Searching journal content for articles similar to Ernst and Kellis 23 (7): 1142.

Displaying results 1-10 of 147

For checked items

view abstracts
download to citation manager

Select this article
Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...” and “innate immune response”. The 288 prevalence of IRF8 motifs within these genes further supports this TF’s role as a critical 289 transcription factor driving interferon-stimulated regulatory networks during poly I:C 290 stimulation. 291 292 Chromatin state dynamics and TFBS using whole ATAC-seq and Ch...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
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. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
..., for conserved genes to mediate consistent phenotypic outcomes, there must also be consistent regulation of such genes by cis-regulatory modules (CRMs). CRMs consist of clusters of transcription factor binding sites (TFBSs) that regulate the expression of target genes through collective or competitive binding...
Select this article
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
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
Select this article
Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...similar to Zymoseptoria tritici(Möller et al. 2023). The regulatory relationships among H3K36me3, H3K27me3, and H4K20me3 warrant further investigation to elucidate their roles in chromatin-based gene regulation.Set2 and Ash1 play essential, distinct roles in chromatin-based regulation affecting fungal...
Select this article
Method: Chromatin interaction–aware gene regulatory modeling with graph attention networks
- Alireza Karbalayghareh,
- Merve Sahin,
- and Christina S. Leslie
Genome Res. May 2022 32: 930-944; Published in Advance April 8, 2022, doi:10.1101/gr.275870.121
...direct transcription factor (TF) targets as validated by CRISPRi TF knockout experiments via in silico ablation of TF binding motifs. GraphReg therefore represents an important advance in modeling the regulatory impact of epigenomic and sequence elements.Transcriptional gene regulation involves...
OPEN ACCESS ARTICLE
Select this article
Method: MEDEA: analysis of transcription factor binding motifs in accessible chromatin
- Luca Mariani,
- Kathryn Weinand,
- Stephen S. Gisselbrecht,
- and Martha L. Bulyk
Genome Res. May 2020 30: 736-748; Published in Advance May 18, 2020, doi:10.1101/gr.260877.120
...@bwh.harvard.eduAbstractDeciphering the interplay between chromatin accessibility and transcription factor (TF) binding is fundamental to understanding transcriptional regulation, control of cellular states, and the establishment of new phenotypes. Recent -wide chromatin accessibility profiling studies have provided catalogs of putative open...
Select this article
Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...experimental designs aimed at investigating the functions of lineage-specific TF regulators within their respective cell types.View larger version: In this window In a new window Figure 5. Gene regulatory network construction in the MES cells. (A) A heatmap displays differential activity of motifs over time...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...and L’EMbeDS, Sant’Anna School of Advanced Studies, Pisa 56127, Italy Approximately 13% of the human at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity...
OPEN ACCESS ARTICLE
Select this article
Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state regulatory potential (esRP) scores for each c...
OPEN ACCESS ARTICLE
Select this article
Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...different biological conditions, suggesting that the “liquid” or “solid” state of chromatin are in fact two sides of the same coin.The structural and dynamical properties of the eukaryotic inside the cell nucleus play crucial roles in many cell functions, such as gene regulation (van Steensel and Furlong...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ernst and Kellis 23 (7): 1142.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: