Searching journal content for articles similar to Wong et al. 11 (12): 1975.

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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
...involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase, which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides...
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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
...such as compaction and accessibility, whereas endogenous DNA allows for in cellulo analysis under physiological conditions. Similarly, proteins can be purified and studied in vitro, expressed exogenously from a plasmid, or endogenously produced within the cell from genomic DNA. Although plasmid-based expression...
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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
...genomics. Early works in molecular biology on gene expression were limited, because purified RNA is unstable and difficult to work with. However, the discovery (and use in the laboratory) of reverse transcriptase, permitting the controlled synthesis of RNAs into cDNAs (Maniatis et al. 1976...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...transcript (transcribed from the same genomic cluster). (D) Expression covariation of miRNA primary transcripts. The color code indicates the Spearman's rank correlation coefficient value. Blue color indicates positively covarying primary transcripts.Most miRNA repression is conferred by miR-17, miR-291...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...and methylome analyses in oocytes revealed that DNA methylation is primarily restricted to transcribed regions (Kobayashi et al. 2012). These transcription events reshape the histone methylation landscape, guiding the DNMT complex to specific genomic regions. Specifically, the transcription-coupled loss of H3K4...
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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
...RNA target regions. To this end, we utilized data sets from DIANA-TarBase v8 (Karagkouni et al. 2018), a curated database of experimentally validated miRNA–mRNA interactions derived from high-throughput techniques such as PAR-CLIP. Each m6A site was tested for overlap with the genomic coordinates...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...)–normalized and Z-score-normalized heatmaps from differential analysis of H3K27me3 over genes between 1-day-old cell types. (E–H) UCSC Genome Browser tracks of repressed domains in the three cell types in young guts. (E) The ANTP-C domain is shared between all three cell types. (F–H) A domain encompassing the pi...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...Científicas, 50059, Zaragoza, Spain; 2European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom; 3University of Liverpool, Institute of Systems, Molecular and Integrative Biology, Liverpool L69 7ZB, United Kingdom; 4Department of Botany...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...Bio) and Oxford Nanopore Technologies (ONT) are revolutionizing genomics: They are making chromosome-level assemblies routine, and full diploid, telomere-to-telomere (T2T) assemblies are becoming the standard for human assemblies. LRS employs single-molecule sequencing, avoiding many biases, errors...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...transcribed rDNA unit. Early replication timing for this genomic location only occurs in GSC-like cells. (D) Pairwise comparison of replication timing differences for Chromosome 2, in which domains (reaching a size at least 20 kb) are evaluated against the hypothesis of having equal replication timing...
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