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LETTER: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere
- Lee H. Wong,
- Kate H. Brettingham-Moore,
- Lyn Chan,
- Julie M. Quach,
- Melissa A. Anderson,
- Emma L. Northrop,
- Ross Hannan,
- Richard Saffery,
- Margaret L. Shaw,
- Evan Williams,
- and K.H. Andy Choo
Genome Res. August 2007 17: 1146-1160; Published in Advance July 10, 2007, doi:10.1101/gr.6022807
...INCENP-interacting protein) at the metaphase centromere. Our data suggest that centromere satellite RNA directly facilitates the accumulation and assembly of centromere-specific nucleoprotein components at the nucleolus and mitotic centromere, and that the sequestration of these components...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Milad Razavi-Mohseni, Weitai Huang, Yu A. Guo, Dustin Shigaki, Shamaine Wei Ting Ho, Patrick Tan, Anders J. Skanderup and Michael A. Beer Genome Research 34: 680–695 (2024)Following genotyping analysis from ATAC-seq and RNA-seq reads, the authors found the ATAC-seq sample labeled SNU484...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...the signal from the rDNA. The RNA expression data are plotted on a log scale. The apparent dips in coverage at the centromeres in the input data are likely to be an artifact of the mapping procedure because reads that map to more than one site in the were discarded. Some reads are also incorrectly mapped...
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Method: Rapid molecular assays to study human centromere genomics
- Rafael Contreras-Galindo,
- Sabrina Fischer,
- Anjan K. Saha,
- John D. Lundy,
- Patrick W. Cervantes,
- Mohamad Mourad,
- Claire Wang,
- Brian Qian,
- Manhong Dai,
- Fan Meng,
- Arul Chinnaiyan,
- Gilbert S. Omenn,
- Mark H. Kaplan,
- and David M. Markovitz
Genome Res. December 2017 27: 2040-2049; Published in Advance November 15, 2017, doi:10.1101/gr.219709.116
...CENPB also stabilizes and maintains cohesion between sister chromatids in pericentric heterochromatin, a separable function that is also required for proper chromosome segregation (Tanno et al. 2015).Recent studies have suggested that centromere sequences, and potentially cognate RNA transcripts...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...the small RNA inferences from human samples. Table 2 shows the top three most enriched terms for cellular component (Gene Ontology) and KEGG pathways. The enriched terms were consistent with the expected functional features of the analyzed data sets. For instance, both the brain and cerebellum expression...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...topological restrictions engage with each other within mRNA and tRNA factories, polycomb domains, the nucleolus, nuclear speckles, and potentially other nuclear subcompartments (Fig. 1A; Bhat et al. 2021). Some of these trans contacts involve specific loci whose interactions are important to gene regulation...
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Research: Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin
- Anastassiia Vertii,
- Jianhong Ou,
- Jun Yu,
- Aimin Yan,
- Hervé Pagès,
- Haibo Liu,
- Lihua Julie Zhu,
- and Paul D. Kaufman
Genome Res. August 2019 29: 1235-1249; Published in Advance June 14, 2019, doi:10.1101/gr.247072.118
...the centromere on the left of this acrocentric chromosome). Unlike MACS2 and EDD, NADfinder was able to call peaks on regions distal from the centromere. (E) A shorter chromosomal region, ∼1.3 Mb from Chr 11qA1, analyzed with the same tracks as C and D, plus MEF RNA-seq data at the bottom (GSM2453367, GSM2453368...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...bees 214 We sought to validate the DESs using Sanger sequencing. Prior to this, we observed 215 a general trend in which CV samples exhibited greater molecular variation compared to 216 GF samples. Principal component analysis (PCA) based on both gene expression and RNA 217 editing levels revealed...
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Corrigendum: Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. January 2024 34: 160; doi:10.1101/gr.278898.123
...Laboratory Press 9509184 10.1101/gr.278898.123 ;34/1/160 ;gr.278898.123 160 gr.278898.123 Corrigendum Corrigendum Corrigenda Ma Qicheng Srivastav Satyam P. Gamez Stephanie Dayama Gargi Feitosa-Suntheimer Fabiana Patterson Edward I. Johnson Rebecca M. Matson Erik M. Gold Alexander S. Brackney Douglas E...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...

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