Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

MicroRNAs: Target Recognition and Regulatory Functions

Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993) · Cell · doi:10.1016/0092-8674(93)90529-y · Cited by 12,948

Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets

Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) · Cell · doi:10.1016/j.cell.2004.12.035 · Cited by 11,855

Untitled work

(2008) · doi:10.1038/nrg2290 · Cited by 5,199

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181

Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia

Calin, G. A., Dumitru, C. D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., Aldler, H., Rattan, S., Keating, M., Rai, K., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242606799 · Cited by 5,111

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans

Wightman, B., Ha, I., & Ruvkun, G. (1993) · Cell · doi:10.1016/0092-8674(93)90530-4 · Cited by 4,292

MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing

Grimson, A., Farh, K. K.-H., Johnston, W. K., Garrett-Engele, P., Lim, L. P., & Bartel, D. P. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.017 · Cited by 3,766

RAS Is Regulated by the let-7 MicroRNA Family

Johnson, S., Großhans, H., Shingara, J., Byrom, M., JARVIS, R., Cheng, A., Labourier, E., Reinert, K. L., Brown, D., & Slack, F. J. (2005) · Cell · doi:10.1016/j.cell.2005.01.014 · Cited by 3,699

A microRNA polycistron as a potential human oncogene

He, L., Thomson, J. M., Hemann, M. T., Hernando, E., Mu, D., Goodson, S. G., Powers, S., Cordon‐Cardo, C., Lowe, S. W., Hannon, G. J., et al. (2005) · Nature · doi:10.1038/nature03552 · Cited by 3,642

Inverted Alu dsRNA structures do not affect localization but can alter translation efficiency of human mRNAs independent of RNA editing

Capshew, C. R., Dusenbury, K. L., & Hundley, H. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks590 · Cited by 62

Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species

Sanfilippo, P., Wen, J., & Lai, E. C. (2017) · Genome biology · doi:10.1186/s13059-017-1358-0 · Cited by 59

Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms

Marondedze, C., Thomas, L. A., Gehring, C., & Lilley, K. S. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1750-x · Cited by 67

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

Thomas, Q. A., Ard, R., Liu, J., Li, B., Wang, J., Pelechano, V., & Marquardt, S. (2020) · Nature Communications · doi:10.1038/s41467-020-16390-7 · Cited by 63

MicroRNA–target interactions: new insights from genome‐wide approaches

Lee, D., & Shin, C. (2012) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2012.06745.x · Cited by 62

Immunoglobulin heavy chain locus chromosomal translocations in B-cell precursor acute lymphoblastic leukemia: rare clinical curios or potent genetic drivers?

Dyer, M. J. S., Akasaka, T., Capasso, M., Dusanjh, P., Lee, Y. F., Karran, E. L., Nagel, I., Vater, I., Cario, G., & Siebert, R. (2009) · Blood · doi:10.1182/blood-2009-09-235986 · Cited by 63

Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism

Sommerkamp, P., Altamura, S., Renders, S., Narr, A., Ladel, L., Zeisberger, P., Eiben, P. L., Fawaz, M., Rieger, M. A., Cabezas‐Wallscheid, N., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.03.003 · Cited by 66

Splicing factor USP39 promotes ovarian cancer malignancy through maintaining efficient splicing of oncogenic HMGA2

Wang, S., Wang, Z., Li, J., Qin, J., Song, J., Li, Y., Zhao, L., Zhang, X., Guo, H., Shao, C., et al. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-03581-3 · Cited by 62

Non-coding RNAs and epithelial mesenchymal transition in cancer: molecular mechanisms and clinical implications

Khanbabaei, H., Ebrahimi, S., García‐Rodríguez, J. L., Ghasemi, Z., Pourghadamyari, H., Mohammadi, M., & Kristensen, L. S. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02488-x · Cited by 67

Positive and negative feedback loops in the p53 and mRNA 3′ processing pathways

Devany, E., Zhang, X., Park, J. Y., Tian, B., & Kleiman, F. E. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1212533110 · Cited by 62

3′UTR shortening and EGF signaling: implications for breast cancer

Akman, H. B., Oyken, M., Tuncer, T., Can, T., & Erson-Bensan, A. E. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv391 · Cited by 62

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

Steinkraus, B. R., Tögel, M., & Fulga, T. A. (2016) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.223 · Cited by 64

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

Llorian, M., Gooding, C., Bellora, N., Hallegger, M., Buckroyd, A., Wang, X., Rajgor, D., Kayikci, M., Feltham, J., Ule, J., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw560 · Cited by 59

Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation

Miles, W. O., Lembo, A., Volorio, A., Brachtel, E. F., Tian, B., Sgroi, D. C., Provero, P., & Dyson, N. J. (2016) · Cancer Research · doi:10.1158/0008-5472.can-16-0844 · Cited by 64

A guide to micro RNA ‐mediated gene silencing

Huberdeau, M. Q., & Simard, M. J. (2018) · FEBS Journal · doi:10.1111/febs.14666 · Cited by 63

RNA-binding proteins in hematopoiesis and hematological malignancy

Hodson, D. J., Screen, M., & Turner, M. (2019) · Blood · doi:10.1182/blood-2018-10-839985 · Cited by 64

Pan-cancer genomic analysis links 3’UTR DNA methylation with increased gene expression in T cells

McGuire, M. H., Herbrich, S. M., Dasari, S. K., Wu, S. Y., Wang, Y., Rupaimoole, R., Lopez‐Berestein, G., Baggerly, K., & Sood, A. K. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.04.045 · Cited by 59

The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics

Nicolet, B. P., & Wolkers, M. C. (2022) · PLOS ONE · doi:10.1371/journal.pone.0276294 · Cited by 62

Identification of recurring tumor-specific somatic mutations in acute myeloid leukemia by transcriptome sequencing

Greif, P. A., Eck, S. H., Konstandin, N. P., Benet‐Pagès, A., Ksienzyk, B., Dufour, A., Vetter, A. T., Popp, H. D., Lorenz‐Depiereux, B., Meitinger, T., et al. (2011) · Leukemia · doi:10.1038/leu.2011.19 · Cited by 61

MicroRNA-340-mediated Degradation of Microphthalmia-associated Transcription Factor (MITF) mRNA Is Inhibited by Coding Region Determinant-binding Protein (CRD-BP)

Goswami, S., Tarapore, R. S., Strong, A. M. P., TeSlaa, J. J., Grinblat, Y., Setaluri, V., & Spiegelman, V. S. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.590158 · Cited by 61

An unexpected ending: Noncanonical 3′ end processing mechanisms

Wilusz, J. E., & Spector, D. L. (2009) · RNA · doi:10.1261/rna.1907510 · Cited by 60

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

Malka, Y., Steiman‐Shimony, A., Rosenthal, E., Argaman, L., Cohen‐Daniel, L., Arbib, E., Margalit, H., Kaplan, T., & Berger, M. (2017) · Nature Communications · doi:10.1038/s41467-017-02099-7 · Cited by 58

Microtubule-Driven Stress Granule Dynamics Regulate Inhibitory Immune Checkpoint Expression in T Cells

Franchini, D.-M., Lanvin, O., Tosolini, M., Patras de Campaigno, E., Cammas, A., Péricart, S., Scarlata, C.-M., Lebras, M., Rossi, C., Ligat, L., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2018.12.014 · Cited by 61

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq.

Xu, G., Fewell, C., Taylor, C., Deng, N., Hedges, D. J., Wang, X., Zhang, K., Lacey, M., Zhang, H., Yin, Q., et al. (2010) · RNA: A publication of the RNA Society · doi:10.1261/rna.2194910 · Cited by 78

On the function and relevance of alternative 3′‐ UTRs in gene expression regulation

Pereira‐Castro, I., & Moreira, A. (2021) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1653 · Cited by 60

Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1

Song, J., Nabeel‐Shah, S., Pu, S., Lee, H., Braunschweig, U., Ni, Z., Ahmed, N., Marcon, E., Zhong, G., Ray, D., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.031 · Cited by 59

The structure of human Cleavage Factor Imhints at functions beyond UGUA-specific RNA binding

Yang, Q., Gilmartin, G. M., & Doublié, S. (2011) · RNA Biology · doi:10.4161/rna.8.5.16040 · Cited by 59

Rejuvenation of Gene Expression Pattern of Aged Human Skin by Broadband Light Treatment: A Pilot Study

Chang, A. L. S., Bitter, P., Qu, K., Lin, M., Rapicavoli, N. A., & Chang, H. Y. (2012) · Journal of Investigative Dermatology · doi:10.1038/jid.2012.287 · Cited by 59

RNA-binding protein CPEB1 remodels host and viral RNA landscapes

Batra, R., Stark, T. J., Clark, A. E., Belzile, J.-P., Wheeler, E. C., Yee, B. A., Huang, H., Gelboin-Burkhart, C. A., Huelga, S. C., Aigner, S., et al. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3310 · Cited by 59

CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression

Tan, S. H., Zhang, M., Shi, X., Ding, K., Zhao, Q., Guo, Q., Wang, H., Wu, Z., Kang, Y., Zhu, T., et al. (2021) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-021-01884-z · Cited by 58

3′UTR heterogeneity and cancer progression

Chan, J. J., Tabatabaeian, H., & Tay, Y. (2022) · Trends in Cell Biology · doi:10.1016/j.tcb.2022.10.001 · Cited by 58

Diversity of animal small RNA pathways and their biological utility

Okamura, K. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.113 · Cited by 59

Single‐cell polyadenylation site mapping reveals 3′ isoform choice variability

Velten, L., Anders, S., Pękowska, A., Järvelin, A. I., Huber, W. K., Pelechano, V., & Steinmetz, L. M. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156198 · Cited by 55

Characterization of Dual PTEN and p53-Targeting MicroRNAs Identifies MicroRNA-638/Dnm2 as a Two-Hit Oncogenic Locus

Tay, Y., Tan, S. M., Karreth, F. A., Lieberman, J., & Pandolfi, P. P. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.06.064 · Cited by 60

Cleavage factor Im (CFIm) as a regulator of alternative polyadenylation

Hardy, J. G., & Norbury, C. J. (2016) · Biochemical Society Transactions · doi:10.1042/bst20160078 · Cited by 57

MiRNAs at the Crossroads between Innate Immunity and Cancer: Focus on Macrophages

Curtale, G. (2018) · Cells · doi:10.3390/cells7020012 · Cited by 58

3′UTR shortening identifies high-risk cancers with targeted dysregulation of the ceRNA network

Li, L., Wang, D., Xue, M., Mi, X., Liang, Y., & Wang, P. (2014) · Scientific Reports · doi:10.1038/srep05406 · Cited by 58

Posttranscriptional Regulation of Cyclooxygenase 2 Expression in Colorectal Cancer

Young, L. E., & Dixon, D. A. (2010) · Current Colorectal Cancer Reports · doi:10.1007/s11888-010-0044-3 · Cited by 57

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries

Grassi, E., Mariella, E., Lembo, A., Molineris, I., & Provero, P. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1254-8 · Cited by 56

Applications of miRNAs in cardiac development, disease progression and regeneration

Pang, J. K. S., Phua, Q. H., & Soh, B.-S. (2019) · Stem Cell Research & Therapy · doi:10.1186/s13287-019-1451-2 · Cited by 57

A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1Preprint

Geißler, R., Simkin, A., Floss, D. M., Patel, R. K., Fogarty, E. A., Scheller, J., & Grimson, A. (2016) · Genes & Development · doi:10.1101/gad.277392.116 · Cited by 56

Introduction to MicroRNAs in Biological Systems

Erson-Bensan, A. E. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-748-8_1 · Cited by 56

Perspectives on the ARE as it turns 25 years old

Beisang, D. J., & Bohjanen, P. R. (2012) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1125 · Cited by 56

Role of RNA Binding Proteins with prion-like domains in muscle and neuromuscular diseases

Picchiarelli, G., & Dupuis, L. (2020) · Cell Stress · doi:10.15698/cst2020.04.217 · Cited by 57

Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiencyPreprint

Fu, Y., Chen, L., Chen, C., Ge, Y., Kang, M., Song, Z., Li, J., Feng, Y., Huo, Z., He, G., et al. (2018) · Genome Research · doi:10.1101/gr.231506.117 · Cited by 57

Selective repression of the oncogene cyclin D1 by the tumor suppressor miR-206 in cancers

Elliman, S. J., Howley, B. V., Mehta, D., Fearnhead, H. O., Kemp, D. M., & Barkley, L. R. (2014) · Oncogenesis · doi:10.1038/oncsis.2014.26 · Cited by 55

Transcriptome and proteome quantification of a tumor model provides novel insights into post‐transcriptional gene regulation

Jüschke, C., Dohnal, I., Pichler, P., Harzer, H., Swart, R., Ammerer, G., Mechtler, K., & Knoblich, J. A. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r133 · Cited by 55

miR in melanoma development: miRNAs and acquired hallmarks of cancer in melanoma

Bennett, P., Bemis, L., Norris, D. A., & Shellman, Y. G. (2013) · Physiological Genomics · doi:10.1152/physiolgenomics.00116.2013 · Cited by 56

Alternative Polyadenylation: Another Foe in Cancer

Erson-Bensan, A. E., & Can, T. (2016) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-15-0489 · Cited by 57

Gain of Additional BIRC3 Protein Functions through 3ʹ-UTR-Mediated Protein Complex Formation

Lee, S., & Mayr, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.006 · Cited by 53

Single cell RNA sequencing for breast cancer: present and future

Ren, L., Li, J., Wang, C., Lou, Z., Gao, S., Zhao, L., Wang, S., Chaulagain, A., Zhang, M., Li, X., et al. (2021) · Cell Death Discovery · doi:10.1038/s41420-021-00485-1 · Cited by 54

Pan-cancer pervasive upregulation of 3′ UTR splicing drives tumourigenesis

Chan, J. J., Zhang, B., Chew, X. H., Salhi, A., Kwok, Z. H., Lim, C. Y., Desi, N., Subramaniam, N., Siemens, A., Kinanti, T., et al. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00913-z · Cited by 56

Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer

Dondi, A., Lischetti, U., Jacob, F., Singer, F., Borgsmüller, N., Coelho, R., Aebersold, R. H., Ak, M., Alquaddoomi, F., Albert, S. I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43387-9 · Cited by 55

Multiplexed single-cell characterization of alternative polyadenylation regulators

Kowalski, M. H., Wessels, H., Linder, J., Dalgarno, C., Mascio, I., Choudhary, S., Hartman, A., Hao, Y., Kundaje, A. B., & Satija, R. (2024) · Cell · doi:10.1016/j.cell.2024.06.005 · Cited by 56

Genome-Wide Polyadenylation Maps Reveal Dynamic mRNA 3′-End Formation in the Failing Human Heart

Creemers, E. E., Bawazeer, A. C., Ugalde, A. P., van Deutekom, H. W. M., van der Made, I., de Groot, N. E., Adriaens, M. E., Cook, S. A., Bezzina, C. R., Hübner, N., et al. (2015) · Circulation Research · doi:10.1161/circresaha.115.307082 · Cited by 54

Alternative Polyadenylation of mRNAs: 3'-Untranslated Region Matters in Gene Expression

Yeh, H.-S., & Yong, J. (2016) · Molecules and Cells · doi:10.14348/molcells.2016.0035 · Cited by 56

RNA processing as an alternative route to attack glioblastoma

Meliso, F. M., Hubert, C. G., Galante, P. A. F., & Penalva, L. O. F. (2017) · Human Genetics · doi:10.1007/s00439-017-1819-2 · Cited by 54

Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder

Falkenberg, K. D., Braverman, N., Moser, A. B., Steinberg, S. J., Klouwer, F. C. C., Schlüter, A., Ruíz, M., Pujol, A., Engvall, M., Naess, K., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.11.007 · Cited by 54

Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expressionPreprint

Gao, Y., Li, L., Amos, C. I., & Li, W. (2021) · Genome Research · doi:10.1101/gr.271346.120 · Cited by 52

mRNA transport, translation, and decay in adult mammalian central nervous system axons

Jung, J., Ohk, J., Kim, H. Y., Holt, C. E., Park, H. J., & Jung, H. (2022) · Neuron · doi:10.1016/j.neuron.2022.12.015 · Cited by 49

Small RNA profiling of low biomass samples: identification and removal of contaminants

Heintz‐Buschart, A., Yusuf, D., Kaysen, A., Etheridge, A., Fritz, J. V., May, P., de Beaufort, C. E., Upadhyaya, B. B., Ghosal, A., Galas, D. J., et al. (2018) · BMC Biology · doi:10.1186/s12915-018-0522-7 · Cited by 53

Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive

Xu, C., & Zhang, J. (2018) · Cell Systems · doi:10.1016/j.cels.2018.05.007 · Cited by 49

Lysine demethylase 5B (KDM5B): A potential anti-cancer drug target

Zheng, Y., Chang, J., Wang, L.-C., Ren, H.-M., Pang, J., & Liu, H. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.10.040 · Cited by 52

SAM homeostasis is regulated by CFIm-mediated splicing of MAT2A

Scarborough, A. M., Flaherty, J. N., Hunter, O. V., Liu, K., Kumar, A., Xing, C., Tu, B. P., & Conrad, N. K. (2021) · eLife · doi:10.7554/elife.64930 · Cited by 54

Single-molecule imaging of microRNA-mediated gene silencing in cells

Kobayashi, H., & Singer, R. H. (2022) · Nature Communications · doi:10.1038/s41467-022-29046-5 · Cited by 59

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeastPreprint

Graber, J. H., Nazeer, F. I., Yeh, P.-C., Kuehner, J. N., Borikar, S., Hoskinson, D. C., & Moore, C. L. (2013) · Genome Research · doi:10.1101/gr.144964.112 · Cited by 53

A PolH Transcript with a Short 3′UTR Enhances PolH Expression and Mediates Cisplatin Resistance

Zhang, J., Sun, W., Ren, C., Kong, X., Yan, W., & Chen, X. (2019) · Cancer Research · doi:10.1158/0008-5472.can-18-3928 · Cited by 53

Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers

Wang, L., Lang, G., Xue, M., Liu, Y., Chen, L., Yao, L., Li, X., Wang, P., Hu, X., & Shao, Z. (2020) · Theranostics · doi:10.7150/thno.40944 · Cited by 52

Omics Technologies Improving Breast Cancer Research and Diagnostics

Orsini, A., Diquigiovanni, C., & Bonora, E. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241612690 · Cited by 52

CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants

Chakrabarti, M., & Hunt, A. G. (2015) · Biomolecules · doi:10.3390/biom5021151 · Cited by 52

Single Nucleotide Polymorphisms in MicroRNA Binding Sites of Oncogenes: Implications in Cancer and Pharmacogenomics

Manikandan, M., & Munirajan, A. K. (2013) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2013.0098 · Cited by 52

Poly(A) polymerase (PAP) diversity in gene expression – Star‐PAP vs canonical PAP

Laishram, R. S. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.05.029 · Cited by 55

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Halpern, K. B., & Itzkovitz, S. (2015) · Methods · doi:10.1016/j.ymeth.2015.11.015 · Cited by 51

High-throughput discovery of post-transcriptional cis-regulatory elements

Wissink, E. M., Fogarty, E. A., & Grimson, A. (2016) · BMC Genomics · doi:10.1186/s12864-016-2479-7 · Cited by 52

Levels of MicroRNA Heterogeneity in Cancer Biology

Petrović, N., Ergün, S., & Isenović, E. R. (2017) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-017-0285-9 · Cited by 52

Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors

Grassi, E., Santoro, R., Umbach, A., Grosso, A., Oliviero, S., Neri, F., Conti, L., Ala, U., Provero, P., Cunto, F. D., et al. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2018.00518 · Cited by 56

Mutations in microRNA Binding Sites of CEP Genes Involved in Cancer

Gopalakrishnan, C., Kamaraj, B., & Purohit, R. (2014) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-014-0153-8 · Cited by 51

PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells

Zhang, X., Devany, E., Murphy, M. R., Glazman, G., Persaud, M., & Kleiman, F. E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv959 · Cited by 56

Single nucleotide variation in the TP53 3′ untranslated region in diffuse large B-cell lymphoma treated with rituximab-CHOP: a report from the International DLBCL Rituximab-CHOP Consortium Program

Li, Y., Gordon, M. W., Xu-Monette, Z. Y., Visco, C., Tzankov, A., Zou, D., Qiu, L., Montes‐Moreno, S., Dybkær, K., Orazi, A., et al. (2013) · Blood · doi:10.1182/blood-2012-12-471722 · Cited by 53

Alternative Transcript Initiation and Splicing as a Response to DNA Damage

Sprung, C. N., Li, J., Hovan, D., McKay, M. J., & Forrester, H. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025758 · Cited by 53

The many functions of mRNA localization during normal development and disease: from pillar to post

Cody, N. A. L., Iampietro, C., & Lécuyer, É. (2013) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.113 · Cited by 51

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation

Mata, J. (2013) · RNA Biology · doi:10.4161/rna.25758 · Cited by 51

Identifying and targeting tumor-initiating cells in the treatment of breast cancer

Wei, W., & Lewis, M. T. (2015) · Endocrine Related Cancer · doi:10.1530/erc-14-0447 · Cited by 52

High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down

Li, X., Pritykin, Y., Concepcion, C. P., Lu, Y., Rocca, G. L., Zhang, M., King, B., Cook, P. J., Au, Y. W., Popow, O., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.05.009 · Cited by 52

Dynamic Variations of 3′UTR Length Reprogram the mRNA Regulatory Landscape

Navarro, E., Mallén, A., & Hueso, M. (2021) · Biomedicines · doi:10.3390/biomedicines9111560 · Cited by 55

KDM5 family as therapeutic targets in breast cancer: Pathogenesis and therapeutic opportunities and challenges

Li, C., Wang, W., Leung, C., Yang, G., & Chen, J. (2024) · Molecular Cancer · doi:10.1186/s12943-024-02011-0 · Cited by 50

Regulation of miRNA Processing and miRNA Mediated Gene Repression in Cancer

Bajan, S., & Hutvágner, G. (2014) · MicroRNA · doi:10.2174/2211536602666140110234046 · Cited by 53

Genetics and Regulatory Impact of Alternative Polyadenylation in Human B-Lymphoblastoid Cells

Yoon, O. K., Hsu, T. Y., Im, J. H., & Brem, R. B. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002882 · Cited by 51

High-Throughput Functional MicroRNAs Profiling by Recombinant AAV-Based MicroRNA Sensor Arrays

Tian, W., Dong, X., Liu, X., Wang, G., Dong, Z., Shen, W., Zheng, G., Lü, J., Chen, J., Wang, Y., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029551 · Cited by 49

RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

Bosia, C., Sgrò, F., Conti, L., Baldassi, C., Brusa, D., Cavallo, F., Cunto, F. D., Turco, E., Pagnani, A., & Zecchina, R. (2017) · Genome biology · doi:10.1186/s13059-017-1162-x · Cited by 49

Enhancers regulate 3′ end processing activity to control expression of alternative 3′UTR isoforms

Kwon, B., Fansler, M. M., Patel, N. D., Lee, J., Ma, W., & Mayr, C. (2022) · Nature Communications · doi:10.1038/s41467-022-30525-y · Cited by 47

ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network

Yang, N., Liu, K., Yang, M., & Gao, X. (2021) · Journal of Oncology · doi:10.1155/2021/4279039 · Cited by 51

3′LIFE: a functional assay to detect miRNA targets in high-throughput

Wolter, J. M., Kotagama, K., Pierre‐Bez, A. C., Firago, M., & Mangone, M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku626 · Cited by 47

Genome-wide profiling of polyadenylation sites reveals a link between selective polyadenylation and cancer metastasis

Lai, D.-P., Tan, S. H., Kang, Y., Wu, J., Ooi, H.-S., Chen, J., Shen, T., Qi, Y., Zhang, X., Guo, Y., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv089 · Cited by 50

A New Chapter in Genetic Medicine: RNA Editing and its Role in Disease Pathogenesis

Gagnidze, K., Rayon-Estrada, V., Harroch, S., Bulloch, K., & Papavasiliou, F. N. (2018) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2018.01.002 · Cited by 48

Spatiotemporal m(i)RNA Architecture and 3′ UTR Regulation in the C. elegans Germline

Diag, A., Schilling, M., Klironomos, F., Ayoub, S., & Rajewsky, N. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.10.005 · Cited by 49

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

Goering, R., Engel, K. L., Gillen, A. E., Fong, N., Bentley, D. L., & Taliaferro, J. M. (2021) · BMC Genomics · doi:10.1186/s12864-021-07781-1 · Cited by 45

ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data

Huang, Z., & Teeling, E. C. (2017) · BMC Genomics · doi:10.1186/s12864-017-4241-1 · Cited by 47

Alternative polyadenylation dependent function of splicing factor SRSF3 contributes to cellular senescence

Shen, T., Li, H., Song, Y., Li, L., Lin, J., Wei, G., & Ni, T. (2019) · Aging · doi:10.18632/aging.101836 · Cited by 48

Glioma glycolipid metabolism: MSI2–SNORD12B–FIP1L1–ZBTB4 feedback loop as a potential treatment target

Dong, W., Liu, X., Yang, C., Wang, D., Xue, Y., Ruan, X., Zhang, M., Song, J., Cai, H., Zheng, J., et al. (2021) · Clinical and Translational Medicine · doi:10.1002/ctm2.411 · Cited by 48

UTR cutbacks give free rein to oncogenes

Atkinson, S. R. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2668 · Cited by 1

Lengthening of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation Is Associated With Tumor Progression and Poor Prognosis of Clear Cell Renal Cell Carcinoma

Zhang, F., Chen, L., Li, W., Yang, C., Xiong, M., Zhou, M., Kazobinka, G., Zhao, J., & Hou, T. (2023) · Laboratory Investigation · doi:10.1016/j.labinv.2023.100125 · Cited by 4

The 3′ UTR Landscape in Cancer

Schmidt, R., Ghosh, S., & Zavolan, M. (2018) · Wiley eBooks · doi:10.1002/9780470015902.a0027958 · Cited by 3

Resolving the complexity of the cancer transcriptome through 3’ UTRs

Erson-Bensan, A. E. (2017) · OpenMETU (Middle East Technical University)

Abstract A14: Alternative polyadenylation drives oncogenic gene expression in pancreatic cancer

Venkat, S., Tisdale, A. A., Eng, K. H., & Feigin, M. E. (2019) · Cancer Research · doi:10.1158/1538-7445.panca19-a14