Searching journal content for articles similar to Kotze et al. 4 (6): 352.

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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...reconstruction (Banecki et al. 2024) by modeling multiple scHi-C maps simultaneously and leveraging their ordering, as determined by a TI method or the scHi-C experiment itself. Themethod incorporates the knowledge about cell order by adding metarestraints to the molecular dynamics simulation (MD; see Methods...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...polymorphism (RFLP) analysis 574 Genomic DNA was amplified by PCR using gene-specific primers and Diastar Taq DNA 575 polymerase (Solgent). The following primer pairs were used for PCR amplification: for 576 EFTUD2: 5′–AGAGTGGCTGTGATACCG–3′ (forward) and 5′–577 GAAGCACTAACAGTGAGGG–3′ (reverse); for KPNB1: 5...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...(Toropainen et al. 2016). Coactivation of both AR and GR led to a substantial increase of hormone-regulated genes compared with DHT-only treatment (Fig. 3B), and only a small proportion of genes lost their hormone regulation upon DexDHT treatment. In support, RT-qPCR analyses performed in PC3-AR cells...
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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
...beads. To focus on individual candidate genes predicted to be bound by the protein of interest, precipitated DNA can be analyzed using qPCR with primers designed specifically against the regulatory sequences of the GOIs. Alternatively, in ChIP-seq following precipitation, cross-links are reversed...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...within the same FunFam. (*) Known cancer genes from CGC.Figure 2, B through D, provide illustrative examples of FIEs in three functional families in which mutations affected the same functional site in multiple paralogs, including those in the known cancer genes EGFR and RAC1. Although this study focused...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...PCR and high-throughput sequencing. No significant off-target effects were detected by this method (Supplemental Fig. S5). RNA-seq analysis of seven-gene-edited cells revealed increased expression of genes involved in DNA replication, repair pathways, p53 signaling, and cancer-related pathways...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
..., it is worthwhile to exploit the ancestor estimation approach based on the prior information from the reference population, which avoids calculating multiple K values.Here, we propose an algorithmic framework, HITSNP, to screen feature SNPs from deep WGS and evaluate its ability in breed diversity estimation...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...to the reference with Burrows-Wheeler Aligner 0.7.18 (Li and Durbin 2010). Sequence Alignment Map (SAM) files were converted into Binary Alignment Maps (BAM) with SAMtools 1.18 (Danecek et al. 2021). Quality filter and removal of PCR duplicates were performed with SAMtools using the view and markdup functions...
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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
...coding gene expression with qPCR-validated targets. Our findings demonstrate that quantifying mRNA fragments from sRNA-seq experiments provides a reliable approach to investigate microRNA–mRNA interactions when total RNA-seq is unavailable.The analysis of gene expression is a cornerstone of functional...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...stem cell–derived SOD1E100G MNs and shows that dysregulation of VGF, INA, and PENK is a strong disease predictor across species and SOD1 mutations. Our study reveals MN population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective...
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