Searching journal content for articles similar to Teschendorff et al. 20 (4): 440.

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  1. Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
    • Xiu Fan,
    • Qili Qian,
    • Wenran Li,
    • Tianzi Liu,
    • Changqing Zeng,
    • Peilin Jia,
    • Huandong Lin,
    • Xin Gao,
    • Li Jin,
    • Mingfeng Xia,
    • Sijia Wang,
    • and Fan Liu
    Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
    ...and stochastic accumulation of epigenetic changes, such as DNA methylation variability, with advancing age. Although increasingly recognized for its potential role in aging biology, its extent, biological significance, and population specificity remain insufficiently characterized. Here, we present the first...
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  2. Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
    • Carmen M. Koch,
    • Kristina Reck,
    • Kaifeng Shao,
    • Qiong Lin,
    • Sylvia Joussen,
    • Patrick Ziegler,
    • Gudrun Walenda,
    • Wolf Drescher,
    • Bertram Opalka,
    • Tobias May,
    • Tim Brümmendorf,
    • Martin Zenke,
    • Tomo Šarić,
    • and Wolfgang Wagner
    Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
    ...Pluripotent stem cells escape from senescence-associated DNA methylation changes Carmen M. Koch 1 , Kristina Reck 1 , Kaifeng Shao 2 , Qiong Lin 3 , Sylvia Joussen 1 , Patrick Ziegler 4 , Gudrun Walenda 1 , Wolf...
  3. 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
    ...with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1628 human samples in which we interrogated 1505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around...
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  4. Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
    • Yutaro Hori,
    • Akira Shimamoto,
    • and Takehiko Kobayashi
    Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
    ...in the other samples (Supplemental Table S1, column 7), we speculate that they are genomic instability “hotspots,” where mutation is frequent in DNA repair compromised cells.Human pluripotent stem cells have a different methylation statusNext, we analyzed rDNA methylation status in human induced pluripotent...
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  5. Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
    • Agustín F. Fernández,
    • Gustavo F. Bayón,
    • Rocío G. Urdinguio,
    • Estela G. Toraño,
    • María G. García,
    • Antonella Carella,
    • Sandra Petrus-Reurer,
    • Cecilia Ferrero,
    • Pablo Martinez-Camblor,
    • Isabel Cubillo,
    • Javier García-Castro,
    • Jesús Delgado-Calle,
    • Flor M. Pérez-Campo,
    • José A. Riancho,
    • Clara Bueno,
    • Pablo Menéndez,
    • Anouk Mentink,
    • Katia Mareschi,
    • Fabian Claire,
    • Corrado Fagnani,
    • Emanuela Medda,
    • Virgilia Toccaceli,
    • Sonia Brescianini,
    • Sebastián Moran,
    • Manel Esteller,
    • Alexandra Stolzing,
    • Jan de Boer,
    • Lorenza Nisticò,
    • Maria A. Stazi,
    • and Mario F. Fraga
    Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
    ...is that the differences in the number of individuals analyzed and different data analyses undertaken make the interpretation of the comparison of age-dependent DNA methylation changes in different cell types difficult. However, the conserved pattern of chromatin signatures in stem and differentiated cells suggests that H...
  6. Research: Age-associated DNA methylation in pediatric populations
    • Reid S. Alisch,
    • Benjamin G. Barwick,
    • Pankaj Chopra,
    • Leila K. Myrick,
    • Glen A. Satten,
    • Karen N. Conneely,
    • and Stephen T. Warren
    Genome Res. April 2012 22: 623-632; Published in Advance February 1, 2012, doi:10.1101/gr.125187.111
    ...Age-associated DNA methylation in pediatric populations Reid S. Alisch 1 , 4 , Benjamin G. Barwick 1 , 4 , Pankaj Chopra 1 , Leila K. Myrick 1 , Glen A. Satten 1 , 2 , Karen N. Conneely 1 and Stephen T. Warren 1 , 3...
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  7. Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
    • Ryan O'Hara,
    • Enzo Tedone,
    • Andrew Ludlow,
    • Ejun Huang,
    • Beatrice Arosio,
    • Daniela Mari,
    • and Jerry W. Shay
    Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
    ...of resting PBMCs.View larger version: In this window In a new window Figure 4. mtDNA in T cells shows stimulation- and age-dependent changes. (A) T cells from 22 healthy donors (aged 33 ± 7) were stimulated at day 0 by anti-CD3/CD28 beads and mtDNA per cell equivalent was measured over a 15-d period...
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  8. Research: A DNA hypermethylation module for the stem/progenitor cell signature of cancer
    • Hariharan Easwaran,
    • Sarah E. Johnstone,
    • Leander Van Neste,
    • Joyce Ohm,
    • Tim Mosbruger,
    • Qiuju Wang,
    • Martin J. Aryee,
    • Patrick Joyce,
    • Nita Ahuja,
    • Dan Weisenberger,
    • Eric Collisson,
    • Jingchun Zhu,
    • Srinivasan Yegnasubramanian,
    • William Matsui,
    • and Stephen B. Baylin
    Genome Res. May 2012 22: 837-849; Published in Advance March 5, 2012, doi:10.1101/gr.131169.111
    ...of their chromatin status in ESCs, we provide evidence that DNA hypermethylation preferentially targets the subset of PcG genes that are developmental regulators, and this may contribute to the stem-like state of cancer. Additionally, the capacity for global methylation profiling to cluster tumors by phenotype may...
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  9. Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • Jakob Skou Pedersen,
    • Eivind Valen,
    • Amhed M. Vargas Velazquez,
    • Brian J. Parker,
    • Morten Rasmussen,
    • Stinus Lindgreen,
    • Berit Lilje,
    • Desmond J. Tobin,
    • Theresa K. Kelly,
    • Søren Vang,
    • Robin Andersson,
    • Peter A. Jones,
    • Cindi A. Hoover,
    • Alexei Tikhonov,
    • Egor Prokhortchouk,
    • Edward M. Rubin,
    • Albin Sandelin,
    • M. Thomas P. Gilbert,
    • Anders Krogh,
    • Eske Willerslev,
    • and Ludovic Orlando
    Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
    ...reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both...
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  10. 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
    ...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 1 , Jihoon E. Joo 2 , 3 , Joseph E. Powell 4 , 5 , Miina...
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