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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...in the early embryo. Scores of -wide surveys in sperm have reported patterns of chromatin accessibility, nucleosome localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...to postmeiotic silencing, with a subset of genes associated with spermiogenesis escaping postmeiotic silencing (Namekawa et al. 2006; Mueller et al. 2008). Of note is that MSCI impacts sex chromosome evolution (Potrzebowski et al. 2008). For example, the X Chromosome is enriched with genes expressed before...
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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
...(Rodríguez Delgado et al. 2009). X-Chromosome inactivation (XCI) in placental mammals involves the spread of the XIST RNA in a proximity-dependent manner governed by three-dimensional chromatin architecture (Wang et al. 2018). The resulting inactive X Chromosome (Xi) also forms a unique bipartite structure...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
..., and chromatin interactions for AGO2 in the nucleus compared with the cytoplasmic compartment during spermatogenic development. We then investigated how conditional loss of AGO2 in male germ cells impacts expression of genes targeted by its nuclear activity. Finally, we examined the phenotypic effects...
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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
...identity elsewhere on the X Chromosome, which may reduce the impact of their loss. Gene families from palindromes shared by human, chimpanzee, and macaque also have conserved expression patterns: 20 of 21 such gene families have the same expression pattern in chimpanzee and human (Supplemental Fig. S7...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...drivers in males (e.g., Larracuente and Presgraves 2012), which may drive the rapid evolution of these repeats to escape the driver (e.g., Cabot et al. 1993; Larracuente 2014). The lack of recombination and male-limited transmission of Y Chromosomes also create opportunities for conflicts involving...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...Origins, evolution, and phenotypic impact of new genes Henrik Kaessmann 1 Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland Abstract Ever since the pre-molecular era, the birth of new genes with novel functions has been...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...been co-opted as retrocopy promoters during evolution. To test our hypothesis, we analyzed ChIP-seq data from matched mouse tissues for two enhancer-associated chromatin marks, monomethylation of histone H3 at lysine K4 (H3K4me1) (Heintzman et al. 2007) and acetylation of histone H3 at lysine 27 (H3K27...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...at the bottom of the panel. (B) Sequence evolution of miRNA families on the X chromosome and autosomes. To limit biases due to age variations, only eutherian-specific miRNA families predating the human-mouse split were considered. Meunier et al. 40 Genome Research www..org protein-coding genes counteracts MSCI...
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Research: The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease
- Laure K. Case,
- Emma H. Wall,
- Julie A. Dragon,
- Naresha Saligrama,
- Dimitry N. Krementsov,
- Mohamad Moussawi,
- James F. Zachary,
- Sally A. Huber,
- Elizabeth P. Blankenhorn,
- and Cory Teuscher
Genome Res. September 2013 23: 1474-1485; Published in Advance June 25, 2013, doi:10.1101/gr.156703.113
...; Case et al. 2012; Charchar et al. 2012). Like autosomal chromosomes, ChrX and ChrYare thought to have once been identical pairs that were free to recombine and exchange genetic material. Over the course of evolution, ChrY became unique from all other chromosomes due to the acquisition of a dominant sex...

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