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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. The double-stranded cDNA fragments were blunted using T4DNA polymerase, KlenowDNA polymerase and T4 PNK. A single “A” nucleotide was added to the 3...
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Resource: A DNA methylation fingerprint of 1628 human samples
- Agustin F. Fernandez,
- Yassen Assenov,
- Jose Ignacio Martin-Subero,
- Balazs Balint,
- Reiner Siebert,
- Hiroaki Taniguchi,
- Hiroyuki Yamamoto,
- Manuel Hidalgo,
- Aik-Choon Tan,
- Oliver Galm,
- Isidre Ferrer,
- Montse Sanchez-Cespedes,
- Alberto Villanueva,
- Javier Carmona,
- Jose V. Sanchez-Mut,
- Maria Berdasco,
- Victor Moreno,
- Gabriel Capella,
- David Monk,
- Esteban Ballestar,
- Santiago Ropero,
- Ramon Martinez,
- Marta Sanchez-Carbayo,
- Felipe Prosper,
- Xabier Agirre,
- Mario F. Fraga,
- Osvaldo Graña,
- Luis Perez-Jurado,
- Jaume Mora,
- Susana Puig,
- Jaime Prat,
- Lina Badimon,
- Annibale A. Puca,
- Stephen J. Meltzer,
- Thomas Lengauer,
- John Bridgewater,
- Christoph Bock,
- and Manel Esteller
Genome Res. February 2012 22: 407-419; Published in Advance May 25, 2011, doi:10.1101/gr.119867.110
...modification affecting gene activity and cellular biology. Determining the complete DNA methylome entails describing all the methylated nucleotides in an organism. The gold standard technique for analyzing the methylation state of individual cytosines is bisulfite sequencing in which unmethylated cytosines...
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Research: DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences
- Yoshiyuki Watanabe,
- Hiroyuki Yamamoto,
- Ritsuko Oikawa,
- Minoru Toyota,
- Masakazu Yamamoto,
- Norihiro Kokudo,
- Shinji Tanaka,
- Shigeki Arii,
- Hiroshi Yotsuyanagi,
- Kazuhiko Koike,
- and Fumio Itoh
Genome Res. March 2015 25: 328-337; Published in Advance February 4, 2015, doi:10.1101/gr.175240.114
..., Rosales C, Lopez-Nieva P, Gra~na O, Ballestar E, Ropero S, Espada J, Melo SA, Lujambio A, Fraga MF, et al. 2009. The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res 19: 438–451. Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
.... Notably, hepatitis B virus (HBV) DNA integration frequently results in the generation of somatic SVs, particularly inducing interchromosomal translocations (TRAs). Although HBV DNA integration into the liver occurs randomly, multisite shared HBV-induced SVs are early driving events in the pathogenesis...
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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
...asexual clonal growth.Given the connection between sRNAs and DNA methylation, we next investigated Spirodela DNA methylation patterns. Methylome analysis by enzymatic methyl-seq (EM-seq) (Feng et al. 2020) showed similar results to those previously published using bisulfite sequencing (Michael et al. 2017...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...fields.View larger version: In this window In a new window Figure 1. RNA modifications and their corresponding writer/editing enzymes: (A) N6-methyladenosine (m6A) deposited by a methyltransferase complex that includes the METTL3–METTL14 heterodimer, (B) 5-methylcytosine (m5C) deposited by the DNA...
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Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
- Musa A. Hassan,
- Vincent Butty,
- Kirk D.C. Jensen,
- and Jeroen P.J. Saeij
Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
.../BXAmice (28 samples in total) before and after stimulation with IFNG/tumor necrosis factor alpha (TNF), inflammatory cytokines important in the immune response against most intracellular pathogens, or CpG, a synthetic double-stranded DNA that activates TLR9, or infection with T. gondii, an obligate...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...; Xiao et al. 2016). Finally, m6A modifications can also be erased by the dioxygenases FTO and ALKBH5, which specifically demethylate m6A RNA (Zhang et al. 2017; Wei et al. 2022).The m6A RNA modification has been identified in several viral genomic RNA, being first described for DNA viruses...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...in the liver. The panel is composed as described for Figure 3A.Macaque TE methylome landscapesExceptions to DNA methylation at specific donor L1 loci appear to facilitate somatic retrotransposition in humans (Faulkner and Billon 2018). However, it was unclear whether similar “escapee” L1s reside in macaque...
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