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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...subclasses (Supplemental Fig. S5A,B). Notably, age-associated DEGs within GABAergic 160 neurons (ID 197), glutamatergic neurons (ID 166), and oligodendrocytes (ID 327) showed the 161 most significant enrichment across both methods. Key PD-related KEGG pathway genes altered 162 in these subclasses included...
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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
...transcriptional changes, independent of the identity of the extra chromosome (e.g., in trans) (Sheltzer et al. 2012; Dürrbaum et al. 2014). To investigate whether aneuploidy is associated with gene expression changes in trans across a large panel of cancer cell lines and to determine where these patterns...
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Research: Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease
- Stephanie Y. Yang,
- Christina A. Castellani,
- Ryan J. Longchamps,
- Vamsee K. Pillalamarri,
- Brian O'Rourke,
- Eliseo Guallar,
- and Dan E. Arking
Genome Res. March 2021 31: 349-358; Published in Advance January 13, 2021, doi:10.1101/gr.269381.120
....89, CI = 0.83; 0.96) and incident neurodegenerative disease (HR = 0.95, 95% CI = 0.91;0.98). The observation that mtDNA-CN measured in blood is associated with gene expression in other tissues suggests that blood-derived mtDNA-CN can reflect metabolic health across multiple tissues. Identification of key...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...to identify transcripts and proteins that change with age (Fig. 1). We quantified 21,016 unique transcripts after filtering out low expressed genes, and 4221 proteins corresponding to 4151 unique Ensembl gene IDs (release 84). To compare age-related changes across transcripts and proteins, we restricted our...
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Research: Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
- Anushka Gupta,
- Farnaz Shamsi,
- Nicolas Altemose,
- Gabriel F. Dorlhiac,
- Aaron M. Cypess,
- Andrew P. White,
- Nir Yosef,
- Mary Elizabeth Patti,
- Yu-Hua Tseng,
- and Aaron Streets
Genome Res. February 2022 32: 242-257; Published in Advance January 18, 2022, doi:10.1101/gr.275509.121
...genes in mature adipocytes (Supplemental Fig. S10J). Although multiple markers for each cluster had conserved expression across scRNA-seq and snRNA-seq, some markers were exclusively enriched in either one of the data sets (Supplemental Fig. S10J), thereby highlighting the importance of performing joint...
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Research: Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
- Daniel W. Bellott and
- David C. Page
Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
...broadly expressed across development as well as across adult tissues.Caenophidian Z–W gene pairs are subject to strong purifying selectionIf surviving X–Y and Z–W gene pairs are extremely dosage sensitive, alleles that alter the ancestral function of the homologs on the X or the Z Chromosomes should...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...of transcription, translation, and protein stability (Bellott et al. 2014; Naqvi et al. 2018), even small sex biases in expression could have cascading effects on genes across the .View larger version: In this window In a new window Figure 1. Estimates of MSY gene expression across 36 human tissues. (A) Outside...
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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
...to their near universal use of polycistronic transcription, limiting their capacity to alter the transcription of individual genes via promoters and instead increasing their reliance on mechanisms of gene expansion and contraction and on post-transcriptional control mechanisms (Teixeira et al. 2012; Dumetz et...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...bodies, suggesting an alternative and nonrepressive function (Wang et al. 2009; Kidder and Palmer 2012; Whyte et al. 2012). In tumor cells, HDAC inhibition reduced the activity of superenhancers (SEs) via aberrant hyperacetylation, causing down-regulation of SE-driven transcription of genes such as Myc...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...in all organs, a combination of various alternative mechanisms may have compensated for the dosage reduction of haploinsufficient genes following Y degeneration. These include the transcriptional up-regulation of individual X-linked genes or down-regulation of selected autosomal partners (Julien et al...
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