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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
..., unlike in tRNAs, m3C sites in poly(A) RNAs are not specifically associated with loop structures.METTL2A downregulates m3C RNAsTo investigate the role of METTL2A in pancreatic cancer cells, we analyzed METTL2A-regulated genes in AsPC-1 cells. Direct RNA sequencing revealed that METTL2A knockdown led...
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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...a comparative analysis of 47,XYY and 47,XXY fibroblasts and iPSC transcriptomes. We reveal a transcriptional feedback mechanism tuning non-PAR X Chromosome gene (NPX) homologs in Y supernumerary cells, a phenomenon not detected in X aneuploid male iPSCs. By ectopically modulating the expression of selected NPY...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...groups is indicated by an asterisk, as determined by Bonferroni-corrected Wilcoxon rank-sum test. Complete list of P-values are available in Supplemental Table 2. (E) Comparison of gene expression levels between autosomal and X Chromosome genes in female and male gonad, head, liver, and muscle tissues...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...the chromosome's genomic sequence separated by intergenic stretches of DNA which are devoid of genes, in a strand-specific manner. However, in practice, the genomic organization is more complex, and genes can in reality occupy the same genomic space as each other and are considered as overlapping genes...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain...
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Method: Estimation of rearrangement phylogeny for cancer genomes
- Chris D. Greenman,
- Erin D. Pleasance,
- Scott Newman,
- Fengtang Yang,
- Beiyuan Fu,
- Serena Nik-Zainal,
- David Jones,
- King Wai Lau,
- Nigel Carter,
- Paul A.W. Edwards,
- P. Andrew Futreal,
- Michael R. Stratton,
- and Peter J. Campbell
Genome Res. February 2012 22: 346-361; Published in Advance October 12, 2011, doi:10.1101/gr.118414.110
...of disrupted chromosomal segments opens the possibility of reverse-engineering the history of rearrangements that have taken place and constructing contigs of digital karyotypes of cancer s to base-pair resolution.Graph theory has seen particular utility in this area of research. For example, frameworks...
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Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
- Joe R. Harman,
- Ross Thorne,
- Max Jamilly,
- Marta Tapia,
- Nicholas T. Crump,
- Siobhan Rice,
- Ryan Beveridge,
- Edward Morrissey,
- Marella F.T.R. de Bruijn,
- Irene Roberts,
- Anindita Roy,
- Tudor A. Fulga,
- and Thomas A. Milne
Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
...rearrangements (KMT2Ar) are chromosome translocations that fuse KMT2A in frame to one of a wide number of partner genes, creating novel fusion proteins (KMT2A-FPs), the most common of which is KMT2A-AFF1 (formerly MLL-AF4 or MLL-MLLT2) (Meyer et al. 2013). KMT2Ar leukemias have few cooperating mutations (Bardini...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...detection. We performed RACA runs on simulated data sets without using read mapping information (similar to the strategy described by Kim et al. 2013) to focus on comparison between the rearrangement models.Given a resulting set of chromosomes, we call an adjacency (a pair of consecutive contigs) correct...
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