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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...). Such experimental approaches have enabled the derivation of patterns enabling the prediction of sequences that can adopt G4 DNA structures.Early computational studies showed that conserved sequence motifs can accurately capture a significant proportion of potential G4-forming regions (Huppert and Balasubramanian...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...in understudied lineages like ruminants. 113 In this study, we aimed to comprehensively characterize the coevolutionary dynamics of 114 KZFPs and TEs across 32 ruminant s. We sought to use a k-mer-based approach to 115 overcome limitations of conserved sequence methods and identify taxon-specific expansions 116...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...the shortest species-specific nucleotide sequences offers insights into species evolution and holds potential practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic “quasi-primes,” the shortest occurring sequences in each of 45...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...). Furthermore, RNA-seq mapping revealed evolutionarily conserved tissue regulation for both events (Fig. 3C). For instance, the alternatively spliced F-actin binding region comprised of the s-exons 15_0 and 15_1 is specifically expressed in the brain and muscles of primates and rodents (Fig. 3C, on the left...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...variants in the transcriptome (Glinos et al. 2022). Furthermore, long-read sequencing enables comprehensive analysis of splicing (Tilgner et al. 2015, 2018; Joglekar et al. 2021) which has fundamental importance for determining mRNA modifications due to their dependence on splicing patterns and transcript...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C...
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Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
.... IPAFinder could recover ∼80% and ∼90% IPA sites at a sequencing coverage of 40× and 60×, respectively (Supplemental Fig. S3A). Furthermore, IPAFinder could exclude the interference of alternative splicing events such as alternative 5′ splice site and intron retention (Supplemental Fig. S3B). Next, we...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...RNA occurrence (Methods) (Fig. 5A). Unlike the coding mRNA component, these long noncoding fractions (median size = 346 nucleotides) are not spliced and are not polyadenylated (Andersson et al. 2014). With the recent advancement in high-throughput sequencing, the occurrence of eRNA along with H3K27ac histone...
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Research: RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
...the generation of long “classical” transcripts (with 5′ and 3′ UTRs) but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of nonpromiscuously expressed SF genes, among which we confirmed RBFOX to be present with AIRE in m...
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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
..., USA; 4Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA; 5Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy; 6Keck MS & Proteomics Resource, Yale University School of Medicine, New...

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