Searching journal content for articles similar to Sundaram et al. 24 (12): 1963.

Displaying results 1-10 of 73

For checked items

view abstracts
download to citation manager

Select this article
Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...(Schmidt et al. 2012; Wang et al. 2012). In mammals, TE-derived sequences contribute up to 40% of -wide binding sites for TFs located in TE-rich regions (Sundaram et al. 2014). It has been proposed that such co-option of TE-regulatory elements for gene regulatory networks can provide substantial...
Select this article
Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...elements and can be used as promoters, enhancers, and insulators, providing fundamental building blocks for gene regulatory networks (Lamprecht et al. 2010; Babaian et al. 2016; Chuong et al. 2017; Sundaram and Wysocka 2020; Karttunen et al. 2023; Lawson et al. 2023; Shah et al. 2023; Liang et al. 2024...
OPEN ACCESS ARTICLE
Select this article
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
..., Guelph, ON N1G 2W1, Canada Corresponding author: michael.wilson@sickkids.caAbstractTransposable elements (TEs) provide a source of transcription factor (TF) binding sites that can rewire gene regulatory networks. NF-kB is an evolutionarily conserved TF complex primarily involved in innate immunity...
Select this article
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
..., Institute of Reproduction and Development, Fudan University, Shanghai 200437, China Corresponding authors: twang@wustl.edu, yue@northwestern.edu, hongboyang@fudan.edu.cnAbstractTransposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive...
OPEN ACCESS ARTICLE
Select this article
Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
....The Cys2-His2 zinc finger (ZNF) is a short nucleic acid binding domain widespread in eukaryotes. ZNFs are often arranged in tandemly repeated arrays, resulting in proteins with versatile nucleic acid binding ability (Wolfe et al. 2000; Klug 2010; Najafabadi et al. 2017). In metazoans, tandem-repeat ZNF...
OPEN ACCESS ARTICLE
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
...active regulatory elements in the Atlantic salmon . 149 150 Immune stimulation remodels chromatin accessibility and histone modifications in 151 Atlantic salmon head kidney 152 Poly I:C stimulation led to widespread changes in chromatin accessibility, with an 153 approximately 25% increase in ATAC...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...relocalization away from the endoplasmic reticulum, suggestive of novel TE dependent protein function in primate evolution. This work highlights the widespread dynamic nature of the spatiotemporal KZFP:TE transcriptome and its importance throughout TE mediated innovation and neurotypical human brain development...
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: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
...controlling wheat adaptation but also propose abundant indications of the widespread ongoing regulatory innovation and expansion introduced by lineage-specific TE insertion, degeneration, and domestication.MethodsPlant materials and growth conditionsTu seeds were surface-sterilized via a 10-min incubation...
Select this article
Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...: 163-189. Smit A, Hubley R, Green P. 2015. RepeatMasker Open-4.0. 2013–2015. Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. 2014. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome research 24: 1963-1976. Sundaram V, Wang T. 2018...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Sundaram et al. 24 (12): 1963.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: