Searching journal content for articles similar to Ettwiller et al. 13 (5): 883.

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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...PGE accurately discovers some crucial TF motifs within prioritized cCREs and reveals the different regulatory types of these cCREs.Cell type–specific gene expression patterns are primarily determined through complex interactions between cis-regulatory elements (CREs) and transcriptional factors, playing...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...) Line graph of gChromVAR Z-scores specific to megakaryocyte traits. (E) Modeling cis-regulatory usage across the erythroid recovery timeline. At early time points in anemia recovery, erythroid precursor cells upregulate expression and activity of JUN and FOS transcription factors at AP-1 motifs...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...-seq (Yang et al. 2020). Together, these data empower us to investigate the cis-regulatory element (CRE) contribution of TEs in zebrafish.Here, we intercalate these multidimensional transcriptome, epi, and three-dimensional structure data to create a comprehensive epigenetic and transcriptional landscape...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...for representing cis-regulatory diversityA high-throughput sequencing experiment typically identifies a set X of genomic regions that are enriched with a specific biochemical activity. We assume that r different regulatory modules may be responsible for the activity and that each module is defined by the presence...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...) introduces the concept of cis-regulatory potential to infer subpopulation-specific GRNs, achieving significantly higher accuracy compared with correlation-based methods. CellOracle (Kamimoto et al. 2023) enables GRN inference by integrating single-cell multi-omics data with prior regulatory knowledge...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...quintiles of network centrality (Supplemental Figs. S22 and S23; Supplemental Table S9). We observed that peripheral genes (Quintile 1) and central genes (Quintile 5) of consensus networks exhibited an excess overlap > 1 of eQTL-deficient genes (those which lacked significant cis-regulatory variants...
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Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
- Dongwon Lee,
- Ashish Kapoor,
- Alexias Safi,
- Lingyun Song,
- Marc K. Halushka,
- Gregory E. Crawford,
- and Aravinda Chakravarti
Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
..., New York, NY 10016, USA; 5University of Texas Health Science Center at Houston, Houston, TX 77030, USA Corresponding authors: aravinda.chakravarti@nyumc.org, dongwon.lee@nyumc.orgAbstractCis-regulatory elements (CRE), short DNA sequences through which transcription factors (TFs) exert regulatory...
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Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
- Julie Dubois-Chevalier,
- Vanessa Dubois,
- Hélène Dehondt,
- Parisa Mazrooei,
- Claire Mazuy,
- Aurélien A. Sérandour,
- Céline Gheeraert,
- Penderia Guillaume,
- Eric Baugé,
- Bruno Derudas,
- Nathalie Hennuyer,
- Réjane Paumelle,
- Guillemette Marot,
- Jason S. Carroll,
- Mathieu Lupien,
- Bart Staels,
- Philippe Lefebvre,
- and Jérôme Eeckhoute
Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
..., how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor...
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Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
- Peng Liu,
- Alexandra A. Soukup,
- Emery H. Bresnick,
- Colin N. Dewey,
- and Sündüz Keleş
Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
...splice junctions, while performing competitively in detecting exonic nucleotides. Applying PRAM to 30 human ENCODE RNA-seq data sets identified unannotated transcripts with epigenetic and RAMPAGE signatures similar to those of recently annotated transcripts. In a case study, we discovered...
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