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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...C regions and flanking ±15-kb non-piC regions of the reference . Scaled piC regions are marked by start and end labels at the bottom of the heatmap. (C) New unified model of piC evolution: “Birth and death” is shown in four steps from left to right.To further test this idea, we examined how TE coverage...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...the regulation of miR-10b and its targets in primary breast tumors. BMC Cancer 19: 86. doi:10.1186/s12885-019-5300-6 ↵Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. 2013. Birth and expression evolution of mammalian microRNA genes. Genome Res 23: 34–45. doi...
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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
...proteins. Correspondingly, Ago2 cKO males show abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male...
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Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
...reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.MicroRNAs (miRNAs) are an extensive class of ∼22-nt RNAs that play important regulatory roles in diverse eukaryotic species (Flynt and Lai 2008; Axtell et al. 2011). In the canonical metazoan pathway...
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Research: The evolution of evolvability in microRNA target sites in vertebrates
- Jin Xu,
- Rui Zhang,
- Yang Shen,
- Guojing Liu,
- Xuemei Lu,
- and Chung-I Wu
Genome Res. November 2013 23: 1810-1816; Published in Advance September 27, 2013, doi:10.1101/gr.148916.112
...and the evolution of tissue identity. Nature 463: 1084–1088. Farh KK-H, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817–1821. Fitch WM. 1976. The molecular evolution of cytochrome c...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum Maria Ninova , Matthew Ronshaugen and Sam Griffiths-Jones Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...in different species would enable better calibration of divergence time by such a CpG-based molecular clock.Several factors in the mature sperm of human and mouse, such as histone retention and modification, CTCF binding, and microRNAs, have been proposed to have regulatory importance in embryonic development...
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Research: Death of new microRNA genes in Drosophila via gradual loss of fitness advantages
- Guang-An Lu,
- Yixin Zhao,
- Hao Yang,
- Ao Lan,
- Suhua Shi,
- Zhongqi Liufu,
- Yumei Huang,
- Tian Tang,
- Jin Xu,
- Xu Shen,
- and Chung-I Wu
Genome Res. September 2018 28: 1309-1318; Published in Advance July 26, 2018, doi:10.1101/gr.233809.117
..., Hurst LD. 2016. Open questions in the study of de novo genes: what, how and why. Nat Rev Genet 17: 567–578. ↵Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. 2013. Birth and expression evolution of mammalian microRNA genes. Genome Res 23: 34...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
..., Sweden Corresponding authors: maria.warnefors@gmail.com, h.kaessmann@zmbh.uni-heidelberg.deAbstractSexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set...
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Research: Evolution of transcript modification by N⁶-methyladenosine in primates
- Lijia Ma,
- Boxuan Zhao,
- Kai Chen,
- Amber Thomas,
- Jigyasa H. Tuteja,
- Xin He,
- Chuan He,
- and Kevin P. White
Genome Res. March 2017 27: 385-392; Published in Advance January 4, 2017, doi:10.1101/gr.212563.116
..., et al. 2014. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15: 707–719. ↵Chen T, Hao YJ, Zhang Y, Li MM, Wang M, Han W, Wu Y, Lv Y, Hao J, Wang L, et al. 2015. m6A RNA methylation is regulated by microRNAs and promotes reprogramming...

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