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Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions
Abstract
A comprehensive representation of the gene content of the long arm of human chromosome 21 (Hsa21q) remains of interest for the study of Down syndrome, its associated phenotypic features, and mouse models. Here we compare transcript catalogs for Hsa21q, chimpanzee chromosome 21 (Ptr21q), and orthologous regions of mouse chromosomes 16, 17, and 10 for open reading frame (ORF) characteristics and conservation. The Hsa21q and mouse catalogs contain 552 and 444 gene models, respectively, of which only 162 are highly conserved. Hsa21q transcripts were used to identify orthologous exons in Ptr21q and assemble 533 putative transcripts. Transcript catalogs for all three organisms are searchable for nucleotide and amino acid sequence features of ORF length, repeat content, experimental support, gene structure, and conservation. For human and mouse comparisons, three additional summaries are provided: (1) the chromosomal distribution of novel ORF transcripts versus potential functional RNAs, (2) the distribution of species-specific transcripts within Hsa21q and mouse models of Down syndrome, and (3) the organization of sense-antisense and putative sense-antisense structures defining potential regulatory mechanisms. Catalogs, summaries, and nucleotide and amino acid sequences of all composite transcripts are available and searchable at http://gfuncpathdb.ucdenver.edu/iddrc/chr21/home.php. These data sets provide comprehensive information useful for evaluation of candidate genes and mouse models of Down syndrome and for identification of potential functional RNA genes and novel regulatory mechanisms involving Hsa21q genes. These catalogs and search tools complement and extend information available from other gene annotation projects.
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“Of 500 genes on chromosome 21, 18 genes influence gene expression, and more than 20 genes are involved in metabolic functioning (Sturgeon and Gardiner 2011).”
From Reactive Oxygen Species, Toxicity, Oxidative Stress, and Antioxidants: Chronic Diseases and Aging (2023) · cites this paper as Sturgeon and Gardiner 2011
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Self-citationTranscriptome analysis by strand-specific sequencing of complementary DNA
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Regulatory roles of natural antisense transcripts
Faghihi, M. A., & Wahlestedt, C. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2738 · Cited by 737
Genome-wide transcription and the implications for genomic organization
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Cognitive deficits and associated neurological complications in individuals with Down's syndrome
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Research works printed but not linked: 1
- CDC (Centers for Disease Control, Prevention) (2006) Improved National Prevalence Estimates for 18 Major Birth Defects. MMWR Morb Mortal Wkly Rep 54:6–12
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“Of the several DSmouse models that have been generated, the most widely used is the Ts65Dn model for studying DS, which is trisomic for 88 of 161 of the ortholog protein coding genes on human chromosome 21 [51].”
MethodSelf-citationDown syndrome: the brain in trisomic mode
Dierssen, M. (2012) · Nature reviews. Neuroscience · doi:10.1038/nrn3314 · Cited by 288
Glutamate Synapses in Human Cognitive Disorders
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Trisomy 21 and early brain development
Haydar, T. F., & Reeves, R. H. (2012) · Trends in Neurosciences · doi:10.1016/j.tins.2011.11.001 · Cited by 200
“[117], and a recent meta-analysis of expression data in trisomy [118]).”
BackgroundDeficits in human trisomy 21 iPSCs and neurons
Weick, J. P., Held, D. L., Bonadurer, G. F., Doers, M. E., Liu, Y., Maguire, C., Clark, A., Knackert, J. A., Molinarolo, K., Musser, M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216575110 · Cited by 205
Human Models Are Needed for Studying Human Neurodevelopmental Disorders
Zhao, X., & Bhattacharyya, A. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.10.009 · Cited by 192
Kleschevnikov, A. M., Belichenko, P. V., Faizi, M., Jacobs, L. F., Htun, K. E., Shamloo, M., & Mobley, W. C. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.1673-12.2012 · Cited by 176
“The Ts65Dn mouse bears an extra copy of approximately half the genes homologous to those on human chromosome 21 (Davisson et al., 1993; Olson et al., 2007; Sturgeon and Gardiner, 2011).”
BackgroundMouse models of Down syndrome: gene content and consequences
Gupta, M., Dhanasekaran, A. R., & Gardiner, K. (2016) · Mammalian Genome · doi:10.1007/s00335-016-9661-8 · Cited by 178
“As illustrated , many gene structures on Hsa21 were identified as antisense to RefSeq protein-coding genes (Sturgeon and Gardiner 2011); mouse orthologs of many of these RefSeq genes are also associated with antisense transcripts.”
BackgroundMethodInfluentialSelf-citationMouse models of Down syndrome as a tool to unravel the causes of mental disabilities
Rueda, N., Flórez, J., & Martínez-Cué, C. (2012) · Neural Plasticity · doi:10.1155/2012/584071 · Cited by 171
“The Dp(10)1Yey mouse is trisomic for the region of Mmu10 syntenic to the distal part of Hsa21 containing 37 orthologous genes [16, 27].”
BackgroundMethodInfluentialHiguera, C., Gardiner, K., & Cios, K. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129126 · Cited by 158
“DS is also particularly challenging because it is not due to a single gene mutation but to an extra copy of a normal chromosome that encodes ~160 protein coding genes of diverse functions, a small number of validated microRNA genes and a few hundred transcripts of undetermined functional properties [3].”
BackgroundSelf-citationVelázquez, R., Ash, J. A., Powers, B. E., Kelley, C. M., Strawderman, M. S., Luscher, Z. I., Ginsberg, S. D., Mufson, E. J., & Strupp, B. J. (2013) · Neurobiology of Disease · doi:10.1016/j.nbd.2013.04.016 · Cited by 124
“A segmental trisomy mouse model of DS, the Ts65Dn mouse (Davisson et al., 1990; Holtzman et al., 1996), is trisomic for the distal portion of mouse chromosome 16 (MMU16), which contains over 100 genes orthologous to those on HSA21 (Patterson and Costa, 2005; Sturgeon and Gardiner, 2011).”
BackgroundKleschevnikov, A. M., Belichenko, P. V., Gall, J., George, L., Nosheny, R., Maloney, M. T., Salehi, A., & Mobley, W. C. (2012) · Neurobiology of Disease · doi:10.1016/j.nbd.2011.10.009 · Cited by 124
“The Ts65Dn mouse is segmentally trisomic for chromosome 16, bearing an extra copy of ~115 genes homologous to those on human chromosome 21 (Davisson et al., 1993; Gardiner et al., 2003; Olson et al., 2007; Sturgeon and Gardiner, 2011).”
BackgroundGardiner, K. (2014) · Drug Design Development and Therapy · doi:10.2147/dddt.s51476 · Cited by 119
“7 Many partial trisomy models have been created using several different methods, and each is trisomic for a unique subset of Hsa21 genes or their mouse orthologs.”
Self-citationGarcía-Cerro, S., Martínez, P., Vidal, V., Corrales, A., Flórez, J., Vidal, R., Rueda, N., Arbonés, M. L., & Martínez-Cué, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106572 · Cited by 104
“This mouse bears a partial trisomy of a segment of Mmu16, containing approximately 92 genes orthologous to Hsa21 genes [48]; in addition, the Ts65Dn mouse also carries a trisomy of ,10 Mb of Mmu17 containing 60 genes that are not homologous to Hsa21 [49].”
BackgroundGarcía-Cerro, S., Rueda, N., Vidal, V., Lantigua, S., & Martínez-Cué, C. (2017) · Neurobiology of Disease · doi:10.1016/j.nbd.2017.06.010 · Cited by 100
Ash, J. A., Velázquez, R., Kelley, C. M., Powers, B. E., Ginsberg, S. D., Mufson, E. J., & Strupp, B. J. (2014) · Neurobiology of Disease · doi:10.1016/j.nbd.2014.06.001 · Cited by 88
“The most well-characterized animal model is the Ts65Dn mouse, which is segmentally trisomic for the distal region of mouse chromosome16 (MMU16)which containsmore than 100 highly conserved genes that are orthologous to those on HSA21 (Sturgeon and Gardiner, 2011).”
Lott, I. T. (2011) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2011.12.010 · Cited by 86
Mouse models of neurodegeneration: Know your question, know your mouse
Fisher, E., & Bannerman, D. M. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aaq1818 · Cited by 80
Prospects for Improving Brain Function in Individuals with Down Syndrome
Costa, A. C. S., & Scott-McKean, J. J. (2013) · CNS Drugs · doi:10.1007/s40263-013-0089-3 · Cited by 83
“The latest published estimate of gene number for HSA21 puts it at more than 500 genes and putative genes [19].”
BackgroundStrupp, B. J., Powers, B. E., Velázquez, R., Ash, J. A., Kelley, C. M., Alldred, M. J., Strawderman, M. S., Caudill, M. A., Mufson, E. J., & Ginsberg, S. D. (2015) · Current Alzheimer Research · doi:10.2174/1567205012666150921100311 · Cited by 72
“One caveat to translational inferences, however, is that the Ts65Dn murine model is only trisomic for approximately 88/161 orthologs on HSA21, and also includes approximately 50 triplicated encoded genes that are not triplicated in HSA21 [14].”
BackgroundInfluentialCorrales, A., Martinez, P. M., García-Cerro, S., Vidal, V., García, E., Flórez, J., Sánchez‐Barceló, E. J., Martínez‐Cué, C., & Rueda, N. (2012) · Journal of Pineal Research · doi:10.1111/jpi.12037 · Cited by 73
“Although both AD and TS animal models overexpress the AbPP gene, TS mice also overexpress 92 genes orthologous to HSA21 genes [5].”
BackgroundAbsence of Prenatal Forebrain Defects in the Dp(16)1Yey/+ Mouse Model of down Syndrome.
Goodliffe, J. W., Olmos-Serrano, J. L., Aziz, N. M., Pennings, J. L. A., Guedj, F., Bianchi, D. W., & Haydar, T. F. (2016) · The Journal of Neuroscience · doi:10.1523/jneurosci.2513-15.2016 · Cited by 65
“Down syndrome (DS), caused by trisomy of 400 – 600 coding and noncoding genes on human chromosome 21 (Hsa21), occurs with an incidence of 1 in 691 live births (Canfield et al., 2006; Cocchi et al., 2010; Sturgeon and Gardiner, 2011) and leads to intellectual disability (Chapman and Hesketh, 2000).”
BackgroundGABAergic over-inhibition, a promising hypothesis for cognitive deficits in Down syndrome
Martín, J. Z. D. S., Delabar, J. M., Bacci, A., & Potier, M. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2017.10.002 · Cited by 70
“Ts65Dn mice have segmental trisomy of murine chromosome 16, containing 92 human orthologs between Mrp139 and Znf295 [97].”
Treating enhanced GABAergic inhibition in Down syndrome: Use of GABA α5-selective inverse agonists
Martínez-Cué, C., Delatour, B., & Potier, M.-C. (2014) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2013.12.008 · Cited by 58
Powers, B. E., Kelley, C. M., Velázquez, R., Ash, J. A., Strawderman, M. S., Alldred, M. J., Ginsberg, S. D., Mufson, E. J., & Strupp, B. J. (2016) · Neuroscience · doi:10.1016/j.neuroscience.2016.11.001 · Cited by 55
“The segmental loci exhibits 55% conservation of known protein coding genes between MMU16 and HSA21 (Davisson et al., 1993; Reeves et al., 1995; Gardiner, 2003; Sturgeon and Gardiner, 2011).”
Luteolin induces hippocampal neurogenesis in the Ts65Dn mouse model of Down syndrome
Zhou, W., Miao, Z., Zhang, B., Long, W., Zheng, F., Kong, J., & Yu, B. (2019) · Neural Regeneration Research · doi:10.4103/1673-5374.248519 · Cited by 53
Pathways to cognitive deficits in Down syndrome
Sturgeon, X., Le, T., Ahmed, M. M., & Gardiner, K. (2012) · Progress in brain research · doi:10.1016/b978-0-444-54299-1.00005-4 · Cited by 52
Self-citationCognitive Impairment, Neuroimaging, and Alzheimer Neuropathology in Mouse Models of Down Syndrome
D. Hamlett, E., A. Boger, H., Ledreux, A., M. Kelley, C., J. Mufson, E., F. Falangola, M., N. Guilfoyle, D., A. Nixon, R., Patterson, D., Duval, N., et al. (2015) · Current Alzheimer Research · doi:10.2174/1567205012666150921095505 · Cited by 46
“There are a minimum of 166 protein coding genes in Hsa21, and the regions on Hsa21 are syntenically conserved with three regions located on murine chromosome (Mmu) 10, 16 and 17 [34, 35].”
BackgroundGoeldner, C., Kishnani, P. S., Skotko, B. G., Casero, J. L., Hipp, J. F., Derks, M., Hernandez, M.-C., Khwaja, O., Lennon-Chrimes, S., Noeldeke, J., et al. (2022) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-022-09418-0 · Cited by 48
“Indeed, it relies solely on findings from the Ts65Dn mouse model of DS which has limitations with regards to predictive and translational relevance [43], and there is currently no clinical evidence of enhanced inhibition in individuals with DS.”
BackgroundAn Anti-β-Amyloid Vaccine for Treating Cognitive Deficits in a Mouse Model of Down Syndrome
Belichenko, P., Madani, R., Rey-Bellet, L., Pihlgren, M., Becker, A., Plassard, A., Vuillermot, S., Giriens, V., Nosheny, R., Kleschevnikov, A., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152471 · Cited by 35
“Down syndrome (DS), or trisomy 21, affects one in 733 newborns [1,2,3,4].”
BackgroundAhmed, M. M., Dhanasekaran, A. R., Block, A., Tong, S., Costa, A. C. S., Stasko, M. R., & Gardiner, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119491 · Cited by 47
“Hsa21 genes that are conserved in mouse include*160 encoding diverse protein functions, five microRNAs, and*45 encoding keratin associated proteins (KRTAPs) [5].”
BackgroundSelf-citationSurvey of Human Chromosome 21 Gene Expression Effects on Early Development in Danio rerio
Edie, S., Zaghloul, N. A., Leitch, C. C., Klinedinst, D. K., Lebron, J., Thole, J. F., McCallion, A. S., Katsanis, N., & Reeves, R. H. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200144 · Cited by 51
Stringer, M., Abeysekera, I., Dria, K. J., Roper, R. J., & Goodlett, C. R. (2015) · Pharmacology Biochemistry and Behavior · doi:10.1016/j.pbb.2015.09.002 · Cited by 42
Scott-McKean, J. J., & Costa, A. C. S. (2011) · Learning & Memory · doi:10.1101/lm.024182.111 · Cited by 47
“For example, it is estimated that up to 4% of brain mRNAs may bind FMRP (Brown et al. 2001), whereas trisomy 21 results in the overexpression of 1% of the genes in the entire genome (Sturgeon and Gardiner 2011).”
BackgroundCosta, A. C. S. (2011) · Developmental Neuroscience · doi:10.1159/000330861 · Cited by 44
Protein profiles in Tc1 mice implicate novel pathway perturbations in the Down syndrome brain
Ahmed, M. M., Dhanasekaran, A. R., Tong, S., Wiseman, F. K., Fisher, E., Tybulewicz, V. L. J., & Gardiner, K. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt017 · Cited by 43
Self-citationBlock, A., Ahmed, M. M., Dhanasekaran, A. R., Tong, S., & Gardiner, K. J. (2015) · Biology of Sex Differences · doi:10.1186/s13293-015-0043-9 · Cited by 43
“Hsa21q encodes ~160 proteins of diverse functions, ~50 members of the keratin-associated protein family, multiple microRNAs, and several hundred human-specific transcripts that may be protein coding, functional RNAs, or transcriptional noise [22, 23].”
BackgroundSelf-citationAltered Distribution of Hippocampal Interneurons in the Murine down Syndrome Model Ts65Dn.
Hernández-González, S., Ballestín, R., López-Hidalgo, R., Gilabert-Juan, J., Blasco-Ibáñez, J. M., Crespo, C., Nácher, J., & Varea, E. (2015) · Neurochemical Research · doi:10.1007/s11064-014-1479-8 · Cited by 41
Alldred, M. J., Lee, S. H., Petkova, E., & Ginsberg, S. D. (2014) · Brain Structure and Function · doi:10.1007/s00429-014-0839-0 · Cited by 41
“The phenotype is presumed to be caused by overexpression of a proportion of the genes triplicated on the HSA21 chromosome, in which current estimates contains [550 genes and putative protein encoding gene transcripts, including [160 known protein encoding transcripts (Sturgeon and Gardiner 2011).”
InfluentialParisotto, E. B., Vidal, V., García-Cerro, S., Lantigua, S., Wilhelm Filho, D., Sanchez-Barceló, E. J., Martínez-Cué, C., & Rueda, N. (2016) · Neurochemical Research · doi:10.1007/s11064-016-2008-8 · Cited by 37
“Among the different mouse models of DS, the Ts65Dn (TS) mouse, that contains three copies of 92 genes orthologous to Hsa21 genes [3], recapitulate numerous phenotypic characteristics of DS, including cognitive deficits and alterations in brain morphology and function [1, 4], that become more pronounced as the animals…”
BackgroundLoss of correlations among proteins in brains of the Ts65Dn mouse model of down syndrome
Ahmed, M. M., Sturgeon, X., Ellison, M., Davisson, M. T., & Gardiner, K. J. (2012) · Journal of Proteome Research · doi:10.1021/pr2011582 · Cited by 39
Self-citationTrazzi, S., Fuchs, C., Franceschi, M. D., Mitrugno, V. M., Bartesaghi, R., & Ciani, E. (2014) · Neurobiology of Disease · doi:10.1016/j.nbd.2014.03.003 · Cited by 40
Alldred, M. J., Penikalapati, S. C., Lee, S. H., Heguy, A., Roussos, P., & Ginsberg, S. D. (2021) · Molecular Neurobiology · doi:10.1007/s12035-021-02453-3 · Cited by 38
“We queried DS murine orthologs triplicated in the Ts mouse model [67, 85], and 64 protein coding trisomic genes were expressed in MSN BFCNs.”
MethodAbeysekera, I., Thomas, J. R., Georgiadis, T. M., Berman, A. G., Hammond, M. A., Dria, K. J., Wallace, J. M., & Roper, R. J. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500781 · Cited by 35
“Bone abnormalities in Ts65Dn DS mice The Ts(1716)65Dn mouse (Ts65Dn), the most widely used and well characterized DS model, displays segmental trisomy of distal mouse chromosome 16 (Mmu16) and carries approximately half the genes conserved between Hsa21 and Mmu16 [10, 11].”
Powers, B. E., Velázquez, R., Kelley, C. M., Ash, J. A., Strawderman, M. S., Alldred, M. J., Ginsberg, S. D., Mufson, E. J., & Strupp, B. J. (2015) · Brain Structure and Function · doi:10.1007/s00429-015-1164-y · Cited by 34
“1996), is trisomic for a segment of mouse chromosome 16 and mouse chromosome 17, with over 100 highly conserved genes that are orthologous to those on HSA21 (Mural et al. 2002; Patterson and Costa 2005; Sturgeon and Gardiner 2011).”
BackgroundInfluentialAlldred, M. J., Chao, H. M., Lee, S. H., Beilin, J., Powers, B. E., Petkova, E., Strupp, B. J., & Ginsberg, S. D. (2018) · Hippocampus · doi:10.1002/hipo.22832 · Cited by 35
“This model translocates a segment of mouse chromosome 16 (MMU16) and mouse chromosome 17 (MMU17) orthologous to HSA21 to <10% of the centromere of MMU17, creating a freely segregating chromosome (Akeson et al., 2001; Kahlem et al., 2004; Reeves et al., 1995) with a conservation of 70% homology for >85 protein coding g…”
BackgroundInfluentialAging and intellectual disability: Insights from mouse models of down syndrome
Ruparelia, A., Pearn, M. L., & Mobley, W. C. (2013) · Developmental Disabilities Research Reviews · doi:10.1002/ddrr.1127 · Cited by 37
Expression profile analysis of vulnerable CA1 pyramidal neurons in young–Middle‐Aged Ts65Dn mice
Alldred, M. J., Lee, S. H., Petkova, E., & Ginsberg, S. D. (2014) · The Journal of Comparative Neurology · doi:10.1002/cne.23663 · Cited by 32
DYRK1A regulates Hap1–Dcaf7/WDR68 binding with implication for delayed growth in Down syndrome
Xiang, J., Yang, S., Xin, N., Gaertig, M. A., Reeves, R. H., Li, S., & Li, X.-J. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614893114 · Cited by 35
“The most widely used DS mouse model, Ts65Dn mice, are trisomic for more than half of the mouse orthologs of genes on human chromosome 21 (59), whereas Ts1Cje mice carry a smaller segmental triplication included in Ts65Dn trisomy (60).”
MethodThomas, J. R., LaCombe, J., Long, R., Lana‐Elola, E., Watson-Scales, S., Wallace, J. M., Fisher, E., Tybulewicz, V. L. J., & Roper, R. J. (2020) · Bone · doi:10.1016/j.bone.2020.115367 · Cited by 28
Kida, E., Rabe, A., Walus, M., Albertini, G., & Golabek, A. A. (2012) · Experimental Neurology · doi:10.1016/j.expneurol.2012.11.022 · Cited by 31
“These animals have an extra copy of part of murine chromosome 16 (MMU16) (from Gabpa/App to Znf295), which is orthologous to HSA21, and are trisomic for 88 of 161 classical protein-coding genes present on HSA21 (Sérégaza et al., 2006; Sturgeon and Gardiner, 2011).”
BackgroundAnti-IL17 treatment ameliorates Down syndrome phenotypes in mice
Rueda, N., Vidal, V., García-Cerro, S., Narcís, J. O., Llorens-Martı́n, M., Corrales, A., Lantigua, S., Iglesias, M., Merino, J., Merino, R., et al. (2018) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2018.05.008 · Cited by 31
Kelley, C. M., Ginsberg, S. D., Alldred, M. J., Strupp, B. J., & Mufson, E. J. (2019) · Developmental Neurobiology · doi:10.1002/dneu.22700 · Cited by 29
“…model has segmental trisomy of murine chromosome (Mmu) 16 and a centromeric low‐coding region of Mmu17 imposed by radiation‐induced reciprocal translocation (Reeves et al., 1995; Akeson et al., 2001; Kahlem et al., 2004; Dierssen et al., 2009; Duchon et al., 2011; Sturgeon and Gardiner, 2011).”
BackgroundAlldred, M. J., Chao, H. M., Lee, S. H., Beilin, J., Powers, B. E., Petkova, E., Strupp, B. J., & Ginsberg, S. D. (2019) · The FASEB Journal · doi:10.1096/fj.201802669rr · Cited by 29
Consequences of trisomy 21 for brain development in Down syndrome
Russo, M. L., Sousa, A. M. M., & Bhattacharyya, A. (2024) · Nature Reviews Neuroscience · doi:10.1038/s41583-024-00866-2 · Cited by 28
“In the 1990s and 2000s, efforts were undertaken to sequence, map and annotate HSA21 in its entirety 202–208 .”
Blazek, J. D., Malik, A. M., Tischbein, M., Arbonés, M. L., Moore, C. S., & Roper, R. J. (2014) · Mechanisms of Development · doi:10.1016/j.mod.2014.12.004 · Cited by 26
“…Ts(1716)65Dn (Ts65Dn) mouse model is the most widely used model in the study of DS. Ts65Dn mice contain segmental trisomy for mouse chromosome 16 (Mmu16) resulting in three copies of approximately half of the gene orthologs triplicated in Ts21 (Davisson et al., 1993; Sturgeon and Gardiner, 2011).”
Kazim, S. F., Blanchard, J., Bianchi, R., & Iqbal, K. (2017) · Scientific Reports · doi:10.1038/srep45561 · Cited by 28
“0001], however, group × age interaction was not significant [F(20,410) = 0.”
Genomic determinants in the phenotypic variability of Down syndrome
Letourneau, A., & Antonarakis, S. E. (2012) · Progress in brain research · doi:10.1016/b978-0-444-54299-1.00002-9 · Cited by 28
Apoptosis in Down’s syndrome: lessons from studies of human and mouse models
Rueda, N., Flórez, J., & Martínez‐Cué, C. (2012) · APOPTOSIS · doi:10.1007/s10495-012-0785-3 · Cited by 31
“a partial trisomy of a segment of Mmu16 that extends from the Mrp139 to the Znf295 gene and contains approximately 92 genes that are orthologous to the Hsa21 genes [14].”
BackgroundExpression of trisomic proteins in Down syndrome model systems
Spellman, C., Ahmed, M. M., Dubach, D., & Gardiner, K. (2012) · Gene · doi:10.1016/j.gene.2012.10.051 · Cited by 25
Self-citationAlldred, M. J., Pidikiti, H., Heguy, A., Roussos, P., & Ginsberg, S. D. (2023) · The FASEB Journal · doi:10.1096/fj.202202111rr · Cited by 21
Gautier, M. K., Kelley, C. M., Lee, S. H., Alldred, M. J., McDaid, J., Mufson, E. J., Stutzmann, G. E., & Ginsberg, S. D. (2023) · Neurobiology of Disease · doi:10.1016/j.nbd.2023.106332 · Cited by 21
“However, HSA21 genes that are syntenic in mice span MMU16, MMU17, and MMU10 (Sturgeon and Gardiner, 2011).”
Lysenko, L. V., Kim, J., Madamba, F., Tyrtyshnaia, A. A., Ruparelia, A., & Kleschevnikov, A. M. (2018) · Neurobiology of Disease · doi:10.1016/j.nbd.2018.03.005 · Cited by 21
Busciglio, J. A., Capone, G. T., O'Byran, J. P., & Gardiner, K. (2013) · Cytogenetic and Genome Research · doi:10.1159/000354306 · Cited by 20
“The number of conserved protein-coding genes is shown below each chromosome [Sturgeon and Gardiner, 2011].”
BackgroundInfluentialSelf-citationBillingsley, C. N., Allen, J., Baumann, D. D., McElyea, S. D., Blazek, J. D., Newbauer, A., Darrah, A., Long, B. C., Young, B. M., Clement, M., et al. (2013) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.36006 · Cited by 17
The Use of Mouse Models for Understanding the Biology of Down Syndrome and Aging
Vacano, G. N., Duval, N., & Patterson, D. W. (2012) · Current Gerontology and Geriatrics Research · doi:10.1155/2012/717315 · Cited by 26
“Mice are small, they have a relatively short generation time, they reproduce rapidly, are inexpensive to maintain and house, and are easy to handle.”
BackgroundCerebellar alterations in a model of Down syndrome: The role of the Dyrk1A gene
García-Cerro, S., Vidal, V., Lantigua, S., Berciano, M. T., Lafarga, M., Ramos‐Cabrer, P., Padró, D., Rueda, N., & Martínez‐Cué, C. (2017) · Neurobiology of Disease · doi:10.1016/j.nbd.2017.12.002 · Cited by 20
“The Ts65Dn (TS) mouse carries a triplication of the distal end of Mmu16, extending from the Mrp139 to the Znf295 genes (Sturgeon and Gardiner, 2011).”
BackgroundRueda, N., Vidal, V., García-Cerro, S., Puente, A., Campa, V. M., Lantigua, S., Narcís, J. O., Bartesaghi, R., & Martínez‐Cué, C. (2020) · Journal of Nutrition · doi:10.1093/jn/nxaa207 · Cited by 17
Santin, M. D., Valabrègue, R., Rivals, I., Pénager, R., Paquin, R., Dauphinot, L., Albac, C., Delatour, B., & Potier, M. (2014) · NMR in Biomedicine · doi:10.1002/nbm.3155 · Cited by 16
Vidal, V., García-Cerro, S., Martinez, P. M., Corrales, A., Lantigua, S., Vidal, R., Rueda, N., Ozmen, L., Hernandez, M., & Martínez‐Cué, C. (2017) · Molecular Neurobiology · doi:10.1007/s12035-017-0675-3 · Cited by 17
“Among these models is the Ts65Dn (TS) mouse, which bears a partial trisomy of a segment of MMU16, which extends from theMrp139 to the Znf295 genes and contains approximately 92 genes that are orthologous to the human chromosome 21 (HSA21) genes [29].”
BackgroundVidal, V., García-Cerro, S., Martinez, P. M., Corrales, A., Flórez, J., Rueda, N., Sharma, A., & Martínez‐Cué, C. (2012) · Neuroscience · doi:10.1016/j.neuroscience.2012.06.031 · Cited by 17
“This mouse bears a partial trisomy of a segment of Mmu16, extending from the Mrp139 to the Znf295 genes, and it contains approximately 92 genes orthologous to Hsa21 genes (Sturgeon and Gardiner, 2011).”
BackgroundMaréchal, D., Pereira, P. L., Duchon, A., & Hérault, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0115302 · Cited by 21
“The long arm of this chromosome (21q) was completely sequenced since 2001 [11], and recent transcription comparisons’ studies report that it contains 696 genes, including at least 235 protein-coding genes and 142 pseudogenes, with a large subset of genes which have a mouse homolog located on regions of synteny carried…”
Hippocampal Network Alterations in Alzheimer's Disease and Down Syndrome: From Structure to Therapy
Sanchez, M. M., Moghadam, S., Naik, P. K., Martin, K. J., & Salehi, A. (2011) · Journal of Alzheimer s Disease · doi:10.3233/jad-2011-0050 · Cited by 17
“However, it has been predicted that the number of genes to be significantly higher (552 genes) [43].”
Meeting at the crossroads: common mechanisms in Fragile X and Down syndrome
Chang, K. T., Ro, H., Wang, W., & Min, K. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.08.007 · Cited by 17
Bi-stream CNN Down Syndrome screening model based on genotyping array
Feng, B. J., Hoskins, W., Zhang, Y., Meng, Z., Samuels, D. C., Wang, J., Xia, R., Liu, C., Tang, J., & Guo, Y. P. (2018) · BMC Medical Genomics · doi:10.1186/s12920-018-0416-0 · Cited by 16
Vidal, V., Puente, A., García-Cerro, S., García‐Unzueta, M. T., Rueda, N., Riancho, J., & Martínez‐Cué, C. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.613211 · Cited by 16
Transcriptional consequences of trisomy 21 on neural induction
Martinez, J. L., Piciw, J. G., Crockett, M., Sorci, I. A., Makwana, N., Sirois, C. L., Giffin-Rao, Y., & Bhattacharyya, A. (2024) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2024.1341141 · Cited by 15
Down syndrome prediction/screening model based on deep learning and illumina genotyping array
Feng, B., Samuels, D. C., Hoskins, W., Guo, Y., Zhang, Y., Tang, J., & Meng, Z.-B. (2017) · IEEE International Conference on Bioinformatics and Biomedicine · doi:10.1109/bibm.2017.8217674 · Cited by 13
“Human chromosome 21(Hsa21) encodes more than 500 genes [19,20], including protein modifiers, transcription factors, RNA splicing factors/modifiers, cell surface receptors and adhesion molecules, and various biochemical pathways components [20,21].”
BackgroundPuente-Bedia, A., Berciano, M. T., Tapia, O., Martínez‐Cué, C., Lafarga, M., & Rueda, N. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031259 · Cited by 12
Hypocellularity in the Murine Model for Down Syndrome Ts65Dn Is Not Affected by Adult Neurogenesis
López‐Hidalgo, R., Ballestín, R., Vega, J., Blasco‐Ibáñez, J. M., Crespo, C., Gilabert‐Juan, J., Nácher, J., & Varea, E. (2016) · Frontiers in Neuroscience · doi:10.3389/fnins.2016.00075 · Cited by 15
“This segment contains approximately 140 genes, many of which are highly conserved between mice and humans (Gardiner et al., 2003; Sturgeon and Gardiner, 2011; Rueda et al., 2012).”
BackgroundKuhn, S. A. C., Ingham, N. J., Pearson, S. A., Gribble, S. M., Clayton, S., Steel, K. P., & Marcotti, W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031433 · Cited by 12
“Details of triplicated genes in Ts65Dn mice [38] were compared with the list of intact Hsa21 genes in Tc1 mice (unpublished data).”
Alldred, M. J., Pidikiti, H., Ibrahim, K. W., Lee, S. H., Heguy, A., Hoffman, G. E., Mufson, E. J., Stutzmann, G. E., & Ginsberg, S. D. (2024) · Journal of Alzheimer s Disease · doi:10.3233/jad-240622 · Cited by 10
Rusu, B., Kukreja, B., Wu, T., Dan, S. J., Feng, M. Y., & Kalish, B. T. (2023) · eNeuro · doi:10.1523/eneuro.0147-23.2023 · Cited by 9
“300 genes of unknown coding or functional potential (Sturgeon and Gardiner, 2011).”
BackgroundPiriform cortex alterations in the Ts65Dn model for down syndrome
Carbonell, J., Blasco‐Ibáñez, J. M., Crespo, C., Nácher, J., & Varea, E. (2020) · Brain Research · doi:10.1016/j.brainres.2020.147031 · Cited by 9
Gautier, M. K., Kelley, C. M., Lee, S. H., Mufson, E. J., & Ginsberg, S. D. (2024) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2024.09.002 · Cited by 8
“Ts65Dn mice are trisomic for portions of mouse chromosome 16 (MMU16) and 17 (MMU17) that are orthologous to the long arm of HSA21 (Gardiner et al., 2003; Sturgeon and Gardiner, 2011).”
BackgroundIshihara, K. (2021) · Genes · doi:10.3390/genes12101598 · Cited by 8
Early increased density of cyclooxygenase-2 (COX-2) immunoreactive neurons in Down syndrome
Mulet, M., Blasco‐Ibáñez, J. M., Crespo, C., Nácher, J., & Varea, E. (2017) · Folia Neuropathologica · doi:10.5114/fn.2017.68582 · Cited by 7
Kulan, H., & Dağ, T. (2019) · PLoS ONE · doi:10.1371/journal.pone.0210954 · Cited by 6
Cholinergic Senescence in the Ts65Dn Mouse Model for Down Syndrome
Kirstein, M., Cambrils, A., Segarra, A., Melero, A., & Varea, E. (2022) · Neurochemical Research · doi:10.1007/s11064-022-03659-0 · Cited by 9
López‐Hidalgo, R., Ballestín, R., Lorenzo, L., Sánchez-Martí, S., Blasco‐Ibáñez, J. M., Crespo, C., Nácher, J., & Varea, E. (2024) · Neurochemistry International · doi:10.1016/j.neuint.2024.105679 · Cited by 6
“…is segmentally trisomic for a portion of the mouse chromosome 16, an orthologue to the long arm of the human chromosome 21, which codes for approximately 140 genes, many of which are highly conserved between mice and humans (Gardiner et al., 2003; Rueda et al., 2012; Sturgeon and Gardiner, 2011).”
Glutamatergic synaptic deficits in the prefrontal cortex of the Ts65Dn mouse model for Down syndrome
Thomazeau, A., Lassalle, O., & Manzoni, O. J. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1171797 · Cited by 6
Dorard, E., Gorisse-Hussonnois, L., Guihenneuc‐Jouyaux, C., Albac, C., Potier, M., & Allinquant, B. (2016) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2016.06.010 · Cited by 5
“…andmost widely used mouse model of DS, trisomic for a segment of chromosome 16 extending between = E. Dorard et al. / Neurobiology of Aging 46 (2016) 43e48 45 genes Mrp139 and Znf295 and containing approximately 92 orthologues of human chromosome 21 genes (Sturgeon and Gardiner, 2011).”
Synaptic Vesicle Recycling Is Unaffected in the Ts65Dn Mouse Model of Down Syndrome
Marland, J. R. K., Smillie, K. J., & Cousin, M. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0147974 · Cited by 5
Abdeldayem, S. S., & ElHefnawi, M. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/333849 · Cited by 5
“This Hsa21 encodes more than 500 gene models [4], where an unknown subset of these genes contributes in the learning deficit [5].”
BackgroundIntellectual Disability in the Elderly
Lim, J. C., Bessey, L. J., Joshi, P., & Boyle, L. L. (2018) · Springer eBooks · doi:10.1007/978-3-319-73078-3_23 · Cited by 4
Kida, E., Walus, M., Albertini, G., & Golabek, A. A. (2021) · Brain Research · doi:10.1016/j.brainres.2021.147535 · Cited by 4
Bioinformatics and Computational Biology
Ali, M. A., Zahoor, A., Niaz, Z., Jabran, M., Anas, M., Shafique, I., Ahmad, H. M., Usama, M., & Abbas, A. (2024) · Springer eBooks · doi:10.1007/978-981-97-0814-7_10 · Cited by 4
Alldred, M. J., Ibrahim, K. W., Pidikiti, H., Lee, S. H., Heguy, A., Chiosis, G., Mufson, E. J., Stutzmann, G. E., & Ginsberg, S. D. (2025) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2025.1546375 · Cited by 4
“…which encompasses a partial triplication of HSA21 orthologs on mouse chromosome 16 (Mmu16; ~90 protein-coding genes), along with a centromeric segment of non-orthologous mouse chromosome 17 (Mmu17; segment 17q1a) (Duchon et al., 2011; Sturgeon and Gardiner, 2011; Akeson et al., 2001).”
Özdemir, H., Kalaycı, H., Yetkinel, S., Çok, T., Çoban, G., & Tarım, E. (2018) · Journal of obstetrics and gynaecology research · doi:10.1111/jog.13636 · Cited by 3
“Hsa21q encodes 161 classical protein-coding genes, 5 microRNAs and >350 additional genes and experimentally supported gene models that cannot be unambiguously classified as protein coding, functional RNA or transcriptional noise.(2,8) Two of these phenotypic features are increased PNT and nuchal edema.”
Background
Metadata
- Authors
- Sturgeon, X., & Gardiner, K. J.
- Affiliations
- University of Colorado Denver (US)
- Corresponding author
- Gardiner, Katheleen J.
- Venue
- Mammalian Genome
- Published
- 2011-03-13
- Volume
- 22
- Issue
- 5-6
- Pages
- 261-271
- ISSN
- 0938-8990 (ISSN-L)
- 1432-1777
- OpenAlex
- W2128527424
- Cited by
- 117
- References
- 38
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 6 · 2023: 5 · 2022: 4 · 2021: 5 · 2020: 5 · 2019: 6 · 2018: 9 · 2017: 8 · 2016: 10 · 2015: 9 · 2014: 12 · 2013: 10 · 2012: 13
- FWCI
- 13.20
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Mammalian Genome (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Anna and John J. Sie Foundation
- National Institutes of Health (5r01hd056235-05)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD056235, R01-HD056235)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- chromosome 21, Down syndrome, orthologous regions, mouse chromosomes, open reading frames, genetic conservation, functional RNA, mouse models of Down syndrome, genome annotation
- MeSH terms
- Animals, Pan troglodytes, Chromosomes, Human, Pair 21, Down Syndrome, Genes, Humans, Species Specificity, Open Reading Frames, Conserved Sequence, DNA, Complementary, Gene Expression Profiling, Regulatory Elements, Transcriptional, Mice
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