Cited by 1,044RNA Research and SplicingRNA regulation and diseaseRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 177 of the 177 references it cites were found in a registry or an index.

Context-dependent control of alternative splicing by RNA-binding proteins

Open access

Fu, Xiang-Dong, Ares, Manuel·2014·Nature Reviews Genetics

Open this paper in CoChat — free account

Abstract

Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the 'splicing code' that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other's functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nrg3778

Cites

177 of 177 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Development and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762
Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873
Mechanisms of Alternative Pre-Messenger RNA Splicing
Black, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161720 · Cited by 2,704
The Spliceosome: Design Principles of a Dynamic RNP Machine
Wahl, M. C., Will, C. L., & Lührmann, R. (2009) · Cell · doi:10.1016/j.cell.2009.02.009 · Cited by 2,665
Expansion of the eukaryotic proteome by alternative splicing
Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,270
Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B. M., Strein, C., Davey, N. E., Humphreys, D. T., Preiss, T., Steinmetz, L. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.031 · Cited by 2,132
Frequent pathway mutations of splicing machinery in myelodysplasia
Yoshida, K., Sanada, M., Shiraishi, Y., Nowak, D., Nagata, Y., Yamamoto, R., Sato, Y., Sato-Otsubo, A., Kon, A., Nagasaki, M., et al. (2011) · Nature · doi:10.1038/nature10496 · Cited by 2,029
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
Kato, M., Han, T. W., Xie, S., Shi, K., Du, X., Wu, L. C., Mirzaei, H., Goldsmith, E. J., Longgood, J., Pei, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.017 · Cited by 2,012
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480
Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS
Kim, H. J., Kim, N. C., Wang, Y., Scarborough, E. A., Moore, J., Diaz, Z., MacLea, K. S., Freibaum, B. D., Li, S., Molliex, A., et al. (2013) · Nature · doi:10.1038/nature11922 · Cited by 1,478

Flagged first, then by citations

Show all 176 references

Sorted by citations

Items 201–300 of 1,000

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomesPreprint
Gazzara, M. R., Mallory, M. J., Roytenberg, R., Lindberg, J., Jha, A., Lynch, K. W., & Barash, Y. (2017) · Genome Research · doi:10.1101/gr.220517.117 · Cited by 61
RBM10: Structure, functions, and associated diseases
Inoue, A. (2021) · Gene · doi:10.1016/j.gene.2021.145463 · Cited by 57
Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis
Carrasco‐López, C., Hernández‐Verdeja, T., Perea-Resa, C., Abia, D., Catalá, R., & Salinas, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx375 · Cited by 57
Poison cassette exon splicing ofSRSF6regulates nuclear speckle dispersal and the response to hypoxia
Machado, C. D. O. F., Schafranek, M., Brüggemann, M., Cañás, M. C. H., Keller, M., Liddo, A. D., Brezski, A., Blümel, N., Arnold, B., Bremm, A., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1225 · Cited by 59
Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay
Sun, Y., Bao, Y., Han, W., Song, F., Shen, X., Zhao, J., Zuo, J., Saffen, D. W., Chen, W., Wang, Z., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx508 · Cited by 57
Messenger RNA Life-Cycle in Cancer Cells: Emerging Role of Conventional and Non-Conventional RNA-Binding Proteins?
Coppin, L., Leclerc, J., Vincent, A., Porchet, N., & Pigny, P. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19030650 · Cited by 60
Rescue of recurrent deep intronic mutation underlying cell type–dependent quantitative NEMO deficiency
Boisson, B., Honda, Y., Ajiro, M., Bustamante, J. C., Bendavid, M., Gennery, A. R., Kawasaki, Y., Ichishima, J., Osawa, M., Nihira, H., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci124011 · Cited by 59
IGF2BP3 May Contributes to Lung Tumorigenesis by Regulating the Alternative Splicing of PKM
Huang, X., Jun, Z., Jiang, Y., Xin, L., Liya, H., Yuanyuan, F., Yuting, Z., Zeng, H., Wu, H., Liu, J., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00679 · Cited by 56
Splicing to Keep Cycling: The Importance of Pre-mRNA Splicing during the Cell Cycle
Petasny, M., Bentata, M., Pawellek, A., Baker, M., Kay, G., & Salton, M. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.08.013 · Cited by 55
Nuclear speckle specific hnRNP D-like prevents age- and AD-related cognitive decline by modulating RNA splicing
Zhang, Q., Zhang, J., Ye, J., Li, X., Liu, H., Ma, X., Wang, C., He, K., Zhang, W., Ji, Y., et al. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00485-w · Cited by 60
Regulation of cancer progression by circRNA and functional proteins
Chen, J., Gu, J., Tang, M., Liao, Z., Tang, R., Zhou, L., Su, M., Jiang, J., Hu, Y., Chen, Y., et al. (2021) · Journal of Cellular Physiology · doi:10.1002/jcp.30608 · Cited by 55
miRNA targeting and alternative splicing in the stress response – events hosted by membrane-less compartments
Kucherenko, M. M., & Shcherbata, H. R. (2018) · Journal of Cell Science · doi:10.1242/jcs.202002 · Cited by 55
The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome
Zhang, L., Song, D., Zhu, B., & Wang, X. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.006 · Cited by 57
Elevated N‐methyltransferase expression induced by hepatic stellate cells contributes to the metastasis of hepatocellular carcinoma via regulation of the CD44v3 isoform
Li, J., Song, Y., Zhang, S., Hu, Q., Wang, F., Chi, X., Zhao, W., Xie, C., Zhang, C., Yu, Y., et al. (2019) · Molecular Oncology · doi:10.1002/1878-0261.12544 · Cited by 54
Transcription Regulation Through Nascent RNA Folding
Schärfen, L., & Neugebauer, K. M. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166975 · Cited by 55
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
Ray, D., Laverty, K. U., Jolma, A., Nie, K., Samson, R., Pour, S. E., Tam, C. L., von Krosigk, N., Nabeel‐Shah, S., Albu, M., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-32245-9 · Cited by 53
The evolution of posttranscriptional regulation
Schaefke, B., Sun, W., Li, Y., Fang, L., & Chen, W. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1485 · Cited by 59
ZRANB2 and SYF2-mediated splicing programs converging on ECT2 are involved in breast cancer cell resistance to doxorubicin
Tanaka, I., Chakraborty, A., Saulnier, O., Benoit‐Pilven, C., Vacher, S., Labiod, D., Lam, E. W. ‐., Bièche, I., Delattre, O., Pouzoulet, F., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1213 · Cited by 53
Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteinsPreprint
Hsiao, Y.-H. E., Bahn, J. H., Lin, X., Chan, T.-M., Wang, R., & Xiao, X. G. (2016) · Genome Research · doi:10.1101/gr.193359.115 · Cited by 54
The implications of alternative pre-mRNA splicing in cell signal transduction
Choi, S., Cho, N., & Kim, K. K. (2023) · Experimental & Molecular Medicine · doi:10.1038/s12276-023-00981-7 · Cited by 54
Pre-mRNA splicing in cancer: the relevance in oncogenesis, treatment and drug resistance
Wojtuszkiewicz, A., Assaraf, Y. G., Maas, M. J., Kaspers, G. J. L., Jansen, G., & Cloos, J. J. (2014) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1517/17425255.2015.993316 · Cited by 52
ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development
Rohacek, A. M., Bebee, T. W., Tilton, R. K., Radens, C. M., McDermott‐Roe, C., Peart, N. J., Kaur, M., Zaykaner, M., Cieply, B. W., Musunuru, K., et al. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.09.026 · Cited by 52
Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis
Yang, J., Thames, S., Best, N. B., Jiang, H., Huang, P., Dilkes, B. P., & Eveland, A. L. (2017) · The Plant Cell · doi:10.1105/tpc.17.00816 · Cited by 52
hnRNP A1/A2 and Sam68 collaborate with SRSF10 to control the alternative splicing response to oxaliplatin-mediated DNA damage
Cloutier, A., Shkreta, L., Toutant, J., Durand, M., Thibault, P., & Chabot, B. (2018) · Scientific Reports · doi:10.1038/s41598-018-20360-x · Cited by 51
SRSF10: an atypical splicing regulator with critical roles in stress response, organ development, and viral replication
Shkreta, L., Delannoy, A., Salvetti, A., & Chabot, B. (2021) · RNA · doi:10.1261/rna.078879.121 · Cited by 51
SRSF10 Plays a Role in Myoblast Differentiation and Glucose Production via Regulation of Alternative Splicing
Wei, N., Cheng, Y., Wang, Z., Liu, Y., Luo, C., Liu, L., Chen, L., Xie, Z., Lu, Y., & Feng, Y. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.038 · Cited by 51
Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements
Ajiro, M., Tang, S., Doorbar, J., & Zheng, Z. (2016) · Journal of Virology · doi:10.1128/jvi.00965-16 · Cited by 53
Normal and altered pre-mRNA processing in the DMD gene
Tuffery‐Giraud, S., Miro, J., Koenig, M., & Claustres, M. (2017) · Human Genetics · doi:10.1007/s00439-017-1820-9 · Cited by 50
A comprehensive expression landscape of RNA-binding proteins (RBPs) across 16 human cancer types
Zhang, B., Babu, K. R., Lim, C. Y., Kwok, Z. H., Li, J., Zhou, S., Yang, H. H., & Tay, Y. (2019) · RNA Biology · doi:10.1080/15476286.2019.1673657 · Cited by 50
Astrocyte senescence contributes to cognitive decline
Csípő, T., Lipécz, Á., Ashpole, N. M., Balasubramanian, P., & Tarantini, S. (2019) · GeroScience · doi:10.1007/s11357-019-00140-9 · Cited by 50
Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals
Torres-Méndez, A., Pop, S., Bonnal, S., Almudí, I., Avola, A., Roberts, R. J. V., Paolantoni, C., Alcaina‐Caro, A., Anduaga, A. M., Haussmann, I. U., et al. (2022) · Science Advances · doi:10.1126/sciadv.abk0445 · Cited by 51
Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation
Ye, R., Hu, N., Cao, C., Su, R., Xu, S., Chen, Y., Zhou, X., & Xue, Y. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.03.001 · Cited by 52
Modulation of Alternative Splicing with Chemical Compounds in New Therapeutics for Human Diseases
Ohe, K., & Hagiwara, M. (2015) · ACS Chemical Biology · doi:10.1021/cb500697f · Cited by 50
Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells
Ajith, S., Gazzara, M. R., Cole, B. S., Shankarling, G. S., Martínez, N. M., Mallory, M. J., & Lynch, K. W. (2016) · RNA Biology · doi:10.1080/15476286.2016.1176663 · Cited by 49
Lin28a Regulates Pathological Cardiac Hypertrophic Growth Through Pck2-Mediated Enhancement of Anabolic Synthesis
Ma, H., Yu, S., Liu, X., Zhang, Y., Fakadej, T., Liu, Z., Yin, C., Shen, W., Locasale, J. W., Taylor, J. M., et al. (2019) · Circulation · doi:10.1161/circulationaha.118.037803 · Cited by 50
The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function
Blake, D., & Lynch, K. W. (2021) · Immunological Reviews · doi:10.1111/imr.13018 · Cited by 49
A niche for the genome
Stotz, K. C., & Griffiths, P. E. (2015) · Biology & Philosophy · doi:10.1007/s10539-015-9507-x · Cited by 48
Regulation of Gene Expression Associated With the N6-Methyladenosine (m6A) Enzyme System and Its Significance in Cancer
Tian, S., Lai, J., Yu, T., Li, Q., & Chen, Q. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2020.623634 · Cited by 49
LINC00924-induced fatty acid metabolic reprogramming facilitates gastric cancer peritoneal metastasis via hnRNPC-regulated alternative splicing of Mnk2
He, Q., Yang, C., Xiang, Z., Huang, G., Wu, H., Chen, T., Dou, R., Song, J., Han, L., Song, T., et al. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05436-x · Cited by 48
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
Zhang, Z., & Xing, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx646 · Cited by 51
Noise-Induced Dysregulation ofQuakingRNA Binding Proteins Contributes to Auditory Nerve Demyelination and Hearing Loss
Panganiban, C. H., Barth, J. L., Darbelli, L., Xing, Y., Zhang, J., Li, H., Noble, K. V., Liu, T., Brown, L. N., Schulte, B. A., et al. (2018) · Journal of Neuroscience · doi:10.1523/jneurosci.2487-17.2018 · Cited by 48
The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes
Chen, J., Cai, Z., Bai, M., Yu, X., Zhang, C., Cao, C., Hu, X. S., Wang, L., Su, R., Wang, L., et al. (2018) · Cell Research · doi:10.1038/s41422-018-0076-9 · Cited by 48
Nucleo-cytoplasmic shuttling of splicing factor SRSF1 is required for development and cilia function
Haward, F., Maslon, M. M., Yeyati, P. L., Bellora, N., Hansen, J. N., Aitken, S., Lawson, J., von Kriegsheim, A., Wachten, D., Mill, P., et al. (2021) · eLife · doi:10.7554/elife.65104 · Cited by 50
Mechanisms of non-coding RNA-modulated alternative splicing in cancer
Wang, X., Hua, J., Li, J., Zhang, J., Dzakah, E. E., Cao, G., & Lin, W. (2022) · RNA Biology · doi:10.1080/15476286.2022.2062846 · Cited by 49
Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translationPreprint
Fagg, W. S., Liu, N., Fair, J. H., Shiue, L., Katzman, S. J., Donohue, J. P., & Ares, M. (2017) · Genes & Development · doi:10.1101/gad.302059.117 · Cited by 48
Self-citation
Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response
Pai, A. A., & Luca, F. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1503 · Cited by 48
EZH2 variants differentially regulate polycomb repressive complex 2 in histone methylation and cell differentiation
Mu, W., Starmer, J., Yee, D., & Magnuson, T. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0242-9 · Cited by 52
QKI-5 regulates the alternative splicing of cytoskeletal gene ADD3 in lung cancer
Wang, J.-Z., Fu, X., Fang, Z., Liu, H., Zong, F.-Y., Zhu, H. M., Yu, Y.-F., Zhang, X.-Y., Wang, S.-F., Huang, Y., et al. (2020) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjaa063 · Cited by 47
Self-citation
Oncogenic dysregulation of pre‐mRNA processing by protein kinases: challenges and therapeutic opportunities
Naro, C., Bielli, P., & Sette, C. (2021) · FEBS Journal · doi:10.1111/febs.16057 · Cited by 49
TDP43 promotes stemness of breast cancer stem cells through CD44 variant splicing isoforms
Guo, L., Hao, K., Zhang, H., Zou, L., Yang, Q., Lu, X., Zhao, L., & Jiao, B. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-04867-w · Cited by 46
The RNA-binding protein QKI governs a muscle-specific alternative splicing program that shapes the contractile function of cardiomyocytes
Montañés-Agudo, P., Aufiero, S., Schepers, E. N., van der Made, I., Ortega, L. C., Ernault, A. C., Richard, S., Kuster, D. W. D., Christoffels, V. M., Pinto, Y. M., et al. (2023) · Cardiovascular Research · doi:10.1093/cvr/cvad007 · Cited by 46
Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells
Tu, Y., Wu, X., Yu, F., Dang, J., Wang, J., Wei, Y., Cai, Z., Zhou, Z., Liao, W., Li, L., et al. (2019) · BMC Immunology · doi:10.1186/s12865-019-0292-1 · Cited by 46
Coordinated Regulation of Pre-mRNA Splicing by the SFPS-RRC1 Complex to Promote Photomorphogenesis
Xin, R., Kathare, P. K., & Huq, E. (2019) · The Plant Cell · doi:10.1105/tpc.18.00786 · Cited by 46
RNA splicing regulators play critical roles in neurogenesis
Fisher, E., & Feng, J. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1728 · Cited by 45
HnRNP L represses cryptic exons
McClory, S. P., Lynch, K. W., & Ling, J. P. (2018) · RNA · doi:10.1261/rna.065508.117 · Cited by 47
Functional Interaction between U1snRNP and Sam68 Insures Proper 3′ End Pre-mRNA Processing during Germ Cell Differentiation
Naro, C., Pellegrini, L., Jolly, A., Farini, D., Cesari, E., Bielli, P., de la Grange, P., & Sette, C. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.058 · Cited by 47
First estimate of the scale of canonical 5′ splice site GT>GC variants capable of generating wild‐type transcripts
Lin, J., Tang, X., Boulling, A., Zou, W., Masson, E., Fichou, Y., Raud, L., Tertre, M. L., Deng, S., Berlivet, I., et al. (2019) · Human Mutation · doi:10.1002/humu.23821 · Cited by 45
αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome
Ji, X., Park, J. W., Bahrami‐Samani, E., Lin, L., Duncan-Lewis, C., Pherribo, G. J., Xing, Y., & Liebhaber, S. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw088 · Cited by 44
Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns
Movassat, M., Crabb, T. L., Busch, A., Yao, C., Reynolds, D. J., Shi, Y., & Hertel, K. J. (2016) · RNA Biology · doi:10.1080/15476286.2016.1191727 · Cited by 45
Post-Translational Modifications and RNA-Binding Proteins
Lovci, M., Bengtson, M. H., & Massirer, K. B. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-29073-7_12 · Cited by 46
Splicing dysregulation in cancer: from mechanistic understanding to a new class of therapeutic targets
Wang, Y., Bao, Y., Zhang, S., & Wang, Z. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1605-0 · Cited by 44
ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing
Lee, S., Wei, L., Zhang, B., Goering, R., Majumdar, S., Wen, J., Taliaferro, J. M., & Lai, E. C. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009439 · Cited by 46
Genomic functions of U2AF in constitutive and regulated splicing
Wu, T., & Fu, X. (2015) · RNA Biology · doi:10.1080/15476286.2015.1020272 · Cited by 48
Self-citation
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA–protein binding sites
Li, Y. E., Xiao, M., Shi, B., Yang, Y., Wang, D., Wang, F., Marcia, M., & Lu, Z. J. (2017) · Genome biology · doi:10.1186/s13059-017-1298-8 · Cited by 44
Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions
Soto, E. J. L., Gandal, M. J., Gonatopoulos-Pournatzis, T., Heller, E. A., Luo, D., & Zheng, S. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.1149-19.2019 · Cited by 44
Alternative Splicing of Pre-mRNA in the Control of Immune Activity
Su, Z., & Huang, D. (2021) · Genes · doi:10.3390/genes12040574 · Cited by 44
Aberrant RNA splicing and mutations in spliceosome complex in acute myeloid leukemia
Zhou, J., & Chng, W. J. (2017) · Stem Cell Investigation · doi:10.21037/sci.2017.01.06 · Cited by 43
FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence
Latorre, E., Ostler, E. L., Faragher, R., & Harries, L. W. (2018) · The FASEB Journal · doi:10.1096/fj.201801154r · Cited by 42
Alternative splicing regulation of doublesex gene by RNA-binding proteins in the silkworm Bombyx mori
Zheng, Z., Sun, X., Zhang, B., Pu, J., Jiang, Z., Li, M., Fan, Y., & Xu, Y.-Z. (2019) · RNA Biology · doi:10.1080/15476286.2019.1590177 · Cited by 42
Active Tonic mTORC1 Signals Shape Baseline Translation in Naive T Cells
Myers, D. R., Norlin, E., Vercoulen, Y., & Roose, J. P. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.037 · Cited by 43
Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers
Nakagaki-Silva, E. E., Gooding, C., Llorian, M., Jacob, A. G., Richards, F., Buckroyd, A., Sinha, S., & Smith, C. W. J. (2019) · eLife · doi:10.7554/elife.46327 · Cited by 42
The functional mechanisms of mutations in myelodysplastic syndrome
Nagata, Y., & Maciejewski, J. P. (2019) · Leukemia · doi:10.1038/s41375-019-0617-3 · Cited by 42
Faulty splicing and cytoskeleton abnormalities in Huntington's disease
Fernández‐Nogales, M., Santos‐Galindo, M., Hernández, I. H., Cabrera, J. R., & Lucas, J. J. (2016) · Brain Pathology · doi:10.1111/bpa.12430 · Cited by 41
The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications
Khan, F. A., Fang, N., Zhang, W., & Ji, S. (2024) · Cell Death and Disease · doi:10.1038/s41419-023-06413-8 · Cited by 44
FUS ‐mediated regulation of alternative RNA processing in neurons: insights from global transcriptome analysis
Masuda, A., Takeda, J., & Ohno, K. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1338 · Cited by 42
Modulation of VEGF-A Alternative Splicing as a Novel Treatment in Chronic Kidney Disease
Stevens, M., & Oltean, S. (2018) · Genes · doi:10.3390/genes9020098 · Cited by 41
Epigenome-based splicing prediction using a recurrent neural network
Lee, D., Zhang, J., Liu, J. J., & Gerstein, M. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008006 · Cited by 43
Therapeutic manipulation of IKBKAP mis-splicing with a small molecule to cure familial dysautonomia
Ajiro, M., Awaya, T., Kim, Y. J., Iida, K., Denawa, M., Tanaka, N., Kurosawa, R., Matsushima, S., Shibata, S., Sakamoto, T., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24705-5 · Cited by 42
Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences
Luo, Z., Zhang, J., Fei, J., & Ke, S. (2022) · Nature Communications · doi:10.1038/s41467-022-30209-7 · Cited by 40
Role of innate immunological/inflammatory pathways in myelodysplastic syndromes and AML: a narrative review
Vegivinti, C. T. R., Keesari, P. R., Veeraballi, S., Maia, C., Mehta, A. K., Lavu, R. R., Thakur, R., Tella, S. H., Patel, R. J., Kakumani, V. K., et al. (2023) · Experimental Hematology and Oncology · doi:10.1186/s40164-023-00422-1 · Cited by 43
Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis
Wang, R., Helbig, I., Edmondson, A. C., Lin, L., & Xing, Y. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad284 · Cited by 42
Molecular basis of titin exon exclusion by RBM20 and the novel titin splice regulator PTB4
Dauksaite, V., & Gotthardt, M. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky165 · Cited by 40
View from an mRNP: The Roles of SR Proteins in Assembly, Maturation and Turnover
Wegener, M., & Müller-McNicoll, M. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-31434-7_3 · Cited by 40
Epigenomic reprogramming in inorganic arsenic-mediated gene expression patterns during carcinogenesis
Eckstein, M., Eleazer, R., Rea, M., & Fondufe‐Mittendorf, Y. N. (2016) · Reviews on Environmental Health · doi:10.1515/reveh-2016-0025 · Cited by 40
Pre-mRNA mis-splicing of sarcomeric genes in heart failure
Zhu, C., Chen, Z., & Guo, W. (2016) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2016.11.008 · Cited by 39
FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1
Cho, S., Chun, Y., He, L., Ramirez, C. B., Ganesh, K. S., Jeong, K., Song, J., Cheong, J., Li, Z., Choi, J., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.07.017 · Cited by 38
Insights into Telomerase/hTERT Alternative Splicing Regulation Using Bioinformatics and Network Analysis in Cancer
Ludlow, A. T., Slusher, A. L., & Sayed, M. (2019) · Cancers · doi:10.3390/cancers11050666 · Cited by 39
The RNA-binding protein QKI controls alternative splicing in vascular cells, producing an effective model for therapy
Caines, R., Cochrane, A., Kelaini, S., González, M. V., Yang, C., Eleftheriadou, M., Moez, A., Stitt, A. W., Zeng, L., Grieve, D., et al. (2019) · Journal of Cell Science · doi:10.1242/jcs.230276 · Cited by 38
Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing
Kutluay, S. B., Emery, A., Penumutchu, S. R., Townsend, D., Tenneti, K., Madison, M. K., Stukenbroeker, A. M., Powell, C., Jannain, D., Tolbert, B. S., et al. (2019) · Journal of Virology · doi:10.1128/jvi.01048-19 · Cited by 39
SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma
Zhan, Y.-T., Li, L., Zeng, T., Zhou, N., Guan, X., & Li, Y. (2020) · Aging · doi:10.18632/aging.202164 · Cited by 38
Alternative splicing of lncRNAs in human diseases.
Chen, J., Liu, Y., Min, J., Wang, H., Li, F., Xu, C., Gong, A., & Xu, M. (2021) · PubMed Central · Cited by 38
Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms
Inamo, J., Suzuki, A., Ueda, M. T., Yamaguchi, K., Nishida, H., Suzuki, K., Kaneko, Y., Takeuchi, T., Hatano, H., Ishigaki, K., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48615-4 · Cited by 37
Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing
Lin, J. J., Hu, Y., Núñez, S., Foulkes, A. S., Cieply, B. W., Xue, C., Gerelus, M., Li, W., Zhang, H., Rader, D. J., et al. (2016) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.116.307573 · Cited by 41
AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors
Hu, J., Khodadadi‐Jamayran, A., Mao, M., Shah, K. K., Yang, Z., Nasim, T., Wang, Z., & Jiang, H. (2016) · Nature Communications · doi:10.1038/ncomms13347 · Cited by 37
Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics?
Grodecká, L., Buratti, E., & Freiberger, T. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18081668 · Cited by 37
Cis‐regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis
Wang, X., Yang, M., Ren, D., Terzaghi, W., Deng, X., & He, G. (2018) · The Plant Journal · doi:10.1111/tpj.14142 · Cited by 38
Post-transcriptional regulation through alternative splicing after infection with Flavobacterium columnare in channel catfish (Ictalurus punctatus)
Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Yang, Y., Gao, D., & Liu, Z. (2019) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2019.05.008 · Cited by 38
A novel role of U1 snRNP: Splice site selection from a distance
Singh, R. N., & Singh, N. N. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.04.004 · Cited by 36
More than a messenger: Alternative splicing as a therapeutic target
Black, A. J., Gamarra, J. R., & Giudice, J. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.06.006 · Cited by 36
Effects of aging on protein expression in mice brain microvessels: ROS scavengers, mRNA/protein stability, glycolytic enzymes, mitochondrial complexes, and basement membrane components
Chandra, P. K., Čikić, S., Rutkai, I., Guidry, J. J., Katakam, P. V. G., Mostany, R., & Busija, D. W. (2021) · GeroScience · doi:10.1007/s11357-021-00468-1 · Cited by 37

Authors: Fu, X.-D., & Ares, M.
Affiliations: University of California San Diego (US)
University of California, Santa Cruz (US)
Corresponding author: Fu, Xiang-Dong
Ares, Manuel
ORCID: Fu, Xiang-Dong
Ares, Manuel
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2014-08-12
Volume: 15
Issue: 10
Pages: 689-701
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg3778
PMC: PMC4440546
OpenAlex: W2029979788
Cited by: 1,044
References: 176
Citations by year: 2026: 67 · 2025: 95 · 2024: 89 · 2023: 93 · 2022: 92 · 2021: 99 · 2020: 93 · 2019: 94 · 2018: 93 · 2017: 94 · 2016: 68 · 2015: 61 · 2014: 5
FWCI: 7.19
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Institute of General Medical Sciences (R01GM052872, GM049369, GM040478, GM052872, R01GM049369, R01GM040478)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: alternative splicing, RNA-binding proteins, splicing regulation, pre-mRNA, combinatorial regulation, cell-type-specific splicing, splicing patterns
MeSH terms: Animals, Binding Sites, Humans, Organ Specificity, Protein Binding, RNA-Binding Proteins, Alternative Splicing, Regulatory Elements, Transcriptional, Cellular Microenvironment

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Context-dependent control of alternative splicing by RNA-binding proteins

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks