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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...into two classes. Class I comprises retrotransposons transposed by copy-and-paste via RNA intermediates, whereas Class II comprises DNA transposons generally transposed by a cut-and-paste mechanism (Wells and Feschotte 2020). Co-option of transposon-encoded proteins has been reported in both groups (Volff...
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Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
- Zhitao Huang,
- Ruiqing Zheng,
- Pengzhen Jia,
- Xuhua Yan,
- Jinmiao Chen,
- and Min Li
Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
...introduce a peak-specific encoder that embeds the raw scATAC-seq peak count data. Building on these, scSHEFT employs a dual alignment strategy using intraomics and interomics loss functions to achieve robust and effective alignment within and across omics. Through comprehensive benchmarking across diverse...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...this method to identify SINE activation in a context that is relevant for normal learning and memory.Retrotransposons are a class of transposable elements (TEs) that integrate into the host through an RNA intermediate (Craig et al. 2015). It is important to be able to examine the transcription of TE RNA...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...Harbor, New York 11724, USA ↵3 These authors contributed equally to this work. Corresponding author: martiens@cshl.eduAbstractIn Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated si...
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Method: Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases
- Young Hoon Sung,
- Jong Min Kim,
- Hyun-Taek Kim,
- Jaehoon Lee,
- Jisun Jeon,
- Young Jin,
- Jung-Hwa Choi,
- Young Ho Ban,
- Sang-Jun Ha,
- Cheol-Hee Kim,
- Han-Woong Lee,
- and Jin-Soo Kim
Genome Res. January 2014 24: 125-131; Published in Advance November 19, 2013, doi:10.1101/gr.163394.113
..., Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–821. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. 2013. RNA-programmed editing in human cells. Elife 2: e00471. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS. 2009. Targeted editing in human cells...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally show how retrotransposon-encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host , in the myriapod Strigamia...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...of the strands to identify cytosine methylation while retaining the original four-bases sequence information on the other strand. As both strands are locked together to link the dual readouts on a single paired-end read, Methyl-SNP-seq allows detecting the methylation status of any DNA even without a reference...
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Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
- Yiming Kang,
- Nikhil R. Patel,
- Christian Shively,
- Pamela Samantha Recio,
- Xuhua Chen,
- Bernd J. Wranik,
- Griffin Kim,
- R. Scott McIsaac,
- Robi Mitra,
- and Michael R. Brent
Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
...Figure 3. Network inference with dual threshold optimization in human cell lines. (A) Medians of number of bound genes, number of perturbation-responsive genes, and number of genes that are both bound and responsive, when comparing ENCODE K562 ChIP-seq data to ENCODE TFKD data. Excludes TFs with either...
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Method: Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
- Seung Woo Cho,
- Sojung Kim,
- Yongsub Kim,
- Jiyeon Kweon,
- Heon Seok Kim,
- Sangsu Bae,
- and Jin-Soo Kim
Genome Res. January 2014 24: 132-141; Published in Advance November 19, 2013, doi:10.1101/gr.162339.113
...in vitro transcribed dualRNA with the method of transfecting sgRNA-encoding plasmids in K562 cells andmeasuredmutation frequencies at the on-target and off-target sites via the T7E1 assay. Three RGENs showed comparable mutation frequencies at on-target and off-target sites regardless of the composition...
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