Searching journal content for articles similar to Buen Abad Najar et al. 32 (7): 1385.

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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...with identifying the TSS, the RNA polymerase recruitment point. TF binding sites near the TSS form the promoter, whereas more distant ones are typically called enhancers (Bateman and Johnson 2022). Some genes have multiple functional TSSs, which complicates regulatory analysis, so alternative promoters must...
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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
...and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address these challenges, we describe the Vertebrate Alternative Splicing and Transcription Database (VastDB), the largest resource of -wide, quantitative...
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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
.... The relationship between exonic splicing regulatory sequences and coding sequences is still poorly understood. We demonstrate that exons that are coregulated by any given splicing factor share a similar nucleotide composition bias and preferentially code for amino acids with similar physicochemical properties...
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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
...accessibility in isolated cardiomyocytes (CMs) from wild-type zebrafish embryos at developmental stages corresponding to heart tube morphogenesis, looping, and maturation. We identified genetic regulatory modules driving crucial events of heart development that contained key cardiac TFs and are associated...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
...alternative splicing events that exhibit reciprocal regulation by the CELF and RBFOX families also change during heart development, myogenesis, and/or in T1D hearts (85.9%) (Supplemental Fig. S6). Genes containing highly consistent, antagonistically coregulated events have previously been implicated...
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Method: Co-expression networks reveal the tissue-specific regulation of transcription and splicing
- Ashis Saha,
- Yungil Kim,
- Ariel D.H. Gewirtz,
- Brian Jo,
- Chuan Gao,
- Ian C. McDowell,
- The GTEx Consortium,
- Barbara E. Engelhardt,
- and Alexis Battle
Genome Res. November 2017 27: 1843-1858; Published in Advance October 11, 2017, doi:10.1101/gr.216721.116
..., Transcriptome-Wide Networks (TWNs), which captures gene relationships that reflect regulation of alternative splicing in an interpretable model. We built TWNs to identify candidate regulators of both splicing and transcription across 16 tissues. Next, we identified Tissue-Specific Networks (TSNs) for 26 tissues...
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Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
- Markus Brosch,
- Gary I. Saunders,
- Adam Frankish,
- Mark O. Collins,
- Lu Yu,
- James Wright,
- Ruth Verstraten,
- David J. Adams,
- Jennifer Harrow,
- Jyoti S. Choudhary,
- and Tim Hubbard
Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
...Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome Markus Brosch 1 , Gary I. Saunders 1 , Adam Frankish , Mark O. Collins , Lu Yu , James Wright...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...seen in Apalone may be close to the ancestral state for turtles; i.e., the karyotype that this softshell turtle has retained since the divergence of its family Trionychidae from other hidden-neck turtles (Crawford et al. 2015). Indeed, a single identifiable large-scale fission event was observed...
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Resource: A time-resolved multi-omic atlas of the developing mouse liver
- Tongqing Gong,
- Chunchao Zhang,
- Xiaotian Ni,
- Xianju Li,
- Jin'e Li,
- Mingwei Liu,
- Dongdong Zhan,
- Xia Xia,
- Lei Song,
- Quan Zhou,
- Chen Ding,
- Jun Qin,
- and Yi Wang
Genome Res. February 2020 30: 263-275; Published in Advance February 12, 2020, doi:10.1101/gr.253328.119
...@bcm.eduAbstractLiver organogenesis and development are composed of a series of complex, well-orchestrated events. Identifying key factors and pathways governing liver development will help elucidate the physiological and pathological processes including those of cancer. We conducted multidimensional omics measurements including...
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Research: The predicted RNA-binding protein regulome of axonal mRNAs
- Raphaëlle Luisier,
- Catia Andreassi,
- Lisa Fournier,
- and Antonella Riccio
Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
...2017; Andreassi et al. 2018; Andreassi et al. 2021). RBP complexes are initially assembled cotranscriptionally and are essential for regulating RNA splicing, polyadenylation site (PAS) choice, alternative polyadenylation (APA), and mRNA nuclear export (Hentze et al. 2018; Van Nostrand et al. 2020...
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