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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...methodological improvement in DRB/TTchem-seq2 is the computational framework used to estimate RNAPII elongation rates. Instead of identifying transcriptional wave peaks, we implemented a new approach to detect the wave fronts of nascent RNA profiles following DRB release (Fig. 1A,B). Whereas wave peaks represent...
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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
..., Powell DR, Akutsu T, Webb G, et al. 2020. Ilearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Brief Bioinform 21: 1047–1057. doi:10.1093/bib/bbz041 ↵Chen Z, Ni P, Wang JX. 2025. Identifying DNA methylation...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
..., specialized DNA sequences that control the timing of transcriptional activation. Two primary types of cis-regulatory element impact transcription in Metazoan species: promoters, which facilitate transcription initiation from an embedded transcription start site, and enhancers, which regulate the rate of mRNA...
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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 RepeatMasker, 146 we found that an average of 20.94% of ruminant s consisted of high-precision TE 147 sequences. The main TE families, by genomic size, included LINE/RTE-BovB (averaging 148 55.7% of total TE content), followed by LINE/L1 (18.13%), SINE/tRNA-Core-RTE 149 (13.07%), and SINE/Core-RTE (8...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
.... In most cases, the dsRNA structure arises from homology between two segments of the same RNA molecule that fold into RNA stem structures. Another possible source of dsRNA is co-transcription of sense and antisense strands of the same genomic region. Binding of these complementary, naturally occurring...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
.... 2023). These small but important molecules are involved in a variety of cellular processes, including development, differentiation, and apoptosis (Ratti et al. 2020). The discovery that miRNAs target transcripts by partial pairwise complementarity permitted the development of multiple target prediction...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...primarily employed RNA sequencing(Jin et al. 2025), which, while 63 informative, does not fully elucidate the complex regulatory mechanisms underlying 64 transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a 65 spatiotemporal manner through precise gene regulatory...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...: In this window In a new window Table 2. Transcription factor binding site motifs enriched in active enhancersTo further validate that the enriched TFBS motifs correlate with TFs that are highly expressed in phNPCs, we analyzed their expression using single-cell RNA-seq (scRNA-seq) data generated in the ph...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...in any eukaryotic organism, TSSPlant (Shahmuradov et al. 2017) designed for plant TSS prediction, and machine learning-enhanced options like DeePromoter (Oubounyt et al. 2019) designed exclusively for mammalian TSSs. Newer CamoTSS specifically calls TSS from actual RNA-seq data (Hou et al. 2023).Most...
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