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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-to-telomere (T2T) assemblies are revolutionizing our understanding of long-hidden biology “dark matter” such as centromeres, rDNA repeats, inter-haplotype variation, and allele-specific expression (ASE), yet insights into dikaryotic fungi that separate their haploid s into distinct nuclei are limited. Here, we...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...Rearrangements of viral and human s at human papillomavirus integration events and their allele-specific impacts on cancer regulation Vanessa L. Porter1,2,3, Michelle Ng1,3, Kieran O'Neill1, Signe MacLennan1,2,3, Richard D. Corbett1, Luka Culibrk1,4, Zeid Hamadeh5,6, Marissa Iden7,8, Rachel Schmidt...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...Innovation, University of Queensland, Brisbane 4072, Australia Corresponding authors: gramarga@usp.br, robert.henry@uq.edu.auAbstractPolyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...the overrepresentation of biological process categories of ASm6A host genes.Enrichment analysis of ASm6AsThe eQTL and sQTL data sets were obtained from the GTEx Consortium (2017). The ASE data sets were obtained from AlleleDB (http://alleledb.gersteinlab.org/). The allele-specific RBP binding data sets were from...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
..., Missouri 63110, USA Corresponding author: hlawson@genetics.wustl.eduAbstractAllele-specific expression (ASE) is a phenomenon in which one allele is preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering the final composition of a gene's product, leading to expression...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...is driven in part by recognition of DNA sequence, genetic variation can influence TF–DNA associations and gene regulation. To identify variants that impact TF binding in human brain tissues, we assessed allele-specific binding (ASB) at heterozygous variants for 94 TFs in nine brain regions from two donors...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...Shuai Wang1,2, Merritt Khaipho-Burch3, Lynn C. Johnson4, Zachary R. Miller4, Peter J. Bradbury5, Doug Speed6, William J. Allen7, M. Cinta Romay4, Jiquan Xue1, Edward S. Buckler3,4,5, Guillaume P. Ramstein6 and Baoxing Song1,2 1Key Laboratory of Maize Biology and Genetic Breeding in Arid Areas...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...methylation H3K27me3 (facultative or developmentally regulated heterochromatin), and the presence of specific histone variants (Henikoff and Smith 2015; Jamge et al. 2023). Upon silencing, TEs accumulate mutations and degenerate into nonautonomous TEs and fragmented remnants or relics (Blumenstiel 2019...
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Research: Allele-specific alternative splicing and its functional genetic variants in human tissues
- Kofi Amoah,
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yiwei Sun,
- Christina Burghard,
- Boon Xin Tan,
- Ei-Wen Yang,
- and Xinshu Xiao
Genome Res. March 2021 31: 359-371; Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
...modulated alternative splicing (GMAS) via identification of allele-specific splicing events. We demonstrate that GMAS events are shared across tissues and individuals more often than expected by chance, consistent with their genetically driven nature. Moreover, although the allelic bias of GMAS exons varies...

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