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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
....Transcriptional similarities between invdupdel(8p) and Trisomy 21Previous reports have noted similarities between the clinical presentation of Down syndrome and other conditions caused by whole-chromosome aneuploidy (Krivega et al. 2022). On a cellular level, different autosomal trisomies result in similar changes in gene...
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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
...in aneuploid cancer cell linesIn the above analysis, we noted that certain gene groups, particularly the ribosome and translation-associated processes, tended to be down-regulated in both highly aneuploid cells and when those genes were encoded on a gained chromosome. We therefore considered the possibility...
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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...and maintaining the alleles in heterozygous sites in one or two of the four chromosome copies.Gene expression from Leish Chr 31 is controlled by down-regulation of all chromosomal copies to a similar extentPrevious works from Prieto Barja et al. (2017) and Dumetz et al. (2017) have demonstrated that having extra...
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Research: Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection
- Konstantin Popadin,
- Stephan Peischl,
- Marco Garieri,
- M. Reza Sailani,
- Audrey Letourneau,
- Federico Santoni,
- Samuel W. Lukowski,
- Georgii A. Bazykin,
- Sergey Nikolaev,
- Diogo Meyer,
- Laurent Excoffier,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. January 2018 28: 1-10; Published in Advance December 13, 2017, doi:10.1101/gr.228411.117
.... Classification of human chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes. Am J Hum Genet 81: 475–491. ↵Antonarakis SE, Petersen MB, McInnis MG, Adelsberger PA, Schinzel AA, Binkert F, Pangalos C, Raoul O, Slaugenhaupt SA, Hafez M. 1992. The meiotic stage of nondisjunction...
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LETTER: The Mouse Brain Transcriptome by SAGE: Differences in Gene Expression between P30 Brains of the Partial Trisomy 16 Mouse Model of Down Syndrome (Ts65Dn) and Normals
- Roman Chrast,
- Hamish S. Scott,
- Marie Pierre Papasavvas,
- Colette Rossier,
- Emmanuel S. Antonarakis,
- Christine Barras,
- Muriel T. Davisson,
- Cecilia Schmidt,
- Xavier Estivill,
- Mara Dierssen,
- Melanie Pritchard,
- and Stylianos E. Antonarakis
Genome Res. December 1, 2000 10: 2006-2021; doi:10.1101/gr.158500
...the first overall analysis of the differences in gene expression in aneuploid versus normal mammalian brain cells. Trisomy 21 (T21), or Down syndrome (DS), is one of a few autosomal aneuploidies in which many cases escape from fetal or early postnatal lethality. DS phenotypes show variable penetrance...
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Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
- Matthew B. Rogers,
- James D. Hilley,
- Nicholas J. Dickens,
- Jon Wilkes,
- Paul A. Bates,
- Daniel P. Depledge,
- David Harris,
- Yerim Her,
- Pawel Herzyk,
- Hideo Imamura,
- Thomas D. Otto,
- Mandy Sanders,
- Kathy Seeger,
- Jean-Claude Dujardin,
- Matthew Berriman,
- Deborah F. Smith,
- Christiane Hertz-Fowler,
- and Jeremy C. Mottram
Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
...(Downing et al. 2011), and L. donovani LV9, a human strain isolated in Ethiopia in 1967 and subsequently maintained by animal passage (Bradley and Kirkley 1977; Stager et al. 2000), were also sequenced. The 19 L. infantum–specific genes appear conserved in L. donovani LV9 and are not clearly absent in L...
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Research: The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome
- M. Reza Sailani,
- Periklis Makrythanasis,
- Armand Valsesia,
- Federico A. Santoni,
- Samuel Deutsch,
- Konstantin Popadin,
- Christelle Borel,
- Eugenia Migliavacca,
- Andrew J. Sharp,
- Genevieve Duriaux Sail,
- Emilie Falconnet,
- Kelly Rabionet,
- Clara Serra-Juhé,
- Stefano Vicari,
- Daniela Laux,
- Yann Grattau,
- Guy Dembour,
- Andre Megarbane,
- Renaud Touraine,
- Samantha Stora,
- Sofia Kitsiou,
- Helena Fryssira,
- Chariklia Chatzisevastou-Loukidou,
- Emmanouel Kanavakis,
- Giuseppe Merla,
- Damien Bonnet,
- Luis A. Pérez-Jurado,
- Xavier Estivill,
- Jean M. Delabar,
- and Stylianos E. Antonarakis
Genome Res. September 2013 23: 1410-1421; Published in Advance June 19, 2013, doi:10.1101/gr.147991.112
...association between variation of the COL6A1 gene region with CHD in Down syndrome (Davies et al. 1995). Also, Grossman et al. (2011) used Drosophila, mouse transgenesis, and a cardiac myoblast H9C2 cell model to show that the overexpression of DSCAM and COL6A2 genes cooperatively contributes to ASD in mice...
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LETTER: Bacterial Contig Map of the 21q11 Region Associated with Alzheimer’s Disease and Abnormal Myelopoiesis in Down Syndrome
- Jürgen Groet,
- Jane H. Ives,
- Andrew P. South,
- Pedro R. Baptista,
- Tania A. Jones,
- Marie-Laure Yaspo,
- Hans Lehrach,
- Marie-Claude Potier,
- Christine Van Broeckhoven,
- and Dean Nižetić
Genome Res. April 1, 1998 8: 385-398; doi:10.1101/gr.8.4.385
...in the telomeric half. Studies of partial trisomies and correlations to phenotypic features of Down syndrome (DS) ( Delabar et al. 1993 ) led to a widespread belief that practically all the dismorphic features were caused by trisomy of the gene(s) in the so-called Down syndrome critical region (DCR). This region...
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ARTICLE: A high-fidelity physical map of human chromosome 21q in yeast artificial chromosomes.
- J R Korenberg,
- X N Chen,
- S Mitchell,
- S Fannin,
- S Gerwehr,
- D Cohen,
- and I Chumakov
Genome Res. December 1995 5: 427-443; doi:10.1101/gr.5.5.427
...in the physical map. This integrated map will facilitate the search for the genes responsible for the Down syndrome phenotypes and provide a better understanding of genome organization and chromosome structure. Footnotes Copyright © Cold Spring Harbor Laboratory Press J R D, Cohen Fannin S...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...Roman et al. 2024), DDX3X expression that is elevated upon addition of Xi does not drive significant gene expression changes in the aneuploid lines. An alternative hypothesis, which is not mutually exclusive with DDX3X auto-regulation, is that DDX3X is negatively modulated by other genes expressed from...
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