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For: Hu J, Lutz CS, Wilusz J, Tian B. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 2005;11:1485-93. [PMID: 16131587 PMCID: PMC1370832 DOI: 10.1261/rna.2107305] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Number Cited by Other Article(s)
151
In vivo methods to assess polyadenylation efficiency. Methods Mol Biol 2008. [PMID: 18369983 DOI: 10.1007/978-1-59745-033-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
152
Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ. Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Res 2008;36:3150-61. [PMID: 18411206 PMCID: PMC2396415 DOI: 10.1093/nar/gkn158] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/19/2008] [Indexed: 12/24/2022]  Open
153
McNally MT. RNA processing control in avian retroviruses. FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2008;13:3869-83. [PMID: 18508481 PMCID: PMC2575692 DOI: 10.2741/2975] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
154
Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment. BMC Genomics 2008;9:189. [PMID: 18439287 PMCID: PMC2413145 DOI: 10.1186/1471-2164-9-189] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 04/25/2008] [Indexed: 11/10/2022]  Open
155
Mandel CR, Bai Y, Tong L. Protein factors in pre-mRNA 3'-end processing. Cell Mol Life Sci 2008;65:1099-122. [PMID: 18158581 PMCID: PMC2742908 DOI: 10.1007/s00018-007-7474-3] [Citation(s) in RCA: 319] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
156
Ibrahim H, Wilusz J, Wilusz CJ. RNA recognition by 3'-to-5' exonucleases: the substrate perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2008;1779:256-65. [PMID: 18078842 PMCID: PMC2365504 DOI: 10.1016/j.bbagrm.2007.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 11/08/2007] [Accepted: 11/09/2007] [Indexed: 12/30/2022]
157
Fujita S, Ito T, Mizutani T, Minoguchi S, Yamamichi N, Sakurai K, Iba H. miR-21 Gene expression triggered by AP-1 is sustained through a double-negative feedback mechanism. J Mol Biol 2008;378:492-504. [PMID: 18384814 DOI: 10.1016/j.jmb.2008.03.015] [Citation(s) in RCA: 349] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Revised: 02/20/2008] [Accepted: 03/09/2008] [Indexed: 12/11/2022]
158
3' end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 2008;27:482-98. [PMID: 18256699 DOI: 10.1038/sj.emboj.7601932] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/24/2007] [Indexed: 12/27/2022]  Open
159
Sartini BL, Wang H, Wang W, Millette CF, Kilpatrick DL. Pre-Messenger RNA Cleavage Factor I (CFIm): Potential Role in Alternative Polyadenylation During Spermatogenesis1. Biol Reprod 2008;78:472-82. [DOI: 10.1095/biolreprod.107.064774] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
160
Messenger RNA 3′ End Formation in Plants. Curr Top Microbiol Immunol 2008;326:151-77. [DOI: 10.1007/978-3-540-76776-3_9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
161
Tharun S. Roles of eukaryotic Lsm proteins in the regulation of mRNA function. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008;272:149-89. [PMID: 19121818 DOI: 10.1016/s1937-6448(08)01604-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
162
Lee JY, Park JY, Tian B. Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and Trace. Methods Mol Biol 2008;419:23-37. [PMID: 18369973 DOI: 10.1007/978-1-59745-033-1_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
163
Loss of polyadenylation protein tauCstF-64 causes spermatogenic defects and male infertility. Proc Natl Acad Sci U S A 2007;104:20374-9. [PMID: 18077340 DOI: 10.1073/pnas.0707589104] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
164
Feng Z, Wu CF, Zhou X, Kuang J. Alternative polyadenylation produces two major transcripts of Alix. Arch Biochem Biophys 2007;465:328-35. [PMID: 17673164 PMCID: PMC4104816 DOI: 10.1016/j.abb.2007.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 06/21/2007] [Accepted: 06/21/2007] [Indexed: 01/23/2023]
165
Graber JH, Salisbury J, Hutchins LN, Blumenthal T. C. elegans sequences that control trans-splicing and operon pre-mRNA processing. RNA (NEW YORK, N.Y.) 2007;13:1409-26. [PMID: 17630324 PMCID: PMC1950753 DOI: 10.1261/rna.596707] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 05/17/2007] [Indexed: 05/04/2023]
166
Maciolek NL, McNally MT. Serine/arginine-rich proteins contribute to negative regulator of splicing element-stimulated polyadenylation in rous sarcoma virus. J Virol 2007;81:11208-17. [PMID: 17670832 PMCID: PMC2045511 DOI: 10.1128/jvi.00919-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
167
Hall-Pogar T, Liang S, Hague LK, Lutz CS. Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3'-UTR. RNA (NEW YORK, N.Y.) 2007;13:1103-15. [PMID: 17507659 PMCID: PMC1894925 DOI: 10.1261/rna.577707] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
168
Kim Guisbert KS, Li H, Guthrie C. Alternative 3' pre-mRNA processing in Saccharomyces cerevisiae is modulated by Nab4/Hrp1 in vivo. PLoS Biol 2007;5:e6. [PMID: 17194212 PMCID: PMC1717019 DOI: 10.1371/journal.pbio.0050006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 11/03/2006] [Indexed: 11/18/2022]  Open
169
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions. BMC Bioinformatics 2007;8:174. [PMID: 17524134 PMCID: PMC1904458 DOI: 10.1186/1471-2105-8-174] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Accepted: 05/24/2007] [Indexed: 12/11/2022]  Open
170
Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE. Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. EMBO J 2007;26:2658-69. [PMID: 17464285 PMCID: PMC1888663 DOI: 10.1038/sj.emboj.7601699] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 04/02/2007] [Indexed: 12/26/2022]  Open
171
Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 2007;35:D165-8. [PMID: 17202160 PMCID: PMC1899096 DOI: 10.1093/nar/gkl870] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
172
Ivanov IP, Atkins JF. Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res 2007;35:1842-58. [PMID: 17332016 PMCID: PMC1874602 DOI: 10.1093/nar/gkm035] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
173
Ji G, Zheng J, Shen Y, Wu X, Jiang R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics 2007;8:43. [PMID: 17286857 PMCID: PMC1805453 DOI: 10.1186/1471-2105-8-43] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 02/07/2007] [Indexed: 11/10/2022]  Open
174
Tian B, Pan Z, Lee JY. Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genes Dev 2007;17:156-65. [PMID: 17210931 PMCID: PMC1781347 DOI: 10.1101/gr.5532707] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Accepted: 11/20/2006] [Indexed: 12/31/2022]
175
Al-Zoghaibi F, Ashour T, Al-Ahmadi W, Abulleef H, Demirkaya O, Khabar KSA. Bioinformatics and experimental derivation of an efficient hybrid 3' untranslated region and use in expression active linear DNA with minimum poly(A) region. Gene 2006;391:130-9. [PMID: 17258873 DOI: 10.1016/j.gene.2006.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2006] [Revised: 12/11/2006] [Accepted: 12/15/2006] [Indexed: 11/25/2022]
176
Dalziel M, Nunes NM, Furger A. Two G-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(A) site of the intronless melanocortin receptor 1 gene are critical for efficient 3' end processing. Mol Cell Biol 2006;27:1568-80. [PMID: 17189425 PMCID: PMC1820467 DOI: 10.1128/mcb.01821-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
177
Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH. Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res 2006;35:234-46. [PMID: 17158511 PMCID: PMC1802579 DOI: 10.1093/nar/gkl919] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
178
Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet 2006;2:e191. [PMID: 17121466 PMCID: PMC1657047 DOI: 10.1371/journal.pgen.0020191] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 09/26/2006] [Indexed: 12/13/2022]  Open
179
Peterson ML, Bingham GL, Cowan C. Multiple features contribute to the use of the immunoglobulin M secretion-specific poly(A) signal but are not required for developmental regulation. Mol Cell Biol 2006;26:6762-71. [PMID: 16943419 PMCID: PMC1592873 DOI: 10.1128/mcb.00889-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
180
Ara T, Lopez F, Ritchie W, Benech P, Gautheret D. Conservation of alternative polyadenylation patterns in mammalian genes. BMC Genomics 2006;7:189. [PMID: 16872498 PMCID: PMC1550727 DOI: 10.1186/1471-2164-7-189] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 07/26/2006] [Indexed: 11/26/2022]  Open
181
Cheng Y, Miura RM, Tian B. Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 2006;22:2320-5. [PMID: 16870936 DOI: 10.1093/bioinformatics/btl394] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
182
Retelska D, Iseli C, Bucher P, Jongeneel CV, Naef F. Similarities and differences of polyadenylation signals in human and fly. BMC Genomics 2006;7:176. [PMID: 16836751 PMCID: PMC1574307 DOI: 10.1186/1471-2164-7-176] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 07/12/2006] [Indexed: 02/02/2023]  Open
183
Chen JM, Férec C, Cooper DN. 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. Hum Genet 2006;120:301-33. [PMID: 16807757 DOI: 10.1007/s00439-006-0218-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 05/29/2006] [Indexed: 12/13/2022]
184
Chen JM, Férec C, Cooper DN. A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview. Hum Genet 2006;120:1-21. [PMID: 16645853 DOI: 10.1007/s00439-006-0180-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 03/26/2006] [Indexed: 10/24/2022]
185
Salisbury J, Hutchison KW, Graber JH. A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics 2006;7:55. [PMID: 16542450 PMCID: PMC1539018 DOI: 10.1186/1471-2164-7-55] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 03/16/2006] [Indexed: 12/18/2022]  Open
186
Pan Z, Zhang H, Hague LK, Lee JY, Lutz CS, Tian B. An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene 2006;366:325-34. [PMID: 16316725 DOI: 10.1016/j.gene.2005.09.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 08/09/2005] [Accepted: 09/22/2005] [Indexed: 01/24/2023]
187
Zhang H, Lee JY, Tian B. Biased alternative polyadenylation in human tissues. Genome Biol 2005;6:R100. [PMID: 16356263 PMCID: PMC1414089 DOI: 10.1186/gb-2005-6-12-r100] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/31/2005] [Accepted: 10/18/2005] [Indexed: 11/15/2022]  Open
188
Gilmartin GM. Eukaryotic mRNA 3' processing: a common means to different ends. Genes Dev 2005;19:2517-21. [PMID: 16264187 DOI: 10.1101/gad.1378105] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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