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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling—“stutter” artifacts—with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed...
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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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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
...methylation. PLoS Comput Biol 16: e1007195. doi:10.1371/journal.pcbi.1007195 ↵de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, et al. 2022. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis Weisheng Wu 1 , 4 , Christapher S. Morrissey 1 , Cheryl A. Keller 1 , Tejaswini Mishra 1 , Maxim...
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Research: Tracing human stem cell lineage during development using DNA methylation
- Lucas A. Salas,
- John K. Wiencke,
- Devin C. Koestler,
- Ze Zhang,
- Brock C. Christensen,
- and Karl T. Kelsey
Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
...-cell-type causal factors. Large-scale population studies must also account for the now well-documented effects of age on a subset of DNA methylation loci, the so-called Horvath clock CpG loci (Horvath 2013), which we show here to be distinct from those forming the FCO signature. Aging in humans is well known...
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Research: Bacterial infection remodels the DNA methylation landscape of human dendritic cells
- Alain Pacis,
- Ludovic Tailleux,
- Alexander M. Morin,
- John Lambourne,
- Julia L. MacIsaac,
- Vania Yotova,
- Anne Dumaine,
- Anne Danckaert,
- Francesca Luca,
- Jean-Christophe Grenier,
- Kasper D. Hansen,
- Brigitte Gicquel,
- Miao Yu,
- Athma Pai,
- Chuan He,
- Jenny Tung,
- Tomi Pastinen,
- Michael S. Kobor,
- Roger Pique-Regi,
- Yoav Gilad,
- and Luis B. Barreiro
Genome Res. December 2015 25: 1801-1811; Published in Advance September 21, 2015, doi:10.1101/gr.192005.115
...Genetics, University of Chicago, Chicago, Illinois 60637, USA; 13Department of Pediatrics, University of Montreal, Montreal, H3T1J4 Canada Corresponding authors: luis.barreiro@umontreal.ca , gilad@uchicago.edu Abstract DNA methylation is an epigenetic mark thought...
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Research: DNA methylation profiles of human active and inactive X chromosomes
- Andrew J. Sharp,
- Elisavet Stathaki,
- Eugenia Migliavacca,
- Manisha Brahmachary,
- Stephen B. Montgomery,
- Yann Dupre,
- and Stylianos E. Antonarakis
Genome Res. October 2011 21: 1592-1600; Published in Advance August 23, 2011, doi:10.1101/gr.112680.110
...) that likely escape XCI with high confidence based on two criteria: (1) Their mean promoter CGI methylation in 46,XX individuals is <0.65; and (2) the difference in mean promoter methylation between 46,XX and 45,X is <0.39 (Supplemental Table 3). We validated a subset of these predictions using transcribed...
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Letter: Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
- Christian Schmidl,
- Maja Klug,
- Tina J. Boeld,
- Reinhard Andreesen,
- Petra Hoffmann,
- Matthias Edinger,
- and Michael Rehli
Genome Res. July 2009 19: 1165-1174; Published in Advance June 3, 2009, doi:10.1101/gr.091470.109
...DNA sequences. Methylation of cytosine residues in genomic DNA is an important epigenetic mark that is essential for normal embryonic development in mammals (Okano et al. 1999), imprinting (Li et al. 1993), X-inactivation (Goto and Monk 1998), and silencing of potential hazardous genetic elements...
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Research: Cell type–specific DNA methylation at intragenic CpG islands in the immune system
- Aimée M. Deaton,
- Shaun Webb,
- Alastair R.W. Kerr,
- Robert S. Illingworth,
- Jacky Guy,
- Robert Andrews,
- and Adrian Bird
Genome Res. July 2011 21: 1074-1086; Published in Advance May 31, 2011, doi:10.1101/gr.118703.110
...are acquired during the later stages of terminal differentiation. A similar conclusion has been drawn by analysis of promoter methylation during the differentiation of embryonic stem cells to neurons (Mohn et al. 2008). We then compared our DNA methylation data with gene expression profiles in the equivalent...
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Method: Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
- Aaron L. Statham,
- Mark D. Robinson,
- Jenny Z. Song,
- Marcel W. Coolen,
- Clare Stirzaker,
- and Susan J. Clark
Genome Res. June 2012 22: 1120-1127; Published in Advance March 30, 2012, doi:10.1101/gr.132076.111
...and cellular differentiation, in both development and disease, including cancer. The -wide distribution of DNA methylation and chromatin modifications is now being revealed by large-scale sequencing studies; however, these techniques only permit correlative studies between chromatin marks and the underlying...

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