like
51:Nature
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920:S2CID
892:(PDF)
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316:S2CID
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680:PMID
622:PMID
573:PMID
524:PMID
474:PMID
425:PMID
376:PMID
308:PMID
259:PMID
198:p300
142:LacZ
126:CMAH
96:CD80
94:-or
65:BLAT
58:and
1004:doi
992:437
959:PMC
951:doi
904:doi
860:PMC
850:doi
801:PMC
793:doi
752:doi
711:doi
670:PMC
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650:328
612:PMC
604:doi
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