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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
...(Ameyar-Zazoua et al. 2012; Taliaferro et al. 2013). Lastly, AGO2 facilitates DNA double-strand break repair in Arabidopsis and cultured human cells (Wei et al. 2012). These studies point to critical nuclear roles for AGO2, but the in vivo relevance of these functions, particularly in mammals, remains...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...from the brain (including the optic bulb), liver, pronephros or head kidney, and meiotic gonads (ovary and testis) from both sexes. The entire organ was extracted, and both nuclear and cytoplasmic RNAs were collected for long-read RNA sequencing (Iso-Seq). On average, 618,000 circular consensus...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...from double-stranded RNA (dsRNA) by Dicer and associate with Argonautes to direct RNA silencing. In Caenorhabditis elegans, 22G-RNAs and 26G-RNAs are often referred to as siRNAs but display distinct characteristics. For example, 22G-RNAs do not originate from dsRNA and do not depend on Dicer, whereas...
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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
..., a wide variety of processes occur requiring distinctive transcriptional programs and regulation (Fig. 1A). In early meiotic prophase, DNA double-strand breaks (DSBs) are formed as a necessary intermediate for meiotic recombination and the subsequent reductional chromosome division during meiosis I...
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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
...elements (LTRs).Testis-specific expression of ERVs in humans and mice was initially reported over 40 years ago (Del Villano and Lerner 1976), and recent studies reveal regulatory functions for TEs in male meiosis. These functions include post-transcriptional regulation of mRNA and long noncoding RNAs (lncRNAs...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...of scaffolds and functional interfaces with target molecules (Uroda et al. 2019; Simko et al. 2020). The single-stranded nature of RNA allows the formation of various secondary structures such as hairpin loops, triplexes, and double-stranded helices, including A-RNA and Z-RNA, that contribute to the stability...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...µg total RNA from each individual was used as input, and double-strand cDNA was produced by following the manufacturer's instructions, except that an alternative Oligo(dT) primer from the SMARTer PCR cDNA Synthesis kit (Clontech Laboratories, Inc.), which also included a random 10-mer sequence...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...(Potter et al. 2017). All of these types of SMs emerge predominantly owing to failure of the repair of double-strand breaks and involve mechanisms that typically depend on either homologous recombination or end-joining (So et al. 2017). Thus, chromosome instability and processes such as nonallelic...
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LETTER: Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome
- Dennis D.Y. Kim,
- Thomas T.Y. Kim,
- Thomas Walsh,
- Yoshifumi Kobayashi,
- Tara C. Matise,
- Steven Buyske,
- and Abram Gabriel
Genome Res. September 2004 14: 1719-1725; doi:10.1101/gr.2855504
...( Versteeg et al. 2003 ; Grover et al. 2004 ). The ADAR (Adenosine Deaminase that Act on RNA) family of RNA editing enzymes found in many metazoans catalyzes adenosine deamination to inosine in double-stranded RNA (dsRNA; Bass 2002 ). By converting AU base pairs to unstable IU wobble base pairs, ADAR can...

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