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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...analyses reveal a highly significant association between 285 endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including 286 HMG domain-containing and chromatin binding factors. Notably, however, the endoderm 287 HCNEs appear to show a greater enrichment of such genes compared...
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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
...to each tissue. Therefore, the FCO signature may be a tool that is useful to explore stem cell heterogeneity more broadly in human development. In conclusion, we defined and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...the influence of genomic location and physiological context on L1 element methylation (Salvador-Palomeque et al. 2019; Sanchez-Luque et al. 2019; Ewing et al. 2020). Together, these results indicate that de novo L1 insertions arising during embryonic development are likely silenced by DNA methylation during...
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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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Letter: DNA methylation programming and reprogramming in primate embryonic stem cells
- Netta Mendelson Cohen,
- Vikas Dighe,
- Gilad Landan,
- Sigrún Reynisdóttir,
- Arnar Palsson,
- Shoukhrat Mitalipov,
- and Amos Tanay
Genome Res. December 2009 19: 2193-2201; Published in Advance November 3, 2009, doi:10.1101/gr.096685.109
...during stem cell derivation. Here we report on DNA methylation patterns in native monkey embryonic stem cells (ESCs), fibroblasts, and ESCs generated through somatic cell nuclear transfer (SCNT), identifying and comparing epi programming and reprogramming. We characterize hundreds of regions...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...-associated box (KRAB) domain and a C-terminal zinc finger array, which for many mediates sequence-specific DNA recognition. The KRAB domain of a majority of KZFPs recruits the transcriptional corepressor TRIM28 (also known as KAP1), which acts as a scaffold for heterochromatin inducers such as the histone methyl...
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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
...material from adult and embryonic stem cells did not completely recapitulate the DNA methylation patterns present in the corresponding primary differentiated tissues, and there were always deficiently methylated CpG sites. Supplemental Table 6 provides examples of these in muscle and neuronal tissues...
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Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
- Lukas Chavez,
- Justyna Jozefczuk,
- Christina Grimm,
- Jörn Dietrich,
- Bernd Timmermann,
- Hans Lehrach,
- Ralf Herwig,
- and James Adjaye
Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
...differentiated human embryonic stem cells and developing human fetal liver. Genome Res 19: 1044–1056. DNA methylation changes in differentiating hESCs Genome Research 1449 www..org Chan EM, Ratanasirintrawoot S, Park IH, Manos PD, Loh YH, Huo H, Miller JD, HartungO, Rho J, Ince TA, et al. 2009. Live cell imaging...
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Research: Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
- Jung H. Kim,
- Saravana M. Dhanasekaran,
- John R. Prensner,
- Xuhong Cao,
- Daniel Robinson,
- Shanker Kalyana-Sundaram,
- Christina Huang,
- Sunita Shankar,
- Xiaojun Jing,
- Matthew Iyer,
- Ming Hu,
- Lee Sam,
- Catherine Grasso,
- Christopher A. Maher,
- Nallasivam Palanisamy,
- Rohit Mehra,
- Hal D. Kominsky,
- Javed Siddiqui,
- Jindan Yu,
- Zhaohui S. Qin,
- and Arul M. Chinnaiyan
Genome Res. July 2011 21: 1028-1041; doi:10.1101/gr.119347.110
...identified differentially methylated regions (DMRs) and revealed novel insights regarding the genomic placement and functional consequences of DNAmethylation in cancer. Results Characterization of DNA methylation by M-NGS in prostate cells To perform a -wide analysis of DNA methylation in prostate cancer, we...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...et al. 2013). Only six DMRs showed differential germline DNA methylation in mouse gametes, but only one locus, orthologous to NAV2, showed a pattern consistent with placental-specific imprinting (Supplemental Fig. 2).Timing of loss of imprinting in human embryonic lineagesTo assess the developmental...
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