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Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
- Dalibor Miklík,
- Jiří Grim,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
...form a valuable tool in the analysis of DNA motifs. So far, studies exploring tDNA composition approached the tDNA as the perfect palindrome or worked on the averaged global alignment of IS sequences. We propose that the shown variability of target site sequences should be considered to understand...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be “insertions” within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...), protein-coding synthetic genes or full-length ORFs were cloned into pETG20A-SBP to create an E. coli expression vector that allows the RBP or RBD cDNAs to be fused N-terminally to thioredoxin+6XHis and C-terminally to SBP-tags. Fusion proteins were then expressed in the Rosetta P3 DE LysS E. coli strain...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...) inclusion of seven full-length stranded cDNA libraries derived from three time points (0 h, 24 h, and 48 h post infection) (Tandel et al. 2019), covering ∼90% of the protein-coding genes in C. parvum; and (2) by using synteny information to construct a consistent annotation between three different closely...
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Research: A novel translational control mechanism involving RNA structures within coding sequences
- Jennifer Jungfleisch,
- Danny D. Nedialkova,
- Ivan Dotu,
- Katherine E. Sloan,
- Neus Martinez-Bosch,
- Lukas Brüning,
- Emanuele Raineri,
- Pilar Navarro,
- Markus T. Bohnsack,
- Sebastian A. Leidel,
- and Juana Díez
Genome Res. January 2017 27: 95-106; Published in Advance November 7, 2016, doi:10.1101/gr.209015.116
...that the positive role of Dhh1 in viral RNA translation is linked to specific RNA folding regulations that may be extended to a specific set of cellular mRNAs. By combining viral studies in the BMV/yeast system with high-throughput RNA-seq, ribosome profiling and CRAC (UV crosslinking and analysis of cDNA) of host...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...networks remains to be seen.Previous work cloning and sequencing DNA from RELA ChIP led to the conclusion that ∼11% of NF-kB-bound regions contain an Alu-derived NF-kB motif (Antonaki et al. 2011). However, the extent to which specific subfamilies of repetitive elements contribute to NF-kB binding in human...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...regions, influenced by the unique tertiary structures of these regions, thereby affecting the sequencing output. In contrast, linear regression analysis was not applicable to data obtained from the oligo(dT)-based protocol. This method uses a poly(T) primer to initiate cDNA synthesis, focusing almost...
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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...′ poly(A) tails of mRNAs were carried out by incubating each mRNA sample for 10 min at room temperature, using a T4 DNA ligase (New England Biolabs). Reverse transcription was performed in a 40 µL reaction volume on a Veriti 96-well fast thermal cycler (Applied Biosystems). The produced cDNA sample...
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Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
- Yasine Malki,
- Guannan Kang,
- W.K. Jacky Lam,
- Qing Zhou,
- Suk Hang Cheng,
- Peter P.H. Cheung,
- Jinyue Bai,
- Ming Lok Chan,
- Chui Ting Lee,
- Wenlei Peng,
- Yiqiong Zhang,
- Wanxia Gai,
- Winsome W.S. Wong,
- Mary-Jane L. Ma,
- Wenshuo Li,
- Xinzhou Xu,
- Zhuoran Gao,
- Irene O.L. Tse,
- Huimin Shang,
- L.Y. Lois Choy,
- Peiyong Jiang,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
..., including the size profile and end motif distributions. The contribution of nucleases was explored using the cleavage profile end motif patterns, and protein quantification of DNASE1L3 in plasma. A machine learning model was trained using fragmentomic features to predict cfDNA concentration. We further...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...(ONT) direct cDNA (Sertkaya et al. 2021) approaches have both been used to demonstrate improvements to lentiviral vectors (LVs), and sequencing has also been applied to other nucleic acid-based therapeutics, such as mRNA vaccines (Gunter et al. 2023). However, there is currently no clear consensus...

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