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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...distribution. Regression was performed using the linear model function in base R, and the P-value of the slope was reported on each plot (Supplemental Code S4).DNA FISHWe chose three K9me3 LADs, four K9me2 LADs, and three K27me3 LADs to target with DNA FISH probes (labeled with fluorophores ATTO467N, ATTO565...
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Method: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
- Mădălina Giurgiu,
- Nadine Wittstruck,
- Elias Rodriguez-Fos,
- Rocío Chamorro González,
- Lotte Brückner,
- Annabell Krienelke-Szymansky,
- Konstantin Helmsauer,
- Anne Hartebrodt,
- Philipp Euskirchen,
- Richard P. Koche,
- Kerstin Haase,
- Knut Reinert,
- and Anton G. Henssen
Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
...models (Supplemental Fig. S6). One limitation of our methods represents the correct decomposition into distinct ecDNA elements for structures containing repetitive regions. This would lead to incomplete structural resolution; for example, the order of the repeat-containing genomic segments might remain...
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Research: Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
- Cui Du,
- Jing Jiang,
- Yuzhuo Li,
- Miao Yu,
- Jian Jin,
- Shuai Chen,
- Hairui Fan,
- Todd S. Macfarlan,
- Bin Cao,
- and Ming-an Sun
Genome Res. February 2023 33: 197-207; Published in Advance February 17, 2023, doi:10.1101/gr.277150.122
..., placenta is abundant with partially methylated domains (Schroeder et al. 2013; Decato et al. 2017) which are also featured in many tumors (Hansen et al. 2011). Mechanistically, one previous study speculated that placenta and tumor share converged DNA methylation pathways that mediate the establishment...
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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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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...that function in the DNA damage response (DDR) also improve phenotypes in Mecp2/Y mice. Association analysis was successful in resolving combinatorial effects of multiple loci. One line, which carries a suppressor mutation in a gene required for cholesterol synthesis, Sqle, carries a second mutation...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...to active coding regions. Although lesswell defined, other DNA-binding proteins and nascent RNA can recruit H3K27 or H3K9 methylases to other genomic regions, resulting in heterochromatic silencing by polycomb complexes (PcG) or HP1, respectively. As a consequence of the above and other mechanistic...
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Research: Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
- Phuc-Loi Luu,
- Hans R. Schöler,
- and Marcos J. Araúzo-Bravo
Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
...Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs Phuc-Loi Luu 1 , Hans R. Schöler 2 , 3 and Marcos J. Araúzo-Bravo 1 , 4 1...
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Method: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
...advantage of a repetitive sequence in the human . Since the long interspersed nuclear element-1 (LINE-1) constitutes ∼17% of the human (up to 600,000 copies), we used real-time PCR targeting the LINE-1 locus to quantify genomic DNA (Phokaew et al. 2008). At first, MCF7 cell lines were tested to validate...
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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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