Searching journal content for articles similar to Xie et al. 20 (6): 804.

Displaying results 1-10 of 17

For checked items

view abstracts
download to citation manager

Select this article
Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
...(Chuong et al. 2016), mammalian development (Chuong et al. 2013; Lynch et al. 2015; Nishihara et al. 2016), evolution of mammalian gene regulatory networks (Xie et al. 2010; Sundaram et al. 2014), or RNA interference in mice (Flemr et al. 2013). Our study represents a remarkable case of ERVL LTRs...
OPEN ACCESS ARTICLE
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
...et al. 2013; Sundaram et al. 2014; Ito et al. 2017; Pehrsson et al. 2019; Miao et al. 2020). TEs contribute to essential components of gene regulatory machinery in both humans and mice, including promoters, enhancers, and insulators. Specific TE subfamilies have rewired gene regulatory networks...
OPEN ACCESS ARTICLE
Select this article
Research: Widespread contribution of transposable elements to the innovation of gene regulatory networks
- Vasavi Sundaram,
- Yong Cheng,
- Zhihai Ma,
- Daofeng Li,
- Xiaoyun Xing,
- Peter Edge,
- Michael P. Snyder,
- and Ting Wang
Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113
...-specific gene functions, suggesting that TEs are an important driving force for regulatory innovation. Taken together, our data suggest that TEs have significantly and continuously shaped gene regulatory networks during mammalian evolution. Footnotes [Supplemental material is available...
Select this article
Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA; 5Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA Abstract Plasticity of gene regulatory encryption can permit DNA sequence divergence...
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: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...paid to farmed fish - where relevant traits to aquaculture rely on early 15 developmental processes. This study reports a regulatory atlas of turbot 16 (Scophthalmus maximus) embryogenesis. 14,560 active genes were identified 17 in the embryonic transcriptome with > 90% showing differential expression...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...RNA-mediated regulatory mechanisms and identify regulatory hubs and functional modules within the network.Here, via integrated molecular-functional analyses, we aimed to identify diapause-associated miRNAs and their larger role within the larger molecular rewiring during the cellular transition into dormancy...
Select this article
Method: High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- Philippe Batut,
- Alexander Dobin,
- Charles Plessy,
- Piero Carninci,
- and Thomas R. Gingeras
Genome Res. January 2013 23: 169-180; Published in Advance August 30, 2012, doi:10.1101/gr.139618.112
.... 2011; Negre et al. 2011; The ENCODE Project Consortium et al. 2012; Shen et al. 2012), their relevance to development and disease (Lindblad-Toh et al. 2011; The ENCODEProject Consortium et al. 2012), and the structure of the gene regulatory networks they implement (Suzuki et al. 2009; Marbach et al...
Select this article
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
...evolution, TEs rewire host transcription networks through transposition and co-option, resulting in a wide variety of TE-derived regulatory elements, including promoters, enhancers, transcription terminators, and chromatin loop anchors (for reviews, see Feschotte and Gilbert 2012; Rebollo et al. 2012...
Select this article
Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...motifs cooperatively modulate gene expression networks that are reused and rewired in the evolutionary acquisition of morphological diversity in metazoans. However, how these cis-regulatory elements diverge in sequence and in function and contribute to new gene regulatory networks and higher...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Xie et al. 20 (6): 804.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: