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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...It is known that satellite DNA and other repetitive sequences can adopt alternative DNA structures (non-B DNA) such as left-handed Z-DNA, three-strand triplexes (H-DNA), four-stranded guanine quadruplexes (G4 DNA), hairpins, etc. (Matos-Rodrigues et al. 2023 and references cited therein). It is also known...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
.... An alternative to arrays would be the use of whole- bisulfite sequencing or long-read sequencing data (Loman et al. 2015). Although these approaches would allow the assessment of allelic DNA methylation across the whole , available sample sizes for these data sets are currently limited. In addition...
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Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
- Kate Liddiard,
- Brian Ruis,
- Taylor Takasugi,
- Adam Harvey,
- Kevin E. Ashelford,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
...a predisposition for the ultimate fusion ligation. We next investigated junction-proximal sequence context and discovered a unique and significant enhancement (sixfold over WT; P≤ 0.001) in the incidence of non-B DNA structures (Cer et al. 2013) within 500 bp of LIG3−/−:LIG4−/− inter-chromosomal fusion junctions...
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Research: Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
- Aneta Mikulasova,
- Daniel Kent,
- Marco Trevisan-Herraz,
- Nefeli Karataraki,
- Kent T.M. Fung,
- Cody Ashby,
- Agata Cieslak,
- Shmuel Yaccoby,
- Frits van Rhee,
- Maurizio Zangari,
- Sharmilan Thanendrarajan,
- Carolina Schinke,
- Gareth J. Morgan,
- Vahid Asnafi,
- Salvatore Spicuglia,
- Chris A. Brackley,
- Anne E. Corcoran,
- Sophie Hambleton,
- Brian A. Walker,
- Daniel Rico,
- and Lisa J. Russell
Genome Res. July 2022 32: 1343-1354; Published in Advance December 21, 2021, doi:10.1101/gr.276042.121
...the opportunity to analyze the consequence of the relocation of an isolated IGH super-enhancer. Using paired-end read targeted DNA sequencing, we precisely mapped the chromosomal changes at the IGH locus (Supplemental Fig. S5). We confirmed two chromosomal breakpoints that occur in the IGHE and IGHA switch...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...conformations (non-B-form DNA), including cruciform DNA, short inverted repeats (SIRs), and G-quadruplexes, all of which can promote instability (Kurahashi et al. 2004; Paeschke et al. 2011; Lu et al. 2015). We extracted the sequence ±500 bp from each breakpoint in Notch and performed permutation tests...
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Research: Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications
- Artur Veloso,
- Killeen S. Kirkconnell,
- Brian Magnuson,
- Benjamin Biewen,
- Michelle T. Paulsen,
- Thomas E. Wilson,
- and Mats Ljungman
Genome Res. June 2014 24: 896-905; Published in Advance April 8, 2014, doi:10.1101/gr.171405.113
...-BDNA sequences can have a negative impact on transcription in vitro (Belotserkovskii et al. 2013), we did not find a correlation between elongation rate and potential non-B DNA sequences, though some of these sequences may not exhibit non-B DNA conformations in vivo. Furthermore, our results suggest...
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Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
- Shang Gao,
- Yang Dai,
- and Jalees Rehman
Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
...for RNA or DNA metabolic processing (Supplemental Fig. S16A). On the other hand, the top-weighted target genes for RELB identified by BITFAM were enriched for processes such as immune cell activation, apoptosis, and proliferation (Supplemental Fig. S16B). There is a limited overlap of the transcription...
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Research: Identification and characterization of centromeric sequences in Xenopus laevis
- Owen K. Smith,
- Charles Limouse,
- Kelsey A. Fryer,
- Nicole A. Teran,
- Kousik Sundararajan,
- Rebecca Heald,
- and Aaron F. Straight
Genome Res. June 2021 31: 958-967; Published in Advance April 19, 2021, doi:10.1101/gr.267781.120
...the centromere by designating the site for new Cenpa assembly after dilution by replication. Vertebrate centromeres assemble on tandem arrays of repetitive sequences, but the function of repeat DNA in centromere formation has been challenging to dissect due to the difficulty in manipulating centromeres in cells...
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Research: Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
- Rob W. Ness,
- Andrew D. Morgan,
- Radhakrishnan B. Vasanthakrishnan,
- Nick Colegrave,
- and Peter D. Keightley
Genome Res. November 2015 25: 1739-1749; Published in Advance August 10, 2015, doi:10.1101/gr.191494.115
...in order to facilitate better predictive models of DNA sequence evolution. Detailed investigations of the process of spontaneous mutation and the extent of mutation rate variation have been limited by the rarity of spontaneous mutations, which has constrained direct observation of sufficient numbers...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...to complete replication and/or resolving the arrested forks prior to the end of telophase and chromosome segregation (Chan et al. 2009). Specific DNA sequences, such as [A/T]n and [AT/TA]n repeats, and/or the formation of non-B DNA secondary structures within aCFSs can inhibit replicative DNA polymerases...

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