Understanding alternative splicing: towards a cellular code

Origin of life: The RNA world

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Listening to silence and understanding nonsense: exonic mutations that affect splicing

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CLIP Identifies Nova-Regulated RNA Networks in the Brain

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A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG

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The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons

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Alternative isoform regulation in human tissue transcriptomes

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Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

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Spliceosome Structure and Function

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Analysis and design of RNA sequencing experiments for identifying isoform regulation

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A day in the life of the spliceosome

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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

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Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

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Molecular mechanisms of ROS production and oxidative stress in diabetes

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Function of alternative splicing

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RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing

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A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons

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Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

Kalyna, M., Simpson, C. G., Syed, N. H., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr932 · Cited by 480

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart

Kalsotra, A., Xiao, X., Ward, A. J., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809045105 · Cited by 508

The human SWI/SNF subunit Brm is a regulator of alternative splicing

Batsché, E., Yaniv, M., & Muchardt, C. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1030 · Cited by 471

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

Lovci, M. T., Ghanem, D., Marr, H., Arnold, J., Gee, S., Parra, M., Liang, T. Y., Stark, T. J., Gehman, L. T., Hoon, S., et al. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2699 · Cited by 385

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

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Neuronal regulation of alternative pre-mRNA splicing

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RNA Quality Control in Eukaryotes

Doma, M. K., & Parker, R. (2007) · Cell · doi:10.1016/j.cell.2007.10.041 · Cited by 345

Crossregulation and Functional Redundancy between the Splicing Regulator PTB and Its Paralogs nPTB and ROD1

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Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

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Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

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Tissue factor as a link between inflammation and coagulation

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The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function

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Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2

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Fox-1 family of RNA-binding proteins

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The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

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A catalytically silent FAAH-1 variant drives anandamide transport in neurons

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Genome-wide Analysis of Alternative Pre-mRNA Splicing

Ben-Dov, C., Hartmann, B., Lundgren, J., & Valcárcel, J. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.r700033200 · Cited by 151

YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

Wei, W.-J., Mu, S.-R., Heiner, M., Fu, X., Cao, L.-J., Gong, X.-F., Bindereif, A., & Hui, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks579 · Cited by 124

Auto- and Cross-Regulation of the hnRNP L Proteins by Alternative Splicing

Rossbach, O., Hung, L.-H., Schreiner, S., Grishina, I., Heiner, M., Hui, J., & Bindereif, A. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01689-08 · Cited by 141

Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

Zhou, H.-L., Hinman, M. N., Barron, V. A., Geng, C., Zhou, G., Luo, G., Siegel, R. E., & Lou, H. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103344108 · Cited by 136

Mouse mammary tumor virus encodes a self-regulatory RNA export protein and is a complex retrovirus

Mertz, J. A., Simper, M. S., Lozano, M. M., Payne, S. M., & Dudley, J. P. (2005) · Journal of Virology · doi:10.1128/jvi.79.23.14737-14747.2005 · Cited by 130

Functional coordination of alternative splicing in the mammalian central nervous system

Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., et al. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r108 · Cited by 120

Alternative pre-mRNA splicing in neurons: growing up and extending its reach

Zheng, S., & Black, D. L. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.04.003 · Cited by 115

ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation

Bhate, A., Parker, D. J., Bebee, T. W., Ahn, J., Arif, W., Rashan, E. H., Chorghade, S., Chau, A., Lee, J.-H., Anakk, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms9768 · Cited by 103

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function

Ezkurdia, I., del Pozo, A., Frankish, A., Rodriguez, J. M., Harrow, J., Ashman, K., Valencia, A., & Tress, M. L. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss100 · Cited by 89

Genome-wide Analysis of Alternative Pre-mRNA Splicing and RNA-Binding Specificities of the Drosophila hnRNP A/B Family Members

Blanchette, M., Green, R. E., MacArthur, S., Brooks, A. N., Brenner, S. E., Eisen, M. B., & Rio, D. C. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.022 · Cited by 86

Alternative Splicing of Cyr61 Is Regulated by Hypoxia and Significantly Changed in Breast Cancer

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SnapShot: The Splicing Regulatory Machinery

Gabut, M., Chaudhry, S., & Blencowe, B. J. (2008) · Cell · doi:10.1016/j.cell.2008.03.010 · Cited by 66

Analyzing Schizophrenia by DNA Microarrays

Horváth, S., Janka, Z., & Mirnics, K. (2011) · Biological Psychiatry · doi:10.1016/j.biopsych.2010.07.017 · Cited by 64

Stepwise assembly of the Nova -regulated alternative splicing network in the vertebrate brain

Irimia, M., Denuc, A., Burguera, D., Somorjai, I., Martín-Durán, J. M., Genikhovich, G., Jimenez-Delgado, S., Technau, U., Roy, S. W., Marfany, G., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012333108 · Cited by 47

Highly accurate isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · doi:10.1101/2022.06.08.495354 · Cited by 40

Structure-guided isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · eLife · doi:10.7554/elife.82556 · Cited by 40

Integrating many co-splicing networks to reconstruct splicing regulatory modules

Dai, C., Li, W., Liu, J., & Zhou, X. J. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-s1-s17 · Cited by 20

The Role of Reactive Oxygen and Nitrogen Species in the Expression and Splicing of Nitric Oxide Receptor

Sharina, I. G., & Martin, E. (2017) · Antioxidants & Redox Signaling · doi:10.1089/ars.2016.6687 · Cited by 19

The discovery, function, and regulation of epithelial splicing regulatory proteins (ESRP) 1 and 2

Derham, J. M., & Kalsotra, A. (2023) · Biochemical Society Transactions · doi:10.1042/bst20221124 · Cited by 16