Searching journal content for articles similar to Mahé et al. 27 (6): 947.

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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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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...- or targeted- sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.Cytosine methylation is the main epigenetic DNA modification found in higher Eukaryotes. In humans...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
...included known promoter binding factors such as the KLF/SP family of transcription factors, which contain guanine/cytosine (G/C) rich sequences. Similarly, top enriched motifs at enhancers contained G/C rich sequences, such as MAZ, ZBTB17, and EGR2. Chromatin interactions frequently connect CpG rich...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...required to reveal a sperm chromatin state distinct from most previous reports. Using ATAC-seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with early development and transcriptional control. Histone modification and chromosome folding profiles also...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...specifically enriched for H3K27me3 modification changes. DNA methylation changes were specifically associated with basal transcriptional factors, the Notch signaling pathway, and the spliceosome. Notably, the polycomb repressive complex was enriched for both H3K27me3 and H3K9me3 modification changes, whereas...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...and landscape, while flies and worms do not, this observation implies that histone marks have a greater role in regulating mRNA expression when cytosine methylation is degenerated within a . Testing the hypothesis that mRNA dosage maintenance is mediated by histone modifications The transcriptional activity...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...in their chromatin environment and transcriptional regulation. We defined promoter regions as 5 kb upstream of and downstream (±5 kb) from the TSS. We then curated chromatin immunoprecipitation (ChIP) experiments for 70 histone modifications and 370 transcription factors, in seven and eleven ENCODE cell lines...
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Resource: Modeling transcriptional regulation of model species with deep learning
- Evan M. Cofer,
- João Raimundo,
- Alicja Tadych,
- Yuji Yamazaki,
- Aaron K. Wong,
- Chandra L. Theesfeld,
- Michael S. Levine,
- and Olga G. Troyanskaya
Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
...states, histone modifications, and binding of transcription factors (TFs). Addressing this challenge across the entire spectrum of genomic variation requires generalizing from the experimental studies (e.g., ChIP-seq data) to learn the regulatory code and thus enable the prediction of effects for any...
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Research: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
- Kasper D. Rasmussen,
- Ivan Berest,
- Sandra Keβler,
- Koutarou Nishimura,
- Lucía Simón-Carrasco,
- George S. Vassiliou,
- Marianne T. Pedersen,
- Jesper Christensen,
- Judith B. Zaugg,
- and Kristian Helin
Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118
...). Yet, whether DNA methylation is causally involved in shaping gene expression patterns, rather than passively mirroring transcriptional states, is still a matter of debate (Schübeler 2015). Here, we present data in support of a role of TET2-mediated cytosine modifications at enhancers to facilitate TF...
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Research: Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
- Yuan Fang,
- Lifen Chen,
- Kande Lin,
- Yilong Feng,
- Pengyue Zhang,
- Xiucai Pan,
- Jennifer Sanders,
- Yufeng Wu,
- Xiu-e Wang,
- Zhen Su,
- Caiyan Chen,
- Hairong Wei,
- and Wenli Zhang
Genome Res. August 2019 29: 1287-1297; Published in Advance July 1, 2019, doi:10.1101/gr.246009.118
...can affect each other, suggesting that a crosstalk exists between R-loops and chromatin modifications in regulating gene expression. R-loops positively correlated with majority of active marks and active gene transcription but were inversely correlated with the repressive mark, H3K27me3, and with low...

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