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Methods: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
- Alayne L. Brunner,
- David S. Johnson,
- Si Wan Kim,
- Anton Valouev,
- Timothy E. Reddy,
- Norma F. Neff,
- Elizabeth Anton,
- Catherine Medina,
- Loan Nguyen,
- Eric Chiao,
- Chuba B. Oyolu,
- Gary P. Schroth,
- Devin M. Absher,
- Julie C. Baker,
- and Richard M. Myers
Genome Res. June 2009 19: 1044-1056; Published in Advance March 9, 2009, doi:10.1101/gr.088773.108
...) 725-1534. [Supplemental material is available online at www.genome.org . Raw Methyl-seq sequence data are available from NCBI's Short Read Archive ( http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi ) (accession no. SRA008154). Processed Methyl-seq data are available for download...
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LETTER: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
- Andrew J. Gentles,
- Matthew J. Wakefield,
- Oleksiy Kohany,
- Wanjun Gu,
- Mark A. Batzer,
- David D. Pollock,
- and Jerzy Jurka
Genome Res. July 2007 17: 992-1004; Published in Advance May 10, 2007, doi:10.1101/gr.6070707
...of SINEs that appear to use RTE elements for mobilization. In contrast to L1-mobilized SINEs, the RTE-mobilized SINEs in Monodelphis appear to shift from G+C-rich to G+C-low regions with time. Endogenous retroviruses have colonized ∼10% of the opossum genome. We found that their density is enhanced...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...fraction seems to play an important role in biological processes (Cheetham et al. 2020). For example, pseudogenes have been associated with the production of truncated proteins that have intact functional domains, with the regulation of transcription and translation through the generation of small...
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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
...Barcelona, Spain Corresponding authors: claudia.carareto@unesp.br, cristina.vieira@univ.lyon1.frAbstractHost shifts in insects are considered a key process with the potential to contribute to reproductive isolation and speciation. Both genomic and transcriptomic variation are attributed to such a process...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...with somatic cells.Mammalian spermatogenesis is the process by which germ cells undergo progressive differentiation to generate mature male gametes. In the mouse, a pool of undifferentiated spermatogonia is recruited with regular periodicity into this process (de Rooij and Russell 2000). Once committed...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...set, we used an equivalent number of randomly selected MMR-containing regions from the background. A summary of the CNN training set generation process is shown in Figure 2A.View larger version: In this window In a new window Figure 2. Allo's neural network training process and accuracy testing. (A...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...get lost over time because of genetic drift. Most human TEs are retrotransposons spreading by a copy-and-paste mechanism, be they LTR (long terminal repeat)-containing endogenous retroviruses (ERVs), long and short interspersed nuclear elements (LINEs and SINEs), or the composite SINE-variable number...
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Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
..., for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...-L1 retrotranscriptase machinery can reshape mammalian s by capturing RNAs and reinserting retrotranscribed copies into the , as in the case for processed pseudogenes (Esnault et al. 2000). We observed an increase of the number of retrocopies with an age matching the evolutionary window as the recent...
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Research: Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity
- Yishay Pinto,
- Orshay Gabay,
- Leonardo Arbiza,
- Aaron J. Sams,
- Alon Keinan,
- and Erez Y. Levanon
Genome Res. May 2016 26: 579-587; Published in Advance April 7, 2016, doi:10.1101/gr.199240.115
...-specific retroviruses and retroelements (Sawyer et al. 2004; Zhang and Webb 2004). While viruses generally infect somatic cells, retroelement integration is mainly destructive when it occurs in the germline. Indeed, A3 members are known to be expressed in the reproductive system, and A3G exhibits the highest expression...
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