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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...on GRCm38 [mm10] release-89 annotation).For the TSRexploreR analysis, a 5′ tag threshold of 3 was used. DESeq2 median-of-ratios approach was used for normalization. For mammalian TSS analysis, the 5′-most tags were grouped into transcript start regions using a maximum distance of 25 bp and a maximum total...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...correlations are light gray. (C) Distribution of functional categories in genes split by VGH decile. Some functional categories like transcription- and translation-associated genes were enriched for small VGH estimates, and others, like receptors, were enriched for high VGH estimates. (D) Correlation of gene...
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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...-quality nuclei with transcription start site enrichment (TSSe) ≥ 10 and uniquely mapped fragments ≥1000 using the function filter_cells in SnapATAC2. Doublets were removed using a modified version of the Scrublet (Wolock et al. 2019) algorithm in SnapATAC2. Briefly, we first added the 500-bp genomic bin features...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
.... The fundamental tasks are to classify or group sequencing reads into distinct genomic bins, each representing a different taxon (e.g., species or strain) within a metagenomic sample (taxonomic binning), and to identify the taxa present while estimating their relative abundances in the sample (taxonomic profiling...
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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
...remarkable versatility in their ability to create new transcripts or genes 66 through exonization, while also modulating gene expression through strategic placement of 67 enhancers or promoters near genes (Guillaume et al. 2018; Sophie and Gaël 2020). Current 68 studies reveals important functional aspects...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...shared peaks. (C,D) Scatterplots of read counts (log2) on shared peaks, IGV (Robinson et al. 2011) tracks, and heatmaps of ±5 kb from the center of transcription start sites (TSSs) or peaks showing the automated ChIP-seq results of H3K27ac (C) and H3K27me3 (D) for evaluating cross-linking conditions, DSG...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...are the gold standard for high-throughput transcriptome profiling (Wang et al. 2009). RNA-sequencing (RNA-seq) has been used to investigate gene expression (The ENCODE Project Consortium 2012), canonical and alternative mRNA splicing (Wright et al. 2022a), noncoding RNAs, and post-transcriptional modifications...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...group from S-adenosyl-l-methionine to cytosine. Importantly, due to the palindromic nature of the CG dinucleotide, CG methylation can be retained after DNA replication by methylation of hemimethylated (i.e., one-strand methylated) DNA. While most mammalian cells exhibit only CG methylation, neurons...
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Research: Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
- Tülay Karakulak,
- Natalia Zajac,
- Hella Anna Bolck,
- Anna Bratus-Neuenschwander,
- Qin Zhang,
- Weihong Qi,
- Debleena Basu,
- Tamara Carrasco Oltra,
- Hubert Rehrauer,
- Christian von Mering,
- Holger Moch,
- and Abdullah Kahraman
Genome Res. April 2025 35: 698-711; Published in Advance March 19, 2025, doi:10.1101/gr.279345.124
...the SCpubr R package to visualize marker expressions and clusters (Blanco-Carmona 2022). Genes expressing ccRCC-specific novel transcripts in ccRCC cells of ccRCC2, ccRCC4, and ccRCC5 were analyzed using ClusterProfiler's enricher function (Yu et al. 2012). For the analysis, a hallmark gene set from MSig...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...varied sequencing technologies and sequencing error rates. We also designed new experiments to profile a normal cell line transcriptome with spiked-in known oncogenic fusion transcripts and nine cancer cell lines using the same long-read sequencing protocol MAS-ISO-seq (Al'Khafaji et al. 2024). In both...
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