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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...that arise from recent demographic events, patterns that are crucial for understanding rare variant effects. To address this challenge, we propose a novel method called spectral components (SPCs), which leverages identity-by-descent (IBD) graphs to capture and transform local, nonlinear fine-scale population...
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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
...(Locke et al. 2011; Rocchi et al. 2012). The new centromere location lacks the repetitive alpha satellites observed at other centromeres. In addition, damage to, or loss of, existing centromeres can be rescued by the formation of new (neo) centromeres at different locations. Neocentromere formation...
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Research: Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
- Jitendra Thakur and
- Kaustuv Sanyal
Genome Res. April 2013 23: 638-652; Published in Advance February 25, 2013, doi:10.1101/gr.141614.112
...chromatin state, is a determinant of centromere/neocentromere identity in C. albicans. Next we compared the strength of CENPA binding on native centromeres and neocentromeres by real-time qPCR analysis on CENPA ChIP DNA from neocentromere-containing strains. Realtime qPCR analysis revealed that native CEN7...
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Corrigendum: Corrigendum: 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. June 2024 34: 979-980; doi:10.1101/gr.279693.124
...the conclusions of the article. The authors apologize for any confusion. Centromere RNA accumulates in the transcriptionally active nucleolus “The results with these antisera confirmed that α-satellite RNA was enriched in the nucleolus (Fig. 1A,C,D,E). Competition with tRNA and rRNA did not affect the detection...
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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
...identity and propagation. CENPA nucleosomes also serve as a platform for kinetochore formation (Supplemental Fig. S1). CENPA can establish functional neocentromeres at ectopic locations that lack canonical centromeric DNA sequence (e.g., human α-satellite repeats) (Amor and Choo 2002; Stimpson and Sullivan...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
...Marseille-Luminy, 13288 Marseille, France Corresponding authors: salvatore.spicuglia@inserm.fr, vahid.asnafi@aphp.frAbstractBroad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain...
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Research: Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles
- Megan E. Aldrup-MacDonald,
- Molly E. Kuo,
- Lori L. Sullivan,
- Kimberline Chew,
- and Beth A. Sullivan
Genome Res. October 2016 26: 1301-1311; Published in Advance August 10, 2016, doi:10.1101/gr.206706.116
...Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles Megan E. Aldrup-MacDonald 1 , 3 , Molly E. Kuo 1 , 3 , Lori L. Sullivan 1 , 3 , Kimberline Chew 1 and Beth A...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
...Science and Engineering, Central South University, Changsha 410083, China Corresponding authors: guofei@csu.edu.cn, jj.tang@siat.ac.cnAbstractCell identity annotation for single-cell transcriptome data is a crucial process for constructing cell atlases, unraveling pathogenesis, and inspiring therapeutic...
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Research: Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
- Shamoni Maheshwari,
- Takayoshi Ishii,
- C. Titus Brown,
- Andreas Houben,
- and Luca Comai
Genome Res. March 2017 27: 471-478; Published in Advance February 21, 2017, doi:10.1101/gr.214619.116
...is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question...
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METHODS: A Novel Chromatin Immunoprecipitation and Array (CIA) Analysis Identifies a 460-kb CENP-A-Binding Neocentromere DNA
- Anthony W.I. Lo,
- Dianna J. Magliano,
- Mandy C. Sibson,
- Paul Kalitsis,
- Jeffrey M. Craig,
- and K.H. Andy Choo
Genome Res. March 1, 2001 11: 448-457; Published in Advance February 8, 2001, doi:10.1101/gr.167601
....F. , Richmond T.J. ( 1997 ) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389 : 251 – 260 . ↵ Maggert K.A. , Karpen G.H. ( 2000 ) Acquisition and metastability of centromere identity and function: Sequence analysis of a human neocentromere. Genome Res. 10 : 725 – 728 . ↵ Muro Y...

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