Searching journal content for articles similar to Floc'hlay et al. 31 (2): 211.

Displaying results 1-10 of 31

For checked items

view abstracts
download to citation manager

Select this article
Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...modifiers, such as cis-acting regulatory elements, trans-acting transcription factors, or epigenetic modifications (Castel et al. 2018; Delaneau et al. 2019; Lee et al. 2020; Tolmacheva et al. 2020). Despite the progress in understanding the factors that influence the penetrance of P/LP variants...
Select this article
Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...and cis variation (Van De Geijn et al. 2015; Hill et al. 2021). Differences in TF binding across a group of genetically diverse individuals can be caused by the impact of genetic variation on either (or both) the target DNA regulatory sequence (cis) or in the TF protein sequence, altering its binding...
OPEN ACCESS ARTICLE
Select this article
Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...were available, resulting in a set of nine tissues: adrenal gland, brain, heart, kidney, large intestine, lung, muscle, stomach, and thymus (Fig. 1A,B). Hence, in this study, we focus on the regulatory evolution across somatic tissues. We called DHS for each tissue separately using a peak caller...
OPEN ACCESS ARTICLE
Select this article
Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...expression regulation. We illustrate how DO gene expression can be27 aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide28 a data resource that documents strain-specific variation in chromatin state and DNA methylation29 in hepatocytes across nine widely...
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...and gene decreased below ∼40 kb. This suggests that few ATAC-seq peaks act as cis silencers on target genes.Generating a catalog of common variants mapping to cis-acting regulatory elementsWe used a previously established catalog of 11,030,905 single-nucleotide variants (SNVs) and 1,705,738 short (≤265-bp...
Select this article
Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
- Can Cenik,
- Elif Sarinay Cenik,
- Gun W. Byeon,
- Fabian Grubert,
- Sophie I. Candille,
- Damek Spacek,
- Bilal Alsallakh,
- Hagen Tilgner,
- Carlos L. Araya,
- Hua Tang,
- Emiliano Ricci,
- and Michael P. Snyder
Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
...in the human population will likely uncover trans-acting and additional cis-acting genetic variants associated with translation and reveal the contribution of population-level variation to translation variability. A recent analysis (Battle et al. 2015) of RNA expression, ribosome occupancy, and protein...
OPEN ACCESS ARTICLE
Select this article
Research: Natural variation in the histone demethylase, KDM4C, influences expression levels of specific genes including those that affect cell growth
- Brittany L. Gregory and
- Vivian G. Cheung
Genome Res. January 2014 24: 52-63; Published in Advance November 27, 2013, doi:10.1101/gr.156141.113
...encoding the histone demethylase, KDM4C, which promotes transcriptional activation by removing the repressive histone mark, H3K9me3, from its target genes. We uncovered cis-acting variants that contribute to extensive individual differences in KDM4C expression. We also identified the target genes of KDM4C...
Select this article
Research: TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
- Helen M. Rowe,
- Adamandia Kapopoulou,
- Andrea Corsinotti,
- Liana Fasching,
- Todd S. Macfarlan,
- Yara Tarabay,
- Stéphane Viville,
- Johan Jakobsson,
- Samuel L. Pfaff,
- and Didier Trono
Genome Res. March 2013 23: 452-461; Published in Advance December 10, 2012, doi:10.1101/gr.147678.112
...) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis -acting activators contained within these retroelements. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced...
Select this article
Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
...often act together with other TFs. Furthermore, TFs are themselves extensively regulated. The study of GRNs has already provided insights into the systems-level mechanisms of gene regulation that control growth, development, physiology, and stress responses. Gene regulatory networks Over the last decade...
Select this article
LETTER: Transcript Level Alterations Reflect Gene Dosage Effects Across Multiple Tissues in a Mouse Model of Down Syndrome
- Pascal Kahlem,
- Marc Sultan,
- Ralf Herwig,
- Matthias Steinfath,
- Daniela Balzereit,
- Barbara Eppens,
- Nidhi G. Saran,
- Mathew T. Pletcher,
- Sarah T. South,
- Gail Stetten,
- Hans Lehrach,
- Roger H. Reeves,
- and Marie-Laure Yaspo
Genome Res. July 2004 14: 1258-1267; doi:10.1101/gr.1951304
...in their composition (e.g., neurons and astrocytes) and their common embryonic origins. Heart and skeletal muscle also shared significant similarities in patterns of gene expression. We obtained a similar order in the clustering of the tissues by analyzing the expression data of the Unigene control genes (data...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Floc'hlay et al. 31 (2): 211.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: