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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...in the context of physical chromosomal features.Multispecies comparative approaches have the power to identify selective pressures that shape these unique aspects of X Chromosome evolution. Mueller et al. (2013) conducted the first fine-scale comparative X Chromosome comparison using the two highest...
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Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
...University, New York, New York 10010, USA ↵9 Present address: Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA Corresponding authors: emily.miraldi@cchmc.org; dan.littman@med.nyu.edu; rbonneau@flatironinstitute.orgAbstractTranscriptional regulatory networks (TRNs) provide insight...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...of novel expression and its causative regulatory sequences can be identified across short evolutionary timescales. Working with the Escherichia coli Long-Term Evolution Experiment (Lenski et al. 1991; Tenaillon et al. 2016; Good et al. 2017), a system in which the ancestral states of all s and each new...
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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
...confirms its robust transferability from animal to microbe groups. Evolutionary analysis further uncovers the functional differentiation of 4mC sequences in biological evolution: Prokaryotic 4mC relies on stable patterns, whereas eukaryotes achieve regulatory plasticity through dynamic sequence...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...of Oncobiology and Epigenetics, University of Lodz, 90-237 Lodz, Poland ↵6 These authors contributed equally to this work. Corresponding authors: urszula.mcclurg@liverpool.ac.uk, mratajewski@cbm.pan.pl, lpulaski@uni.lodz.plAbstractTranscriptional regulation lies at the heart of cellular identity and function...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...higher than newly acquired mutations.Although TP53 has a rather extensive and complex regulatory network, we seem to have unveiled a simple principle from both transcriptional and epigenomic aspects: TP53 activated promoter activities of TEs through direct binding to TE loci with TP53 binding motifs...
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Research: A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes
- Stefanie Mühlhausen,
- Peggy Findeisen,
- Uwe Plessmann,
- Henning Urlaub,
- and Martin Kollmar
Genome Res. July 2016 26: 945-955; Published in Advance May 6, 2016, doi:10.1101/gr.200931.115
...A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes Stefanie Mühlhausen 1 , Peggy Findeisen 1 , Uwe Plessmann 2 , Henning Urlaub 2 , 3 and Martin Kollmar 1 1Group Systems...
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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...diversity. They anticorrelate at the genomic scale, so that protein families with many paralogs tend to have fewer transcript variants and vice versa (Talavera et al. 2007). It is therefore expected that some genes shifted from one strategy to the other during evolution: The function of an alternative...
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Research: High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
- Bianca M. Schmitt,
- Konrad L.M. Rudolph,
- Panagiota Karagianni,
- Nuno A. Fonseca,
- Robert J. White,
- Iannis Talianidis,
- Duncan T. Odom,
- John C. Marioni,
- and Claudia Kutter
Genome Res. November 2014 24: 1797-1807; Published in Advance August 13, 2014, doi:10.1101/gr.176784.114
...codons that must be translated by tRNA anticodons is consistently and robustly found within transcriptomes throughout development and across evolution. These triplet codons in mRNA transcripts form transient, noncovalent hydrogen bonds with decoding tRNAs, creating the molecular interface that connects...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...NRC-1), a hydrogenotrophic methanogen ( Methanococcus maripaludis S2), an acidophilic and aerobic thermophile ( Sulfolobus solfataricus P2), and an anaerobic hyperthermophile ( Pyrococcus furiosus DSM 3638). We demonstrate how the evolution of transcriptional elements (promoters and terminators...

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