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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...a karyotypically normal, immortalized human aortic endothelial cell line (TeloHAEC) (Fish et al. 2017; Alizada et al. 2021). This profiling was achieved using ChRO-seq (Chromatin Run-On sequencing [Chu et al. 2018]) which reveals bi-directional transcription of enhancer RNAs (eRNAs), a hallmark of active enhancers...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
..., and MHG H3K27ac peaks as indicated. Enrichment in both human and zebrafish HCNE sequences is shown. RNA-seq expression of TF genes corresponding to enriched motifs is indicated as fragments Per Kilobase of transcript per Million mapped reads (FPKM) for both human and zebrafish data sets as indicated. (AFG...
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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
...capture (3C), HiC, and ChIA-PET data on chromatin loops.Direct TF bindingThere are two main original sources of data on specific TF binding to the regulatory sequences of your GOI: major -wide programs (such as the above-mentioned ENCODE or FANTOM, which are especially rich in data on ncRNAs...
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Method: Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
- Wanqing Shao and
- Ting Wang
Genome Res. January 2021 31: 88-100; Published in Advance December 21, 2020, doi:10.1101/gr.265173.120
..., Washington University School of Medicine, St. Louis, Missouri 63108, USA Corresponding author: twang@wustl.eduAbstractTransposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...; Won et al. 2008). Typically, during active transcription, looser chromatin structures facilitate binding of TFs and RNA polymerases to trigger target gene expression. For instance, acetylation of a lysine residue of H3 histone weakens the binding between the histone and negatively charged DNA...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
..., current protocols for -wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5′ ends from as little as 50 ng total RNA...
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Research: The predicted RNA-binding protein regulome of axonal mRNAs
- Raphaëlle Luisier,
- Catia Andreassi,
- Lisa Fournier,
- and Antonella Riccio
Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
.... The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3′ Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...with transcriptional regulatory elements carrying active epigenetic modifications. Drug-induced promoter-proximal RNA polymerase II pausing promotes nearby G4 formation. In contrast, G4 stabilization by G4-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
....4 × 10−4 for CRC and P = 4.6 × 10−12 for T-ALL). The global loss of CC indicates a localization tendency of the network (Ahmad et al. 2020). Nodes with the highest 10% CC in the normal colon contain genes enriched in the regulation of transcription from RNA polymerase II promoter and cell cycle...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...RNA bait library specifically targeting 4650 regions that accumulate H3K27me3 and included a subset of loci differentially methylated between shoots and roots (Supplemental Fig. S9). The comparison of both Hi-C and C-Hi-C matrixes allowed us to identify a significant enrichment of chromatin contacts...

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