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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...al. 2013). Epigenetic regulation of non-LTR retrotransposons may also be important during disease processes. Cancer s are characterized by global hypomethylation and gene-specific hypermethylation (Baylin and Jones 2011). In tumor samples, L1s are variably hypomethylated, whereas hypermethylated...
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Research: A heterozygous IDH1^R132H/WT mutation induces genome-wide alterations in DNA methylation
- Christopher G. Duncan,
- Benjamin G. Barwick,
- Genglin Jin,
- Carlo Rago,
- Priya Kapoor-Vazirani,
- Doris R. Powell,
- Jen-Tsan Chi,
- Darell D. Bigner,
- Paula M. Vertino,
- and Hai Yan
Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
...A heterozygous IDH1 R132H/WT mutation induces genome-wide alterations in DNA methylation Christopher G. Duncan 1 , 6 , Benjamin G. Barwick 2 , 6 , Genglin Jin 1 , Carlo Rago 3 , Priya Kapoor-Vazirani 4 , Doris R. Powell 4...
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Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
...of differentially methylated regions (DMRs) typically involves the detection of consecutive CpGs groups that show significant changes in their average methylation levels. However, the methylation state of a genomic region can also be characterized by a mixture of patterns (epialleles) with variable frequencies...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
...Comprehensive analysis of structural variants in breast cancer s using single-molecule sequencing Sergey Aganezov1, Sara Goodwin2, Rachel M. Sherman1, Fritz J. Sedlazeck3, Gayatri Arun2, Sonam Bhatia2, Isac Lee4, Melanie Kirsche1, Robert Wappel2, Melissa Kramer2, Karen Kostroff5, David L. Spector2...
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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
....DNA–RNA hybrids, also referred to as R-loops, are three-stranded nucleic acid structures, and each is composed of a DNA–RNA duplex and a DNA strand displaced in a single-stranded conformation. R-loops were first found in the f1 phage in 1967 (Milman et al. 1967) and were subsequently characterized in Escherichia...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...polyadenylation (IPA) is a key mechanism driving transcriptome diversity, yet its detection 10 and functional characterization remain challenging due to complex splicing patterns and 11 complexity of intronic regions. Here, we introduce IPAseek, a dynamic programming-based 12 computational framework...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...-associated epigenetic changes in LEps are directly related to elevated cancer risk.Although numerous studies have characterized the DNA methylomes of individual epithelial cell populations in human and mouse breast tissue (Bloushtain-Qimron et al. 2008; Dos Santos et al. 2015), there are not many studies that have...
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Research: The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
- Ronan Chaligné,
- Tatiana Popova,
- Marco-Antonio Mendoza-Parra,
- Mohamed-Ashick M. Saleem,
- David Gentien,
- Kristen Ban,
- Tristan Piolot,
- Olivier Leroy,
- Odette Mariani,
- Hinrich Gronemeyer,
- Anne Vincent-Salomon,
- Marc-Henri Stern,
- and Edith Heard
Genome Res. April 2015 25: 488-503; Published in Advance February 4, 2015, doi:10.1101/gr.185926.114
...chromosome, with highly abnormal 3D nuclear organization and global perturbations of heterochromatin, including gain of euchromatic marks and aberrant distributions of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...technologies for SV discovery in breast cancer patients-derived organoids.More recent studies demonstrated the feasibility of producing long-read sequencing from various clinical tumor samples. For example, Sakamoto et al. (2020b) characterized regions of clustered copy number changes, inversions...
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