Searching journal content for articles similar to Santini et al. 13 (6a): 1111.

Displaying results 1-10 of 222

For checked items

view abstracts
download to citation manager

Select this article
Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
.... 2016). TADs are, therefore, three-dimensional structures that organize the into functional and physical units by bringing together genes and regulatory elements that interact primarily with each other (Dixon et al. 2012; Nora et al. 2012). TADs are thought to form through loop extrusion: as cohesin...
OPEN ACCESS ARTICLE
Select this article
Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...variants versus identification of their target genes.Multitask training to predict multiple regulatory genomic assays across different cell and tissue types enables information sharing between the different contexts (Kelley et al. 2018). However, performance remains limited by the training sequence space...
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
...common and cell-type-specific regeneration-responsive gene (RRG) programs and cis-regulatory elements, as well as key TFs associated with stages and cell types during regeneration, enhancing our understanding of tissue regeneration.ResultsSingle-nucleus multiomic profiling of zebrafish caudal fin...
OPEN ACCESS ARTICLE
Select this article
Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...BGC.gBGC promotes parallel alterations in genes and the proximal conserved elementsStrong gBGC can lead to severe W → S substitutions in both coding and flanking noncoding regions (Ratnakumar et al. 2010). Therefore, a conspicuous GC-biased substitution pattern in proximal conserved elements may be a potential...
Select this article
Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...the spatial and temporal dynamics of enhancer–promoter interactions. Understanding how enhancers interact with promoters will deepen our understanding of the regulation of gene expression and the molecular underpinnings of transcriptional control.Gene expression programs are encoded by cis-regulatory elements...
Select this article
Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we map caQTLs in liver tissue from 138 human donors and identify caQTLs for 35,361 regulatory elements, including population-specific caQTLs driven...
Select this article
Research: Genome-wide oscillations in G + C density and sequence conservation
- Zarmik Moqtaderi,
- Susan Brown,
- and Welcome Bender
Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
...by Kawahara Keiga.Mammalian s are more problematic; they are much larger and contain numerous repetitive elements. However, there are some regions with fewer mobile elements and higher sequence conservation. These include genes or gene clusters with extensive cis-regulatory regions, such as the human HOX loci...
Select this article
Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
- Joe R. Harman,
- Ross Thorne,
- Max Jamilly,
- Marta Tapia,
- Nicholas T. Crump,
- Siobhan Rice,
- Ryan Beveridge,
- Edward Morrissey,
- Marella F.T.R. de Bruijn,
- Irene Roberts,
- Anindita Roy,
- Tudor A. Fulga,
- and Thomas A. Milne
Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
.... These observations suggest that although the core GRN motifs represent common regulatory wiring that enables an oncogenic transcription program, levels of gene and protein expression likely also contribute to oncogenesis.To explore the primary RNA-seq data in detail, we clustered node activity patterns into five...
OPEN ACCESS ARTICLE
Select this article
Resource: Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
- Bony De Kumar,
- Mark E. Parrish,
- Brian D. Slaughter,
- Jay R. Unruh,
- Madelaine Gogol,
- Christopher Seidel,
- Ariel Paulson,
- Hua Li,
- Karin Gaudenz,
- Allison Peak,
- William McDowell,
- Brian Fleharty,
- Youngwook Ahn,
- Chengqi Lin,
- Edwin Smith,
- Ali Shilatifard,
- and Robb Krumlauf
Genome Res. August 2015 25: 1229-1243; Published in Advance May 29, 2015, doi:10.1101/gr.184978.114
...Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA AbstractThe clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity...
OPEN ACCESS ARTICLE
Select this article
Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...of conservation in the genomic distribution of chromatin modifications and gene regulatory elements between cnidarians and bilaterians. Promoter histone modifications are shared in most eukaryotes, and enhancers are marked by the same histone modifications in Nematostella and bilaterian model organisms. While...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Santini et al. 13 (6a): 1111.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: