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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...sacrificed for this study. Total genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit and quantified on the Qubit DNA quantification system (Thermo Fisher Scientific) using Qubit broad range assay reagents, following the manufacturer's protocol. DNA concentration across all samples...
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Method: A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney,
- Olivia Cheronet,
- Daniel M. Fernandes,
- Kendra Sirak,
- Matthew Mah,
- Rebecca Bernardos,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Ann Marie Lawson,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Francesca Candilio,
- Mihai Constantinescu,
- Alfredo Coppa,
- Ion Ciobanu,
- János Dani,
- Zsolt Gallina,
- Francesco Genchi,
- Emese Gyöngyvér Nagy,
- Tamás Hajdu,
- Magdolna Hellebrandt,
- Antónia Horváth,
- Ágnes Király,
- Krisztián Kiss,
- Barbara Kolozsi,
- Péter Kovács,
- Kitti Köhler,
- Michaela Lucci,
- Ildikó Pap,
- Sergiu Popovici,
- Pál Raczky,
- Angela Simalcsik,
- Tamás Szeniczey,
- Sergey Vasilyev,
- Cristian Virag,
- Nadin Rohland,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2021 31: 472-483; Published in Advance February 12, 2021, doi:10.1101/gr.267534.120
...where a third tooth root was available, we extracted ancient DNA using the cementum-targeting approach described by Damgaard et al. (2015) (Method “D” for “Damgaard”). We also generated extracts from powder produced from petrous bones for 10 of the same individuals using the method described by Pinhasi...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...-bound instances (4.6-fold enrichment; one example is shown in Fig. 2D). A clear example of an ancient RELA-associated TE was MER81, a 114-bp non-autonomous DNA transposon (Bao et al. 2015). MER81 was enriched for RELA binding in all three species (10.9-fold change in human, 10.6-fold change in mouse, and 6.2-fold...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
..., Cervantes MD, Hamilton EP. 2011. Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic s. Res Microbiol 162: 578–586. doi:10.1016/j.resmic.2011.05.001 Pannunzio NR, Watanabe G, Lieber MR. 2018. Nonhomologous DNA endjoining for repair of DNA double-strand breaks. J Biol Chem 293...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...are incubated with BrdU, followed by nuclei isolation. GFP-positive nuclei are then sorted by DNA content, separating into one of four S-phase fractions: early, early-mid, late-mid, or late replicating. Next, the BrdU-containing DNA is immunoprecipitated and prepared for sequencing to identify genomic locations...
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Method: Human auditory ossicles as an alternative optimal source of ancient DNA
- Kendra Sirak,
- Daniel Fernandes,
- Olivia Cheronet,
- Eadaoin Harney,
- Matthew Mah,
- Swapan Mallick,
- Nadin Rohland,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Francesca Candilio,
- Ann Marie Lawson,
- Kirsten Mandl,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Juraj Bartík,
- Alfredo Coppa,
- Tumen Dashtseveg,
- Sándor Évinger,
- Zdeněk Farkaš,
- Tamás Hajdu,
- Jamsranjav Bayarsaikhan,
- Lauren McIntyre,
- Vyacheslav Moiseyev,
- Mercedes Okumura,
- Ildikó Pap,
- Michael Pietrusewsky,
- Pál Raczky,
- Alena Šefčáková,
- Andrei Soficaru,
- Tamás Szeniczey,
- Béla Miklós Szőke,
- Dennis Van Gerven,
- Sergey Vasilyev,
- Lynne Bell,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119
...in England, English Heritage Publishing, Swindon, UK. ↵Pinhasi R, Fernandes DM, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, Gerritsen F, Moiseyev V, Gromov A, Raczky P, et al. 2015. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10: e0129102. doi:10...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...large that this time has come for ancient human DNA.MethodsDNA extraction and library preparationWe extracted DNA from tooth or bone powder using a manual (Dabney et al. 2013; Korlević et al. 2015) or automated protocol (Rohland et al. 2018) using “Dabney” buffer and silica-coated magnetic beads. We...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...Science and Technology of China, Quzhou 324000, Zhejiang, China; 3College of Biomedical Engineering, Sichuan University, Chengdu 610041, Sichuan, China Corresponding author: luoximei@uestc.edu.cnAbstractDNA N4-methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication...
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Method: Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples
- Lukas Bokelmann,
- Isabelle Glocke,
- and Matthias Meyer
Genome Res. October 2020 30: 1449-1457; Published in Advance September 22, 2020, doi:10.1101/gr.263863.120
...from single-stranded libraries, we extracted DNA from a small quantity of bone powder (3 mg) of a well-preserved Neanderthal bone fragment from Vindija Cave, Croatia (Vindija 33.19) from which a high-coverage sequence was previously obtained (Prüfer et al. 2017). DNA extraction was performed using...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
...Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations Yasine Malki1,2,3,5, Guannan Kang1,2,3,5, W.K. Jacky Lam1,2,3,4,5, Qing Zhou1,2,3, Suk Hang Cheng1,2,3, Peter P.H. Cheung2,3, Jinyue Bai1,2,3, Ming Lok Chan2,3, Chui...
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