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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
..., Ye J, Ou H, Jiang T, Guo B, Yang Q, Liang W, et al. 2021. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Mol Psychiatry 26: 6630–6642. doi:10.1038/s41380...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...Tong University, Shanghai 200030, China ↵4 These authors contributed equally to this work. Corresponding authors: jtshi@sibcb.ac.cn, fh12355@rjh.com.cnAbstractDNA methylation and associated regulatory elements play a crucial role in gene expression regulation. Previous studies have focused primarily...
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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
...loci that show unusual and biologically interesting patterns of ASE, including allele-specific alternative splicing and transcription termination sites. Our methodology provides a rigorous, quantitative, and high-resolution tool for profiling ASE across whole genomes. Footnotes ↵ 3...
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Method: A pooling-based approach to mapping genetic variants associated with DNA methylation
- Irene M. Kaplow,
- Julia L. MacIsaac,
- Sarah M. Mah,
- Lisa M. McEwen,
- Michael S. Kobor,
- and Hunter B. Fraser
Genome Res. June 2015 25: 907-917; Published in Advance April 24, 2015, doi:10.1101/gr.183749.114
...that cover &lt;2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite...
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Research: Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
- Wei Qu,
- Shin-ichi Hashimoto,
- Atsuko Shimada,
- Yoichiro Nakatani,
- Kazuki Ichikawa,
- Taro L. Saito,
- Katsumi Ogoshi,
- Kouji Matsushima,
- Yutaka Suzuki,
- Sumio Sugano,
- Hiroyuki Takeda,
- and Shinichi Morishita
Genome Res. August 2012 22: 1419-1425; Published in Advance June 11, 2012, doi:10.1101/gr.140236.112
.... Allele-specificmethylation is prevalent and is contributed by CpG-SNPs in the human . Genome Res 20: 883–889. Sved J, Bird A. 1990. The expected equilibrium of the CpG dinucleotide in vertebrate s under a mutation model. Proc Natl Acad Sci 87: 4692–4696. Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki...
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Research: Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence
- Lavinia Gordon,
- Jihoon E. Joo,
- Joseph E. Powell,
- Miina Ollikainen,
- Boris Novakovic,
- Xin Li,
- Roberta Andronikos,
- Mark N. Cruickshank,
- Karen N. Conneely,
- Alicia K. Smith,
- Reid S. Alisch,
- Ruth Morley,
- Peter M. Visscher,
- Jeffrey M. Craig,
- and Richard Saffery
Genome Res. August 2012 22: 1395-1406; Published in Advance July 16, 2012, doi:10.1101/gr.136598.111
..., the range of heritability within the top 5% of probes in the Boks and colleagues study (0.62–0.94) is similar to that found for the top 5% of probes for CBMCs in our study (0.48–0.94). Studies of allele-specific methylation (ASM) have also found evidence for a high heritability of DNA methylation...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...using human genomic DNA, we assessed whether the joint identification of SNPs and methylation is comparable with commonly used techniques. We also took advantage of the dual readout to question whether allele-specific methylation (ASM) can be identified. We next applied Methyl-SNP-seq in conjunction...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...to damage and efficiency of base excision repair (BER) would impact both CpG and non-CpG mutation rate. Thus, comparison of CpG and non-CpG SNP densities along the chromosome may be informative about relative contributions of forces influencing mutation rate. To analyze changes in the variation rate along...
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Research: Methylomic trajectories across human fetal brain development
- Helen Spiers,
- Eilis Hannon,
- Leonard C. Schalkwyk,
- Rebecca Smith,
- Chloe C.Y. Wong,
- Michael C. O’Donovan,
- Nicholas J. Bray,
- and Jonathan Mill
Genome Res. March 2015 25: 338-352; Published in Advance February 3, 2015, doi:10.1101/gr.180273.114
...in the methyl-CpG binding protein 2 ( MECP2 ) gene. However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited. We quantified genome-wide patterns of DNA methylation at ∼400,000 sites in 179 human fetal brain samples (100 male, 79 female...
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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
...(SNPs). However, these CpG SNPs appear to have little effect when located in regions of differential methylation that are determined by cis-regulatory factors (Shoemaker et al. 2010).Because the P. picta Y Chromosome is highly degraded and our reference was assembled from sequencing female tissue...

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