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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...are therefore likely to impact evolution of gene regulation. Yet, the role of TEs in regulatory evolution after WGDs is not well understood. Here we used Atlantic salmon as a model system to explore how TE activity after the salmonid WGD ∼100 MYA shaped CRE evolution. We identified 55,080 putative TE-CREs using...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...haplotypes, termed cenhaps, observed in humans (Langley et al. 2019), within which satellite arrays also evolve dynamically (Logsdon et al. 2023). Together, these patterns are consistent with unidirectional allelic or nonallelic gene conversion mediating array evolution, or unequal crossover between sister...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
.... 2017; Heger et al. 2020), and in species whose s have been sequenced, ZNF gene copy number spans three orders of magnitude, from fewer than ten in many nematodes to hundreds, if not thousands, in some vertebrates, arthropods, and mollusks (Goodstadt et al. 2007; Albertin et al. 2015; Panfilio et al...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...role in the evolution of our species (Perry et al. 2007; Dennis et al. 2012; Huttner et al. 2024).TBC1D3 is a primate-specific SD gene family (Paulding et al. 2003). This gene family is dispersed across the two arms of Chromosome 17, although most copies in humans map to two expansion blocks at locus...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...largely agrees with previous works that find structural variation alters gene expression in humans and nonhuman primates (Marques-Bonet et al. 2009; Lazar et al. 2018). Although expression analysis was limited to a single cell type, we report an enrichment of DEGs within and nearby (<100 kbp) inversion...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...to that of the nucleotide mutation rate (Adrion et al. 2017). New TE insertions can be a major source of loss-of-function mutations (Hirsch and Springer 2017), including those that directly disrupt genes and those that indirectly lead to ectopic chromatin formation (Wells and Feschotte 2020), and over evolutionary time TEs...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...) insertions and deletions in palindrome arms and spacers during the last 25 million years of primate evolution were depleted around protein-coding genes, and molecular analyses demonstrate purifying selection on protein-coding genes in X-palindrome arms and spacers. All 12 X palindromes conserved between...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
..., sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one ormultiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...16802, USA Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNAseq to characterize gene expression in the same...
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