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Research: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes
- Pierre Chymkowitch,
- Aurélie Nguéa P,
- Håvard Aanes,
- Christian J. Koehler,
- Bernd Thiede,
- Susanne Lorenz,
- Leonardo A. Meza-Zepeda,
- Arne Klungland,
- and Jorrit M. Enserink
Genome Res. June 2015 25: 897-906; Published in Advance March 23, 2015, doi:10.1101/gr.185793.114
...promoters was also strongly reduced under these conditions, suggesting that Rap1 sumoylation mediates recruitment of TFIID (Fig. 5B). We tested this hypothesis directly by coimmunoprecipitation experiments. Although the TFIID subunit Taf4 efficiently coimmunoprecipitated with HAtagged Rap1 in WT cells...
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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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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...in nucleosome occupancy, reflecting the decrease in gene expression. The opposite was observed in target genes responding to deleted repressors, which suggests that the loss of a promoter-bound repressor will lead to a subsequent recruitment of other DNA-binding factors to promote transcription (Fig. 4B). We...
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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
...a robust and powerful method for RNAPII transcription elongation rate measurement.Transcription elongation by RNA polymerase II (RNAPII) is one of the essential steps that give rise to precursor mRNAs in eukaryotes. Productive elongation begins when RNAPII is released from promoter-proximal pausing...
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Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
- Angela Jimeno-Martín,
- Erick Sousa,
- Rebeca Brocal-Ruiz,
- Noemi Daroqui,
- Miren Maicas,
- and Nuria Flames
Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
...de la Salud, Universidad San Jorge, 50830, Villanueva de Gállego, Zaragoza, Spain Corresponding author: nflames@ibv.csic.esAbstractTo systematically investigate the complexity of neuron specification regulatory networks, we performed an RNA interference (RNAi) screen against all 875 transcription...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...at both the gene and isoform levels. Here, ribosomal protein S2 (RPS2) is fused to APOBEC1, an RNA editing enzyme that catalyzes C-to-U editing on RNA transcripts, to enable simultaneous measurements of mRNA translation and mRNA levels (Fig. 1A).View larger version: In this window In a new window Figure 1...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...reduces the expression of a subset of genes. In addition, HDAC activity is required for interferon-induced transcriptional initiation of the immediate-early genes (Chang et al. 2004; Sakamoto et al. 2004). In mammalian cells, HDACs are enriched at transcriptionally active enhancers, promoters, and gene...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...of aligned transcripts over genes that were either upregulated (Myd88) or downregulated (Thbs1) in multiple depletions. (E) Gene Ontology analysis of all significantly downregulated genes found in at least two or three depletion conditions. (F) ChromHMM analysis of promoters (500 bp upstream of transcription...

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