Mechanisms and Consequences of Alternative Polyadenylation

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works

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 · see citing works

Frequent deletions and down-regulation of micro- RNA genes <i>miR15</i> and <i>miR16</i> 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 4,269 · see citing works

Regulation of mRNA Translation and Stability by microRNAs

Fabian, M. R., Sonenberg, N., & Filipowicz, W. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060308-103103 · Cited by 3,214 · see citing works

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479 · see citing works

let-7 Regulates Self Renewal and Tumorigenicity of Breast Cancer Cells

Yu, F., Yao, H., Zhu, P., Zhang, X., Pan, Q., Gong, C., Huang, Y., Hu, X., Su, F., Lieberman, J., et al. (2007) · Cell · doi:10.1016/j.cell.2007.10.054 · Cited by 1,906 · see citing works

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

Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613 · see citing works

Dynamic Regulation of Nucleosome Positioning in the Human Genome

Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,396 · see citing works

Analysis and design of RNA sequencing experiments for identifying isoform regulation

Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010) · Nature Methods · doi:10.1038/nmeth.1528 · Cited by 1,353 · see citing works

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · cited 7× · see citing works

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008) · Science · doi:10.1126/science.1155390 · Cited by 1,349 · see citing works

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284 · see citing works

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,160 · see citing works

Regulation of Alternative Splicing by Histone Modifications

Luco, R. F., Pan, Q., Tominaga, K., Blencowe, B. J., Pereira‐Smith, O. M., & Misteli, T. (2010) · Science · doi:10.1126/science.1184208 · Cited by 1,099 · see citing works

Integrating mRNA Processing with Transcription

Proudfoot, N. J., Furger, A., & Dye, M. J. (2002) · Cell · doi:10.1016/s0092-8674(02)00617-7 · Cited by 1,084 · see citing works

AU-rich elements and associated factors: are there unifying principles?

Barreau, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki1012 · Cited by 1,033 · see citing works

Formation of mRNA 3′ Ends in Eukaryotes: Mechanism, Regulation, and Interrelationships with Other Steps in mRNA Synthesis

Zhao, J., Hyman, L. E., & Moore, C. L. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.405-445.1999 · Cited by 1,024 · see citing works

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P., & Krause, H. M. (2007) · Cell · doi:10.1016/j.cell.2007.08.003 · Cited by 967 · see citing works

A large-scale analysis of mRNA polyadenylation of human and mouse genes

Tian, B. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki158 · Cited by 944 · see citing works

The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

McCracken, S. A., Fong, N., Yankulov, K., Ballantyne, S. M., Pan, G., Greenblatt, J., Patterson, S. D., Wickens, M., & Bentley, D. L. (1997) · Nature · doi:10.1038/385357a0 · Cited by 925 · see citing works

Two mRNAs can be produced from a single immunoglobulin μ gene by alternative RNA processing pathways

Early, P. (1980) · Cell · doi:10.1016/0092-8674(80)90617-0 · Cited by 890 · see citing works

Multiple promoters direct tissue-specific expression of the rat BDNF gene

Timmusk, T., Palm, K., Metsis, M., Reintam, T., Paalme, V., Saarma, M., & Persson, H. (1993) · Neuron · doi:10.1016/0896-6273(93)90335-o · Cited by 858 · see citing works

Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability

Jing, Q., Huang, S., Guth, S., Zarubin, T., Motoyama, A. B., Chen, J., Padova, F. D., Lin, S., Gram, H., & Han, J. (2005) · Cell · doi:10.1016/j.cell.2004.12.038 · Cited by 849 · see citing works

Mechanism and regulation of mRNA polyadenylation

Colgan, D. F., & Manley, J. L. (1997) · Genes &amp; Development · doi:10.1101/gad.11.21.2755 · Cited by 784 · see citing works

Epigenetics in Alternative Pre-mRNA Splicing

Luco, R. F., Alló, M., Schor, I. E., Kornblihtt, A. R., & Misteli, T. (2011) · Cell · doi:10.1016/j.cell.2010.11.056 · Cited by 783 · see citing works

A Slow RNA Polymerase II Affects Alternative Splicing In Vivo

de la Mata, M., Alonso, C. R., Kadener, S., Fededa, J. P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D., & Kornblihtt, A. R. (2003) · Molecular Cell · doi:10.1016/j.molcel.2003.08.001 · Cited by 683 · see citing works

Patterns of Variant Polyadenylation Signal Usage in Human GenesPreprint

Beaudoing, E., Freier, S. M., Wyatt, J. R., Claverie, J., & Gautheret, D. (2000) · Genome Research · doi:10.1101/gr.10.7.1001 · Cited by 676 · see citing works

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomePreprint

Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I. U., & Pugh, B. F. (2008) · Genome Research · doi:10.1101/gr.078261.108 · Cited by 673 · see citing works

Two mRNAs with different 3′ ends encode membrane-bound and secreted forms of immunoglobulin μ chain

Rogers, J. (1980) · Cell · doi:10.1016/0092-8674(80)90616-9 · Cited by 670 · see citing works

Distinct Role of Long 3′ UTR BDNF mRNA in Spine Morphology and Synaptic Plasticity in Hippocampal Neurons

An, J. J., Gharami, K., Liao, G., Woo, N. H., Lau, A. G., Vanevski, F., Torre, E. R., Jones, K. R., Feng, Y., Lu, B., et al. (2008) · Cell · doi:10.1016/j.cell.2008.05.045 · Cited by 670 · see citing works

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

Kaida, D., Berg, M. G., Younis, I., Kasim, M., Singh, L. N., Wan, L., & Dreyfuss, G. (2010) · Nature · doi:10.1038/nature09479 · Cited by 638 · see citing works

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625 · see citing works

Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

Ji, Z., Lee, J. Y., Pan, Z., Jiang, B., & Tian, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900028106 · Cited by 595 · see citing works

Recognition of Trimethylated Histone H3 Lysine 4 Facilitates the Recruitment of Transcription Postinitiation Factors and Pre-mRNA Splicing

Sims, R. J., Millhouse, S., Chen, C.-F., Lewis, B. A., Erdjument‐Bromage, H., Tempst, P., Manley, J. L., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.010 · Cited by 581 · see citing works

Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3′ ends

Alt, F. W. (1980) · Cell · doi:10.1016/0092-8674(80)90615-7 · Cited by 576 · see citing works

RNA polymerase II and the integration of nuclear eventsPreprint

Hirose, Y., & Manley, J. L. (2000) · Genes & Development · doi:10.1101/gad.14.12.1415 · Cited by 575 · see citing works

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

Shi, Y., Giammartino, D. C. D., Taylor, D. J., Sarkeshik, A., Rice, W. J., Yates, J. R., Frank, J., & Manley, J. L. (2009) · Molecular Cell · doi:10.1016/j.molcel.2008.12.028 · Cited by 560 · see citing works

Cell-type-specific signatures of microRNAs on target mRNA expression

Sood, P., Krek, A., Zavolan, M., Macino, G., & Rajewsky, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0511045103 · Cited by 547 · see citing works

The 3′ untranslated region of messenger RNA: A molecular ‘hotspot’ for pathology?

Conne, B., Stutz, A., & Vassalli, J. (2000) · Nature Medicine · doi:10.1038/76211 · Cited by 530 · see citing works

An RNA map predicting Nova-dependent splicing regulation

Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., & Darnell, R. B. (2006) · Nature · doi:10.1038/nature05304 · Cited by 528 · see citing works

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

Jan, C. H., Friedman, R. C., Ruby, J. G., & Bartel, D. P. (2010) · Nature · doi:10.1038/nature09616 · Cited by 482 · see citing works

Targeted 3′ Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

Liu, F., Marquardt, S., Lister, C., et al. (2009) · Science · doi:10.1126/science.1180278 · Cited by 481 · see citing works

FY Is an RNA 3′ End-Processing Factor that Interacts with FCA to Control the Arabidopsis Floral Transition

Simpson, G. G., Dijkwel, P. P., Quesada, V., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00425-2 · Cited by 447 · see citing works

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

Shepard, P. J., Choi, E., Lu, J., Flanagan, L. A., Hertel, K. J., & Shi, Y. (2011) · RNA · doi:10.1261/rna.2581711 · Cited by 432 · see citing works

The Polyadenylation Factor CstF-64 Regulates Alternative Processing of IgM Heavy Chain Pre-mRNA during B Cell Differentiation

Takagaki, Y., Seipelt-Thiemann, R. L., Peterson, M. L., & Manley, J. L. (1996) · Cell · doi:10.1016/s0092-8674(00)82000-0 · Cited by 425 · see citing works

Protein factors in pre-mRNA 3′-end processing

Mandel, C. R., Bai, Y., & Tong, L. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-7474-3 · Cited by 415 · see citing works

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S. J. M., Hirst, M., & Iyer, V. R. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060065 · Cited by 401 · see citing works

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

Ozsolak, F., Kapranov, P., Foissac, S., Kim, S. W., Fishilevich, E., Monaghan, A. P., John, B., & Milos, P. M. (2010) · Cell · doi:10.1016/j.cell.2010.11.020 · Cited by 400 · see citing works

Alternate splicing produces a novel cyclin D1 transcript.

Betticher, D., Thatcher, N., Altermatt, H. J., Hoban, P. R., Ryder, W. D. J., & Heighway, J. (1995) · PubMed · Cited by 399 · see citing works

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

Millevoi, S., & Vagner, S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1176 · Cited by 393 · see citing works

Biased chromatin signatures around polyadenylation sites and exons

Nielsen, C. B., Padgett, R. A., Spies, N., & Burge, C. B. (2009) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 390 · see citing works

α-Thalassaemia caused by a polyadenylation signal mutation

Higgs, D. R., Goodbourn, S. E. Y., Lamb, J., Clegg, J. B., Weatherall, D. J., & Proudfoot, N. J. (1983) · Nature · doi:10.1038/306398a0 · Cited by 386 · see citing works

Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast

Takizawa, P. A., Sil, A., Swedlow, J. R., et al. (1997) · Nature · doi:10.1038/38015 · Cited by 386 · see citing works

Biased Chromatin Signatures around Polyadenylation Sites and Exons

Spies, N., Nielsen, C. B., Padgett, R. A., & Burge, C. B. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.10.008 · Cited by 385 · see citing works

The RNA polymerase II core promoter — the gateway to transcription

Juven-Gershon, T., Hsu, J.-Y., Theisen, J. W., & Kadonaga, J. T. (2008) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.03.003 · Cited by 367 · see citing works

Cyclin D1: polymorphism, aberrant splicing and cancer risk

Knudsen, K. E., Diehl, J. A., Haiman, C. A., & Knudsen, E. S. (2006) · Oncogene · doi:10.1038/sj.onc.1209371 · Cited by 363 · see citing works

RNA polymerase II is an essential mRNA polyadenylation factor

Hirose, Y., & Manley, J. L. (1998) · Nature · doi:10.1038/25786 · Cited by 359 · see citing works

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

Perales, R., & Bentley, D. L. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.09.018 · Cited by 355 · see citing works

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter, K. M., Kim, S., Espinosa, J. M., & Bentley, D. L. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1352 · Cited by 343 · see citing works

To localize or not to localize: mRNA fate is in 3′UTR ends

Andreassi, C., & Riccio, A. (2009) · Trends in Cell Biology · doi:10.1016/j.tcb.2009.06.001 · Cited by 338 · see citing works

Transcription termination by nuclear RNA polymerasesPreprint

Richard, P., & Manley, J. L. (2009) · Genes & Development · doi:10.1101/gad.1792809 · Cited by 326 · see citing works

The Arabidopsis RNA-Binding Protein FCA Requires a Lysine-Specific Demethylase 1 Homolog to Downregulate FLC

Liu, F., Quesada, V., Crevillén, P., Bäurle, I., Świeżewski, S., & Dean, C. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.10.018 · Cited by 326 · see citing works

Translational Regulation and RNA Localization in Drosophila Oocytes and Embryos

Johnstone, O., & Lasko, P. F. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.090756 · Cited by 322 · see citing works

Functional Interaction of Yeast Pre-mRNA 3′ End Processing Factors with RNA Polymerase II

Licatalosi, D. D., Geiger, G., Minet, M., Schroeder, S. C., Cilli, K., McNeil, J. B., & Bentley, D. L. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00518-x · Cited by 316 · see citing works

Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA

Dantonel, J.-C., Murthy, K. G. K., Manley, J. L., et al. (1997) · Nature · doi:10.1038/38763 · Cited by 307 · see citing works

3′ end mRNA processing: molecular mechanisms and implications for health and disease

Danckwardt, S., Hentze, M. W., & Kulozik, A. E. (2008) · The EMBO Journal · doi:10.1038/sj.emboj.7601932 · Cited by 296 · see citing works

Biased alternative polyadenylation in human tissues

Zhang, H., Lee, J. Y., & Tian, B. (2005) · Genome biology · doi:10.1186/gb-2005-6-12-r100 · Cited by 292 · see citing works

Putting RNAs in the right place at the right time: RNA localization in the frog oocyte

King, M. L., Messitt, T. J., & Mowry, K. L. (2005) · Biology of the Cell · doi:10.1042/bc20040067 · Cited by 291 · see citing works

Increased efficiency of mRNA 3′ end formation: a new genetic mechanism contributing to hereditary thrombophilia

Gehring, N. H., Frede, U., Neu‐Yilik, G., Hundsdoerfer, P., Vetter, B., Hentze, M. W., & Kulozik, A. E. (2001) · Nature Genetics · doi:10.1038/ng578 · Cited by 277 · see citing works

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

Ji, Z., & Tian, B. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008419 · Cited by 264 · see citing works

Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival

Wiestner, A. U., Tehrani, M., Chiorazzi, M., Wright, G. W., Gibellini, F., Nakayama, K., Liu, H., Rosenwald, A., Müller‐Hermelink, H. K., Ott, G., et al. (2007) · Blood · doi:10.1182/blood-2006-08-039859 · Cited by 252 · see citing works

Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

HU, J., Lutz, C. S., Wilusz, J., & Tian, B. (2005) · RNA · doi:10.1261/rna.2107305 · Cited by 249 · see citing works

The Landscape of C. elegans 3′UTRs

Mangone, M., Manoharan, A. P., Thierry‐Mieg, D., Thierry‐Mieg, J., Han, T., Mackowiak, S. D., Mis, E. K., Zegar, C., Gutwein, M. R., Khivansara, V., et al. (2010) · Science · doi:10.1126/science.1191244 · Cited by 247 · see citing works

How and why does β‐actin mRNA target?

Condeelis, J. S., & Singer, R. H. (2005) · Biology of the Cell · doi:10.1042/bc20040063 · Cited by 240 · see citing works

A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA→AAUGAA) leads to the IPEX syndrome

Bennett, C. L., Brunkow, M. E., Ramsdell, F., O'Briant, K. C., Zhu, Q., Fuleihan, R., Shigeoka, A. O., Ochs, H. D., & Chance, P. F. (2001) · Immunogenetics · doi:10.1007/s002510100358 · Cited by 240 · see citing works

An alternatively spliced cyclin D1 isoform, cyclin D1b, is a nuclear oncogene.

Lu, F., Gladden, A. B., & Diehl, J. A. (2003) · PubMed · Cited by 239 · see citing works

The Spen Family Protein FPA Controls Alternative Cleavage and Polyadenylation of RNA

Hornyik, C., Terzi, L. C., & Simpson, G. G. (2010) · Developmental Cell · doi:10.1016/j.devcel.2009.12.009 · Cited by 229 · see citing works

A Mechanism for the Regulation of Pre-mRNA 3′ Processing by Human Cleavage Factor Im

Brown, K. M., & Gilmartin, G. M. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00453-2 · Cited by 226 · see citing works

Distinct 3′UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF)

Lau, A. G., Irier, H. A., Gu, J., Tian, D., Ku, L., Liu, G., Xia, M., Fritsch, B., Zheng, J. Q., Dingledine, R. J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002929107 · Cited by 225 · see citing works

Levels of Polyadenylation Factor CstF-64 Control IgM Heavy Chain mRNA Accumulation and Other Events Associated with B Cell Differentiation

Takagaki, Y., & Manley, J. L. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80291-9 · Cited by 223 · see citing works

Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognitionPreprint

Venkataraman, K., Brown, K. M., & Gilmartin, G. M. (2005) · Genes & Development · doi:10.1101/gad.1298605 · Cited by 223 · see citing works

Cyclin D1 Splice Variants

Solomon, D. A., Wang, Y., Fox, S. R., Lambeck, T. C., Giesting, S., Lan, Z., Senderowicz, A. M., & Knudsen, E. S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303969200 · Cited by 218 · see citing works

Translational Efficiency Is Regulated by the Length of the 3′ Untranslated Region

Tanguay, R. L., & Gallie, D. R. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.1.146 · Cited by 204 · see citing works

An interaction between U2AF 65 and CF Im links the splicing and 3′ end processing machineries

Millevoi, S., Loulergue, C., Dettwiler, S., Karaa, Z. S., Keller, W., Antoniou, M. N., & Vagner, S. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601331 · Cited by 203 · see citing works

Direct Interactions between Subunits of CPSF and the U2 snRNP Contribute to the Coupling of Pre-mRNA 3′ End Processing and Splicing

Kyburz, A., Friedlein, A., Langen, H., & Keller, W. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.05.037 · Cited by 198 · see citing works

Thalassemia due to a mutation in the cleavage‐polyadenylation signal of the human beta‐globin gene.

Orkin, S. H., Cheng, T. C., Antonarakis, S. E., et al. (1985) · The EMBO Journal · doi:10.1002/j.1460-2075.1985.tb03650.x · Cited by 193 · see citing works

Fox-1 family of RNA-binding proteins

Kuroyanagi, H. (2009) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-009-0120-5 · Cited by 187 · see citing works

Last but Not Least

Barabino, S. M. L., & Keller, W. D. (1999) · Cell · doi:10.1016/s0092-8674(00)80057-4 · Cited by 179 · see citing works

The basal initiation machinery: beyond the general transcription factors

Sikorski, T. W., & Buratowski, S. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.03.006 · Cited by 176 · see citing works

mRNA export: an assembly line from genes to nuclear pores

Vinciguerra, P., & Stutz, F. (2004) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2004.03.013 · Cited by 174 · see citing works

Crystal structure of the human symplekin–Ssu72–CTD phosphopeptide complex

Xiang, K., Nagaike, T., Xiang, S., Kilic, T., Beh, M. M., Manley, J. L., & Tong, L. (2010) · Nature · doi:10.1038/nature09391 · Cited by 171 · see citing works

Cell-cycle related regulation of poly(A) polymerase by phosphorylation

Colgan, D. F., Murthy, K. G. K., Prives, C. L., et al. (1996) · Nature · doi:10.1038/384282a0 · Cited by 164 · see citing works

Regulation of alternative polyadenylation by genomic imprintingPreprint

Wood, A. J., Schulz, R., Woodfine, K., Koltowska, K., BEECHEY, C. V., Peters, J., Bourc’his, D., & Oakey, R. J. (2008) · Genes & Development · doi:10.1101/gad.473408 · Cited by 163 · see citing works

Alternative Polyadenylation Events Contribute to the Induction of NF-ATc in Effector T Cells

Chuvpilo, S. A., Zimmer, M., Kerstan, A., et al. (1999) · Immunity · doi:10.1016/s1074-7613(00)80026-6 · Cited by 162 · see citing works

Polypyrimidine Tract Binding Protein Modulates Efficiency of Polyadenylation

Castelo‐Branco, P., Furger, A., Wollerton, M., Smith, C. W. J., Moreira, A., & Proudfoot, N. J. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.10.4174-4183.2004 · Cited by 162 · see citing works

The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3′ end formation by two distinct mechanismsPreprint

Moreira, A., Takagaki, Y., Brackenridge, S., Wollerton, M., Manley, J. L., & Proudfoot, N. J. (1998) · Genes & Development · doi:10.1101/gad.12.16.2522 · Cited by 156 · see citing works

Global Changes in Processing of mRNA 3′ Untranslated Regions Characterize Clinically Distinct Cancer Subtypes

Singh, P., Alley, T. L., Wright, S., Kamdar, S. J., Schott, W. H., Wilpan, R. Y., Mills, K. D., & Graber, J. H. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-2236 · Cited by 156 · see citing works

A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants

Chen, J., Férec, C., & Cooper, D. N. (2006) · Human Genetics · doi:10.1007/s00439-006-0218-x · Cited by 143 · see citing works

Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3′-UTRs

Kubo, T., Wada, T., Yamaguchi, Y., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl794 · Cited by 143 · see citing works

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse

Halees, A. S., El-Badrawi, R., & Khabar, K. S. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm959 · Cited by 142 · see citing works

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors

Rozenblatt–Rosen, O., Nagaike, T., Francis, J. M., Kaneko, S., Glatt, K. A., Hughes, C. M., LaFramboise, T., Manley, J. L., & Meyerson, M. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812023106 · Cited by 141 · see citing works

Conserved and variable regions in the subunits of brain type II Ca2+/calmodulin-dependent protein kinase

Bulleit, R. F., Bennett, M. K., Molloy, S. S., Hurley, J. B., & Kennedy, M. B. (1988) · Neuron · doi:10.1016/0896-6273(88)90210-3 · Cited by 137 · see citing works

Transcription elongation factor ELL2 directs immunoglobulin secretion in plasma cells by stimulating altered RNA processing

Martincic, K., Alkan, S., Jarvela, A. M. C., et al. (2009) · Nature Immunology · doi:10.1038/ni.1786 · Cited by 137 · see citing works

RNA polymerase II kinetics in polo polyadenylation signal selection

Pinto, P. A. B., Henriques, T., Freitas, M. O., Martins, T., Domingues, R. G., Wyrzykowska, P. S., Coelho, P. A., Carmo, A. M., Sunkel, C. E., Proudfoot, N. J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.156 · Cited by 136 · see citing works

Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis

Liu, D., Brockman, J. M., Dass, B., Hutchins, L. N., Singh, P., McCarrey, J. R., MacDonald, C. C., & Graber, J. H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl919 · Cited by 130 · see citing works

Determinants of mRNA localization

Kislauskis, E., & Singer, R. H. (1992) · Current Opinion in Cell Biology · doi:10.1016/0955-0674(92)90128-y · Cited by 128 · see citing works

Cyclin D1b variant influences prostate cancer growth through aberrant androgen receptor regulation

Burd, C. J., Petre, C. E., Morey, L. M., Wang, Y., Revelo, M. P., Haiman, C. A., Lu, S., Fenoglio‐Preiser, C. M., Li, J., Knudsen, E. S., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506281103 · Cited by 125 · see citing works

The role of the AU-rich elements of mRNAs in controlling translation

Espel, E. (2004) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2004.11.008 · Cited by 124 · see citing works

Transcriptional Activators Enhance Polyadenylation of mRNA Precursors

Nagaike, T., Logan, C. J., Hotta, I., Rozenblatt–Rosen, O., Meyerson, M. M., & Manley, J. L. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.01.022 · Cited by 116 · see citing works

THE LANDSCAPE OF

Matul, M., McCord, M. J., Phily, C., et al. (2010) · Cited by 108 · see citing works

SRm160 Splicing Coactivator Promotes Transcript 3′-End Cleavage

McCracken, S. A., Lambermon, M. H. L., & Blencowe, B. J. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.1.148-160.2002 · Cited by 106 · see citing works

Identification of a cis‐acting dendritic targeting element in the mRNA encoding the alpha subunit of Ca2+/calmodulin‐dependent protein kinase II

Blichenberg, A., Rehbein, M., Müller, R., Garner, C. C., Richter, D., & Kindler, S. (2001) · European Journal of Neuroscience · doi:10.1046/j.0953-816x.2001.01565.x · Cited by 98 · see citing works

Multiple, Conserved Iron-responsive Elements in the 3′-Untranslated Region of Transferrin Receptor mRNA Enhance Binding of Iron Regulatory Protein 2

Erlitzki, R., Long, J. C., & Theil, E. C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207918200 · Cited by 94 · see citing works

Cyclin D1 Splice Variants: Polymorphism, Risk, and Isoform-Specific Regulation in Prostate Cancer

Comstock, C. E. S., Augello, M. A., Benito, R. P., Karch, J. M., Tran, T. H., Utama, F. E., Tindall, E. A., Wang, Y., Burd, C. J., Groh, E. M., et al. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-08-2865 · Cited by 92 · see citing works

A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence

Nunes, N. M., Li, W., Tian, B., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.42 · Cited by 91 · see citing works

To polyadenylate or to deadenylate

Zhang, X., Virtanen, A., & Kleiman, F. E. (2010) · Cell Cycle · doi:10.4161/cc.9.22.13887 · Cited by 86 · see citing works

Splicing factors stimulate polyadenylation via USEs at non‐canonical 3′ end formation signals

Danckwardt, S., Kaufmann, I., Gentzel, M., Förstner, K. U., Gantzert, A.-S., Gehring, N. H., Neu‐Yilik, G., Bork, P., Keller, W., Wilm, M. S., et al. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601699 · Cited by 86 · see citing works

Loss of polyadenylation protein τCstF-64 causes spermatogenic defects and male infertility

Dass, B., Tardif, S., Park, J. Y., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707589104 · Cited by 85 · see citing works

Heterogeneous nuclear ribonucleoproteins F and H/H′ show differential expression in normal and selected cancer tissues

Honoré, B., Baandrup, U. T., & Vorum, H. (2003) · Experimental Cell Research · doi:10.1016/j.yexcr.2003.11.011 · Cited by 83 · see citing works

Reexamining the polyadenylation signal: were we wrong about AAUAAA?

MacDonald, C. C., & Redondo, J.-L. (2002) · Molecular and Cellular Endocrinology · doi:10.1016/s0303-7207(02)00044-8 · Cited by 83 · see citing works

Differential Interactions of the Autonomous Pathway RRM Proteins and Chromatin Regulators in the Silencing of Arabidopsis Targets

Bäurle, I., & Dean, C. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002733 · Cited by 80 · see citing works

p38 MAPK Controls Prothrombin Expression by Regulated RNA 3′ End Processing

Danckwardt, S., Gantzert, A.-S., Macher‐Goeppinger, S., Probst, H. C., Gentzel, M., Wilm, M. S., Gröne, H., Schirmacher, P., Hentze, M. W., & Kulozik, A. E. (2011) · Molecular Cell · doi:10.1016/j.molcel.2010.12.032 · Cited by 78 · see citing works

Moving molecules: mRNA trafficking in mammalian oligodendrocytes and neurons

Smith, R. (2004) · The Neuroscientist · doi:10.1177/1073858404266759 · Cited by 67 · see citing works

A physical and functional link between splicing factors promotes pre-mRNA 3′ end processing

Millevoi, S., Decorsière, A., Loulergue, C., Iacovoni, J. S., Bernat-Fabre, S., Antoniou, M. N., & Vagner, S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp470 · Cited by 67 · see citing works

Differential Repression of Alternative Transcripts: A Screen for miRNA Targets

Legendre, M., Ritchie, W., Lopez, F., & Gautheret, D. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020043 · Cited by 66 · see citing works

Cyclin D1b Is Aberrantly Regulated in Response to Therapeutic Challenge and Promotes Resistance to Estrogen Antagonists

Wang, Y., Dean, J. L., Millar, E. K. A., Tran, T. H., McNeil, C. M., Burd, C. J., Henshall, S. M., Utama, F. E., Witkiewicz, A. K., Rui, H., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-3170 · Cited by 66 · see citing works

Sumoylation regulates multiple aspects of mammalian poly(A) polymerase functionPreprint

Vethantham, V., Rao, N., & Manley, J. L. (2008) · Genes & Development · doi:10.1101/gad.1628208 · Cited by 62 · see citing works

Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development

Peterson, M. L. (2007) · Immunologic Research · doi:10.1007/bf02686094 · Cited by 53 · see citing works

Conservation of alternative polyadenylation patterns in mammalian genes

Ara, T., Lopez, F., Ritchie, W., Benech, P. D., & Gautheret, D. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-189 · Cited by 53 · see citing works

MicroRNAs in C. elegans Aging: Molecular Insurance for Robustness?

Ibáñez‐Ventoso, C., & Driscoll, M. (2009) · Current Genomics · doi:10.2174/138920209788185243 · Cited by 46 · see citing works

Finishing touches: Post-translational modification of protein factors involved in mammalian pre-mRNA 3′ end formation

Ryan, K., & Bauer, D. L. V. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.03.016 · Cited by 42 · see citing works

An RNA–protein complex links enhanced nuclear 3′ processing with cytoplasmic mRNA stabilization

Ji, X., Kong, J., & Liebhaber, S. A. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.171 · Cited by 35 · see citing works

From Transcription to mRNA: PAF Provides a New Path

Rosonina, E., & Manley, J. L. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.10.004 · Cited by 33 · see citing works

HL60 Cells Halted in G1 or S Phase Differentiate Normally

Brown, G. E. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5654 · Cited by 29 · see citing works

Alternative 3′ UTR polyadenylation of Bzw1 transcripts display differential translation efficiency and tissue-specific expression

Yu, M., Sha, H., Gao, Y., et al. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.04.113 · Cited by 24 · see citing works

Polyadenylation proteins CstF-64 and τCstF-64 exhibit differential binding affinities for RNA polymers

Monarez, R. R., MacDonald, C. C., & Dass, B. (2007) · Biochemical Journal · doi:10.1042/bj20061097 · Cited by 22 · see citing works

Differences in polyadenylation site choice between somatic and male germ cells

McMahon, K. W., Hirsch, B. A., & MacDonald, C. C. (2006) · BMC Molecular Biology · doi:10.1186/1471-2199-7-35 · Cited by 21 · see citing works

Chromatin: The Final Frontier in Splicing Regulation?

Fox-Walsh, K. L., & Fu, X. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.03.002 · Cited by 21 · see citing works

Spermatogenetic but not immunological defects in mice lacking the τCstF-64 polyadenylation protein

Hockert, K. J., Martincic, K., Mendis-Handagama, S. M. L. C., et al. (2011) · Journal of Reproductive Immunology · doi:10.1016/j.jri.2011.01.018 · Cited by 15 · see citing works

Alternative Polyadenylation Blooms

Rosonina, E., & Manley, J. L. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.02.001 · Cited by 11 · see citing works

A potential regulatory role for mRNA secondary structures within the prothrombin 3'UTR

Liu, X., Jiang, Y., & Russell, J. (2010) · Thrombosis Research · doi:10.1016/j.thromres.2010.04.010 · Cited by 9 · see citing works

U1 snRNP regulates cancer cell migration and invasion in vitro

Oh, J.-M., Venters, C. C., Di, C., Pinto, A. M., Wan, L., Younis, I., Cai, Z., Arai, C., So, B. R., Duan, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13993-7 · Cited by 7,157 · see citing works

Molecular regulation of stem cell quiescence

Cheung, T. H., & Rando, T. A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3591 · Cited by 1,148 · see citing works

Coupling mRNA processing with transcription in time and space

Bentley, D. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3662 · Cited by 828 · see citing works

Assessment of transcript reconstruction methods for RNA-seq

The RGASP Consortium, Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., Guigó, R., Harrow, J., & Bertone, P. (2013) · Nature Methods · doi:10.1038/nmeth.2714 · Cited by 699 · see citing works

Dynamic integration of splicing within gene regulatory pathways

Braunschweig, U., Gueroussov, S., Plocik, A. M., Graveley, B. R., & Blencowe, B. J. (2013) · Cell · doi:10.1016/j.cell.2013.02.034 · Cited by 406 · see citing works

Translational control by changes in poly(A) tail length: recycling mRNAs

Weill, L., Belloc, E., Bava, F.-A., & Méndez, R. (2012) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.2311 · Cited by 328 · see citing works

Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease

Batra, R., Charizanis, K., Manchanda, M., Mohan, A., Li, M., Finn, D. J., Goodwin, M., Zhang, C., Sobczak, K., Thornton, C. A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.027 · Cited by 292 · see citing works

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

Shi, Y., & Manley, J. L. (2015) · Genes &amp; Development · doi:10.1101/gad.261974.115 · Cited by 249 · see citing works

An RNA toolbox for cancer immunotherapy

Pastor, F., Berraondo, P., Etxeberria, I., Frederick, J., Sahin, U., Gilboa, E., & Melero, I. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.132 · Cited by 229 · see citing works

Reprogramming the assembly of unmodified DNA with a small molecule

Avakyan, N., Greschner, A. A., Aldaye, F., Serpell, C. J., Toader, V., Petitjean, A., & Sleiman, H. F. (2016) · Nature Chemistry · doi:10.1038/nchem.2451 · Cited by 148 · see citing works

3′ UTR lengthening as a novel mechanism in regulating cellular senescence.

Chen, M., Lyu, G., Han, M., Nie, H., Shen, T., Chen, W., Niu, Y., Song, Y., Li, X., Li, H., et al. (2018) · Genome Research · doi:10.1101/gr.224451.117 · Cited by 111 · see citing works

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 · see citing works

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in <i>Drosophila melanogaster</i>

Liu, X., Freitas, J., Zheng, D., Oliveira, M. S., Hoque, M., Martins, T., Henriques, T., Tian, B., & Moreira, A. (2017) · RNA · doi:10.1261/rna.062661.117 · Cited by 67 · see citing works

Aminopeptidase N Activatable Nanoprobe for Tracking Lymphatic Metastasis and Guiding Tumor Resection Surgery via Optoacoustic/NIR-II Fluorescence Dual-Mode Imaging

Chen, J., Chen, L., Zeng, F., & Wu, S. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01241 · Cited by 50 · see citing works

Control by a hair’s breadth: the role of microRNAs in the skin

Ning, M. S., & Andl, T. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-1117-z · Cited by 48 · see citing works

Involved microRNAs in alternative polyadenylation intervene in breast cancer via regulation of cleavage factor “CFIm25”

Tamaddon, M., Shokri, G., Hosseini Rad, S. M. A., Rad, I., Emami Razavi, À., & Kouhkan, F. (2020) · Scientific Reports · doi:10.1038/s41598-020-68406-3 · Cited by 25 · see citing works

Global 3′ UTR shortening has a limited effect on protein abundance in proliferating T cells

Gruber, A. J., Martin, G., Müller, P., Schmidt, A., Gruber, A. J., Gumienny, R., Mittal, N., Jayachandran, R., Pieters, J., Keller, W., et al. (2014) · Nature Communications · doi:10.1038/ncomms6465 · Cited by 196 · see citing works

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 54 · see citing works

Guinea Pig p53 mRNA: Identification of New Elements in Coding and Untranslated Regions and Their Functional and Evolutionary Implications

D’Erchia, A. M., Pesole, G., Tullo, A., Saccone, C., & Sbisà, E. (1999) · Genomics · doi:10.1006/geno.1999.5794 · Cited by 21 · see citing works

Alternative polyadenylation in the regulation and dysregulation of gene expression

Turner, R. E., Pattison, A., & Beilharz, T. H. (2017) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2017.08.056 · Cited by 76 · see citing works

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 · see citing works