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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
...that do not cluster consistently with their tissue of origin and function (endocrine pancreas, liver, right lobe of liver, gastrocnemius medialis, bipolar neuron), were not included in the subsequent analyses (Supplemental Table 1; see Methods).View larger version: In this window In a new window Figure 1...
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Resource: An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
- Javier Tapial,
- Kevin C.H. Ha,
- Timothy Sterne-Weiler,
- André Gohr,
- Ulrich Braunschweig,
- Antonio Hermoso-Pulido,
- Mathieu Quesnel-Vallières,
- Jon Permanyer,
- Reza Sodaei,
- Yamile Marquez,
- Luca Cozzuto,
- Xinchen Wang,
- Melisa Gómez-Velázquez,
- Teresa Rayon,
- Miguel Manzanares,
- Julia Ponomarenko,
- Benjamin J. Blencowe,
- and Manuel Irimia
Genome Res. October 2017 27: 1759-1768; Published in Advance August 30, 2017, doi:10.1101/gr.220962.117
..., epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin. Genome Res 24: 511–521. Mauger O, Lemoine F, Scheiffele P. 2016. Targeted intron retention and excision for rapid gene regulation in response to neuronal activity.Neuron 92: 1266–1278. Melé M...
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Research: Interplay between coding and exonic splicing regulatory sequences
- Nicolas Fontrodona,
- Fabien Aubé,
- Jean-Baptiste Claude,
- Hélène Polvèche,
- Sébastien Lemaire,
- Léon-Charles Tranchevent,
- Laurent Modolo,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. May 2019 29: 711-722; Published in Advance April 8, 2019, doi:10.1101/gr.241315.118
...et al. 2010; Lin et al. 2011; Shabalina et al. 2013; Savisaar and Hurst 2017a,b). Therefore, coding and exonic splicing regulatory sequences could evolve independently because of the variation of the third nucleotides of codons. In this setting, it has recently been shown that splicing regulatory...
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Method: A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1
- Dror Hollander,
- Maya Donyo,
- Nir Atias,
- Keren Mekahel,
- Zeev Melamed,
- Sivan Yannai,
- Galit Lev-Maor,
- Asaf Shilo,
- Schraga Schwartz,
- Iris Barshack,
- Roded Sharan,
- and Gil Ast
Genome Res. April 2016 26: 541-553; Published in Advance February 9, 2016, doi:10.1101/gr.193169.115
...on splicing aberrations in cancer, we analyzed transcriptome-wide data of cancerous and normal tissues spanning 24,426 alternative splicing events and 18,093 genes (Castle et al. 2008), identifying alternative splicing events that exhibit significant splicing differences in tumors compared with corresponding...
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Resource: Identification of protein features encoded by alternative exons using Exon Ontology
- Léon-Charles Tranchevent,
- Fabien Aubé,
- Louis Dulaurier,
- Clara Benoit-Pilven,
- Amandine Rey,
- Arnaud Poret,
- Emilie Chautard,
- Hussein Mortada,
- François-Olivier Desmet,
- Fatima Zahra Chakrama,
- Maira Alejandra Moreno-Garcia,
- Evelyne Goillot,
- Stéphane Janczarski,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. June 2017 27: 1087-1097; Published in Advance April 18, 2017, doi:10.1101/gr.212696.116
...variations (deltaPSI) of the 81 exons of the “Mes-Epi” list, as measured by RT-PCR (x-axis) and by RNA-seq (y-axis). Exons are differentially spliced between normal fibroblast (Fibro) and normal epithelial (Epi) cells (left panel) and between Claudin-Low (mesenchymal-like) versus luminal (epithelial...
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Method: Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
- Mengjie Chen,
- Qi Zhan,
- Zepeng Mu,
- Lili Wang,
- Zhaohui Zheng,
- Jinlin Miao,
- Ping Zhu,
- and Yang I. Li
Genome Res. April 2021 31: 698-712; Published in Advance March 19, 2021, doi:10.1101/gr.261115.120
...for 95 annotated cell types (e.g., epithelial cells, fibroblasts and endothelial cells, etc.) were used for projection. This processed reference panel is downloaded directly from R package RCA (Li et al. 2017). To identify subpopulations from the observed single cells, we projected all cells from our sc...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...tissue. (A) Clusters of 510,171 human heart cells from 11 male and nine female individuals. Cells within the dashed box are glia, which are colored by subtypes. (EC) Endothelial cells, (FB) fibroblasts, (aCM) atrial cardiomyocytes, (vCM) ventricular cardiomyocytes, (mSchwann) myelinating Schwann, (nm...
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Methods: Genome-wide discovery of human heart enhancers
- Leelavati Narlikar,
- Noboru J. Sakabe,
- Alexander A. Blanski,
- Fabio E. Arimura,
- John M. Westlund,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
..., endothelial cells, and fibroblasts that are most probably controlled by different genetic pathways. In other words, heart enhancers are not likely to be bound by the same set of TFs or have sequence similarities if they are active in different cellular contexts. Therefore, learning a common ‘‘heart enhancer...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...family member (Sierant et al. 2025). This indicates that although most defects can be explained in large part by patient genetics, our current knowledge is insufficient to pinpoint the full genetic origin of most individual cases. In addition to environmental factors, unexplained cases presumably involve...
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Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- Piotr J. Balwierz,
- Mikhail Pachkov,
- Phil Arnold,
- Andreas J. Gruber,
- Mihaela Zavolan,
- and Erik van Nimwegen
Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
...,B6,B7}) are enriched for developmental genes and transcription factors. The genes in these pathways are most likely involved in the transition of the tissue from squamous to columnar epithelial that occurs during differentiation. Thus, in contrast to the methods used in the original study (Ross et...
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