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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
...as only one allele is expressed. Allele-specific DNA methylation and chromatin composition are two well-established epigenetic systems that control imprinted gene expression (Fournier et al. 2002; Singh et al. 2010; Prendergast et al. 2012).ASE can reflect differential rates of transcription, m...
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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
..., referred to as DMR hotspots (Methods). HPV integration sites were then intersected with the DMR hotspots to identify events that potentially affected DNA methylation in an allele-specific manner. Across the samples in our data set, 33 integration event loci overlapped autosomal DMR hotspots (Fig. 6A...
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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
....Deciphering the genotype-to-phenotype map remains a fundamental quest in biology. Gene expression is a promising focal point, because it is an intermediate step between DNA sequence and gross phenotype. Gene expression itself is a complex trait regulated by genetic, epigenetic, and environmental factors (Pastinen 2010...
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Research: Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
...expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these regulatory “layers” are buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin...
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Method: Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
- Pejman Mohammadi,
- Stephane E. Castel,
- Andrew A. Brown,
- and Tuuli Lappalainen
Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
...of Geneva Medical School, Geneva, 1211, Switzerland; 4Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, 1211, Switzerland; 5Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland Mapping cis-acting expression quantitative trait loci (cis-eQTL) has become a popular...
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Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...by ligation to TruSeq Illumina adapters with T4 DNA ligase (Enzymatics). BAM files were filtered to remove read-pairs which mapped to ribosomal DNA sequences.Allele-specific alignment and data analysisReads of quality scores above 30 were independently mapped to 129/sv and castaneus reference s using Bowtie 2...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
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Research: Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
- Robert Shoemaker,
- Jie Deng,
- Wei Wang,
- and Kun Zhang
Genome Res. July 2010 20: 883-889; Published in Advance April 23, 2010, doi:10.1101/gr.104695.109
...al. 2008. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 40: 904–908. Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. 2009. A robust approach to identifying tissue-specific gene expression regulatory...
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Method: A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- Daniel A. Skelly,
- Marnie Johansson,
- Jennifer Madeoy,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
...haplotype A or B, which served as input to our Bayesian model. As the RNA-seq data from Pickrell et al. (2010) were not accompanied by genomic DNA sequence data, we used the same estimates of the dispersion in read counts as our full analysis of the yeast data (i.e., the analysis of Illumina and ABI Allele-specific...
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Methods: SNP-specific array-based allele-specific expression analysis
- Hans T. Bjornsson,
- Thomas J. Albert,
- Christine M. Ladd-Acosta,
- Roland D. Green,
- Michael A. Rongione,
- Christina M. Middle,
- Rafael A. Irizarry,
- Karl W. Broman,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 771-779; Published in Advance March 27, 2008, doi:10.1101/gr.073254.107
...analysis was performed on a PSQ HS96 Pyrosequencer (Biotage) according to the manufacturer’s protocol. All allele-specific expression analysis was performed in triplicate (Supplemental Table 3). Oligonucleotide reconstitution experiment We synthesized 130 biotinylated 45-nt oligonucleotides (Integrated DNA...

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