[1]
|
Mayr, C. (2019) What Are 3’ UTRs Doing? Cold Spring Harbor Perspectives in Biology, 11, a034728. https://doi.org/10.1101/cshperspect.a034728
|
[2]
|
Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. and Burge, C.B. (2008) Proliferating Cells Express MRNAs with Shortened 3’ Untranslated Regions and Fewer MicroRNA Target Sites. Science, 320, 1643-1647. https://doi.org/10.1126/science.1155390
|
[3]
|
Mayr, C. and Bartel, D.P. (2009) Widespread Shortening of 3’UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells. Cell, 138, 673-684. https://doi.org/10.1016/j.cell.2009.06.016
|
[4]
|
Wang, R., Nambiar, R., Zheng, D. and Tian, B. (2018) PolyA_DB 3 Catalogs Cleavage and Polyadenylation Sites Identified by Deep Sequencing in Multiple Genomes. Nucleic Acids Research, 46, D315-D319. https://doi.org/10.1093/nar/gkx1000
|
[5]
|
Herrmann, C.J., Schmidt, R., Kanitz, A., Artimo, P., Gruber, A.J. and Zavolan, M. (2020) PolyASite 2.0: A Consolidated Atlas of Polyadenylation Sites from 3’ End Sequencing. Nucleic Acids Research, 48, D174-D179. https://doi.org/10.1093/nar/gkz918
|
[6]
|
Marini, F., Scherzinger, D. and Danckwardt, S. (2021) TREND-DB-A Transcriptome-Wide Atlas of the Dynamic Landscape of Alternative Polyadenylation. Nucleic Acids Research, 49, D243-D253. https://doi.org/10.1093/nar/gkaa722
|
[7]
|
Turner, R.E., Pattison, A.D. and Beilharz, T.H. (2018) Alternative Polyadenylation in the Regulation and Dysregulation of Gene Expression. Seminars in Cell & Developmental Biology, 75, 61-69. https://doi.org/10.1016/j.semcdb.2017.08.056
|
[8]
|
Hong, W., Ruan, H., Zhang, Z., Ye, Y., Liu, Y., Li, S., Jing, Y., Zhang, H., Diao, L., Liang, H. and Han, L. (2020) APAatlas: Decoding Alternative Polyadenylation across Human Tissues. Nucleic Acids Research, 48, D34-D39. https://doi.org/10.1093/nar/gkz876
|
[9]
|
Tian, B., Pan, Z. and Lee, J.Y. (2007) Widespread MRNA Polyadenylation Events in Introns Indicate Dynamic Interplay Between Polyadenylation and Splicing. Genome Research, 17, 156-165. https://doi.org/10.1101/gr.5532707
|
[10]
|
Zhang, Y., Liu, L., Qiu, Q., Zhou, Q., Ding, J., Lu, Y. and Liu, P. (2021) Alternative Polyadenylation: Methods, Mechanism, Function, and Role in Cancer. Journal of Experimental & Clinical Cancer Research, 40, Article No. 51. https://doi.org/10.1186/s13046-021-01852-7
|
[11]
|
Tian, B. and Manley, J.L. (2017) Alternative Polyadenylation of MRNA Precursors. Nature Reviews Molecular Cell Biology, 18, 18-30. https://doi.org/10.1038/nrm.2016.116
|
[12]
|
Yuan, F., Hankey, W., Wagner, E.J., Li, W. and Wang, Q. (2021) Alternative Polyadenylation of MRNA and Its Role in Cancer. Genes & Diseases, 8, 61-72. https://doi.org/10.1016/j.gendis.2019.10.011
|
[13]
|
Lin, J., Xu, R., Wu, X., Shen, Y. and Li, Q.Q. (2017) Role of Cleavage and Polyadenylation Specificity Factor 100: Anchoring Poly(A) Sites and Modulating Transcription Termination. The Plant Journal, 91, 829-839. https://doi.org/10.1111/tpj.13611
|
[14]
|
Mandel, C.R., Kaneko, S., Zhang, H., Gebauer, D., Vethantham, V., Manley, J.L. and Tong, L. (2006) Polyadenylation Factor CPSF-73 Is the Pre-MRNA 3’-End-Processing Endonuclease. Nature, 444, 953-956. https://doi.org/10.1038/nature05363
|
[15]
|
Eaton, J.D., Davidson, L., Bauer, D.L.V., Natsume, T., Kanemaki, M.T. and West, S. (2018) Xrn2 Accelerates Termination by RNA Polymerase II, Which Is Underpinned by CPSF73 Activity. Genes & Development, 32, 127-139. https://doi.org/10.1101/gad.308528.117
|
[16]
|
Chan, S.L., Huppertz, I., Yao, C., Weng, L., Moresco, J.J., Yates III, J.R., Ule, J., Manley, J.L. and Shi, Y. (2014) CPSF30 and Wdr33 Directly Bind to AAUAAA in Mammalian MRNA 3’ Processing. Genes & Development, 28, 2370-2380. https://doi.org/10.1101/gad.250993.114
|
[17]
|
Schönemann, L., Kühn, U., Martin, G., Schäfer, P., Gruber, A.R., Keller, W., Zavolan, M. and Wahle, E. (2014) Reconstitution of CPSF Active in Polyadenylation: Recognition of the Polyadenylation Signal by WDR33. Genes & Development, 28, 2381-2393. https://doi.org/10.1101/gad.250985.114
|
[18]
|
Yang, W., Hsu, P.L., Yang, F., Song, J.E. and Varani, G. (2018) Reconstitution of the CstF Complex Unveils a Regulatory Role for CstF-50 in Recognition of 3’-End Processing Signals. Nucleic Acids Research, 46, 493-503. https://doi.org/10.1093/nar/gkx1177
|
[19]
|
Fonseca, D., Baquero, J., Murphy, M.R., Aruggoda, G., Varriano, S., Sapienza, C., Mashadova, O., Rahman, S. and Kleiman, F.E. (2018) MRNA Processing Factor CstF-50 and Ubiquitin Escort Factor P97 Are BRCA1/BARD1 Cofactors Involved in Chromatin Remodeling During the DNA Damage Response. Molecular and Cellular Biology, 38, e00364-17. https://doi.org/10.1128/MCB.00364-17
|
[20]
|
Hwang, H.W., Park, C.Y., Goodarzi, H., Fak, J.J., Mele, A., Moore, M.J., Saito, Y. and Darnell, R.B. (2016) PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-Canonical Poly(A) Site Usage. Cell Reports, 15, 423-435. https://doi.org/10.1016/j.celrep.2016.03.023
|
[21]
|
Takagaki, Y., Seipelt, R.L., Peterson, M.L. and Manley, J.L. (1996) The Polyadenylation Factor CstF-64 Regulates Alternative Processing of IgM Heavy Chain Pre-MRNA During B Cell Differentiation. Cell, 87, 941-952. https://doi.org/10.1016/S0092-8674(00)82000-0
|
[22]
|
Hockert, J.A., Yeh, H.J. and MacDonald, C.C. (2010) The Hinge Domain of the Cleavage Stimulation Factor Protein CstF-64 Is Essential for CstF-77 Interaction, Nuclear Localization, and Polyadenylation. Journal of Biological Chemistry, 285, 695-704. https://doi.org/10.1074/jbc.M109.061705
|
[23]
|
Grozdanov, P.N., Masoumzadeh, E., Latham, M.P. and MacDonald, C.C. (2018) The Structural Basis of CstF-77 Modulation of Cleavage and Polyadenylation through Stimulation of CstF-64 Activity. Nucleic Acids Research, 46, 12022-12039. https://doi.org/10.1093/nar/gky862
|
[24]
|
Rüegsegger, U., Blank, D. and Keller, W. (1998) Human Pre-MRNA Cleavage Factor Im Is Related to Spliceosomal SR Proteins and Can Be Reconstituted in Vitro from Recombinant Subunits. Molecular Cell, 1, 243-253. https://doi.org/10.1016/S1097-2765(00)80025-8
|
[25]
|
Rüegsegger, U., Beyer, K. and Keller, W. (1996) Purification and Characterization of Human Cleavage Factor Im Involved in the 3’ End Processing of Messenger RNA Precursors. Journal of Biological Chemistry, 271, 6107-6113. https://doi.org/10.1074/jbc.271.11.6107
|
[26]
|
Martin, G., Gruber, A.R., Keller, W. and Zavolan, M. (2012) Genome-Wide Analysis of Pre-MRNA 3’ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3’ UTR Length. Cell Reports, 1, 753-763. https://doi.org/10.1016/j.celrep.2012.05.003
|
[27]
|
Gruber, A.R., Martin, G., Keller, W. and Zavolan, M. (2012) Cleavage Factor Im Is a Key Regulator of 3’ UTR Length. RNA Biology, 9, 1405-1412. https://doi.org/10.4161/rna.22570
|
[28]
|
Gruber, A.J. and Zavolan, M. (2019) Alternative Cleavage and Polyadenylation in Health and Disease. Nature Reviews Genetics, 20, 599-614. https://doi.org/10.1038/s41576-019-0145-z
|
[29]
|
Schäfer, P., Tüting, C., Schönemann, L., Kühn, U., Treiber, T., Treiber, N., Ihling, C., Graber, A., Keller, W., Meister, G., Sinz, A. and Wahle, E. (2018) Reconstitution of Mammalian Cleavage Factor II Involved in 3’ Processing of MRNA Precursors. RNA, 24, 1721-1737. https://doi.org/10.1261/rna.068056.118
|
[30]
|
Stroup, E.K. and Ji, Z. (2023) Deep Learning of Human Polyadenylation Sites at Nucleotide Resolution Reveals Molecular Determinants of Site Usage and Relevance in Disease. Nature Communications, 14, Article No. 7378. https://doi.org/10.1038/s41467-023-43266-3
|
[31]
|
Ji, G., Tang, Q., Zhu, S., Zhu, J., Ye, P., Xia, S. and Wu, X. (2023) StAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies. Genomics, Proteomics & Bioinformatics, 21, 601-618. https://doi.org/10.1016/j.gpb.2023.01.003
|
[32]
|
Imada, E.L., Wilks, C., Langmead, B. and Marchionni, L. (2023) REPAC: Analysis of Alternative Polyadenylation from RNA-Sequencing Data. Genome Biology, 24, Article No. 22. https://doi.org/10.1186/s13059-023-02865-5
|
[33]
|
Wang, G., Xie, Z., Su, J., Chen, M., Du, Y., Gao, Q., Zhang, G., Zhang, H., Chen, X., Liu, H., Han, L. and Ye, Y. (2022) Characterization of Immune-Related Alternative Polyadenylation Events in Cancer Immunotherapy. Cancer Research, 82, 3474-3485. https://doi.org/10.1158/0008-5472.CAN-22-1417
|
[34]
|
Linder, J., Koplik, S.E., Kundaje, A. and Seelig, G. (2022) Deciphering the Impact of Genetic Variation on Human Polyadenylation Using APARENT2. Genome Biology, 23, Article No. 232. https://doi.org/10.1186/s13059-022-02799-4
|
[35]
|
Li, Z., Li, Y., Zhang, B., Li, Y., Long, Y., Zhou, J., Zou, X., Zhang, M., Hu, Y., Chen, W. and Gao, X. (2022) DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. Genomics, Proteomics & Bioinformatics, 20, 483-495. https://doi.org/10.1016/j.gpb.2020.05.004
|
[36]
|
Ye, C., Zhao, D., Ye, W., Wu, X., Ji, G., Li, Q.Q. and Lin, J. (2021) QuantifyPoly(A): Reshaping Alternative Polyadenylation Landscapes of Eukaryotes with Weighted Density Peak Clustering. Briefings in Bioinformatics, 22, bbab268. https://doi.org/10.1093/bib/bbab268
|
[37]
|
Lusk, R., Stene, E., Banaei-Kashani, F., Tabakoff, B., Kechris, K. and Saba, L.M. (2021) Aptardi Predicts Polyadenylation Sites in Sample-Specific Transcriptomes Using High-Throughput RNA Sequencing and DNA Sequence. Nature Communications, 12, Article No. 1652. https://doi.org/10.1038/s41467-021-21894-x
|
[38]
|
Lin, E., Liu, X., Liu, Y., Zhang, Z., Xie, L., Tian, K., Liu, J. and Yu, Y. (2021) Roles of the Dynamic Tumor Immune Microenvironment in the Individualized Treatment of Advanced Clear Cell Renal Cell Carcinoma. Frontiers in Immunology, 12, Article 653358. https://doi.org/10.3389/fimmu.2021.653358
|
[39]
|
Li, G.W., Nan, F., Yuan, G.H., Liu, C.X., Liu, X., Chen, L.L., Tian, B. and Yang, L. (2021) SCAPTURE: A Deep Learning-Embedded Pipeline That Captures Polyadenylation Information from 3’ Tag-Based RNA-Seq of Single Cells. Genome Biology, 22, Article No. 221. https://doi.org/10.1186/s13059-021-02437-5
|
[40]
|
Gao, Y., Li, L., Amos, C.I. and Li, W. (2021) Analysis of Alternative Polyadenylation from Single-Cell RNA-Seq Using ScDaPars Reveals Cell Subpopulations Invisible to Gene Expression. Genome Research, 31, 1856-1866. https://doi.org/10.1101/gr.271346.120
|
[41]
|
Ma, X., Cheng, S., Ding, R., Zhao, Z., Zou, X., Guang, S., Wang, Q., Jing, H., Yu, C., Ni, T. and Li, L. (2023) IpaQTL-Atlas: An Atlas of Intronic Polyadenylation Quantitative Trait Loci across Human Tissues. Nucleic Acids Research, 51, D1046-D1052. https://doi.org/10.1093/nar/gkac736
|
[42]
|
Zhu, S., Lian, Q., Ye, W., Qin, W., Wu, Z., Ji, G. and Wu, X. (2022) ScAPAdb: A Comprehensive Database of Alternative Polyadenylation at Single-Cell Resolution. Nucleic Acids Research, 50, D365-D370. https://doi.org/10.1093/nar/gkab795
|
[43]
|
Yang, X., Tong, Y., Liu, G., Yuan, J. and Yang, Y. (2022) ScAPAatlas: An Atlas of Alternative Polyadenylation across Cell Types in Human and Mouse. Nucleic Acids Research, 50, D356-D364. https://doi.org/10.1093/nar/gkab917
|
[44]
|
Cui, Y., Peng, F., Wang, D., Li, Y., Li, J.S., Li, L. and Li, W. (2022) 3’aQTL-Atlas: An Atlas of 3’UTR Alternative Polyadenylation Quantitative Trait Loci across Human Normal Tissues. Nucleic Acids Research, 50, D39-D45. https://doi.org/10.1093/nar/gkab740
|
[45]
|
Lin, Y., Li, Z., Ozsolak, F., Kim, S.W., Arango-Argoty, G., Liu, T.T., Tenenbaum, S.A., Bailey, T., Monaghan, A.P., Milos, P.M. and John, B. (2012) An In-Depth Map of Polyadenylation Sites in Cancer. Nucleic Acids Research, 40, 8460-8471. https://doi.org/10.1093/nar/gks637
|
[46]
|
Xiang, Y., Ye, Y., Lou, Y., Yang, Y., Cai, C., Zhang, Z., Mills, T., Chen, N.Y., Kim, Y., Muge Ozguc, F., Diao, L., Karmouty-Quintana, H., Xia, Y., Kellems, R.E., Chen, Z., Blackburn, M.R., Yoo, S.H., Shyu, A.B., Mills, G.B. and Han, L. (2018) Comprehensive Characterization of Alternative Polyadenylation in Human Cancer. Journal of the National Cancer Institute, 110, 379-389. https://doi.org/10.1093/jnci/djx223
|
[47]
|
Di Giammartino, D.C., Li, W., Ogami, K., Yashinskie, J.J., Hoque, M., Tian, B. and Manley, J.L. (2014) RBBP6 Isoforms Regulate the Human Polyadenylation Machinery and Modulate Expression of MRNAs with AU-Rich 3’ UTRs. Genes & Development, 28, 2248-2260. https://doi.org/10.1101/gad.245787.114
|
[48]
|
Fu, Y., Chen, L., Chen, C., Ge, Y., Kang, M., Song, Z., Li, J., Feng, Y., Huo, Z., He, G., Hou, M., Chen, S. and Xu, A. (2018) Crosstalk between Alternative Polyadenylation and MiRNAs in the Regulation of Protein Translational Efficiency. Genome Research, 28, 1656-1663. https://doi.org/10.1101/gr.231506.117
|
[49]
|
Chen, L., Dong, W., Zhou, M., Yang, C., Xiong, M., Kazobinka, G., Chen, Z., Xing, Y. and Hou, T. (2023) PABPN1 Regulates MRNA Alternative Polyadenylation to Inhibit Bladder Cancer Progression. Cell & Bioscience, 13, Article No. 45. https://doi.org/10.1186/s13578-023-00997-6
|
[50]
|
Xiong, M., Liu, C., Li, W., Jiang, H., Long, W., Zhou, M., Yang, C., Kazobinka, G., Sun, Y., Zhao, J. and Hou, T. (2023) PABPN1 Promotes Clear Cell Renal Cell Carcinoma Progression by Suppressing the Alternative Polyadenylation of SGPL1 and CREG1. Carcinogenesis, 44, 576-586. https://doi.org/10.1093/carcin/bgad049
|
[51]
|
Tan, Y., Zheng, T., Su, Z., Chen, M., Chen, S., Zhang, R., Wang, R., Li, K. and Na, N. (2023) Alternative Polyadenylation Reprogramming of MORC2 Induced by NUDT21 Loss Promotes KIRC Carcinogenesis. JCI Insight, 8, e162893. https://doi.org/10.1172/jci.insight.162893
|
[52]
|
Witkowski, M.T., Lee, S., Wang, E., Lee, A.K., Talbot, A., Ma, C., Tsopoulidis, N., Brumbaugh, J., Zhao, Y., Roberts, K.G., Hogg, S.J., Nomikou, S., Ghebrechristos, Y.E., Thandapani, P., Mullighan, C.G., Hochedlinger, K., Chen, W., Abdel-Wahab, O., Eyquem, J. and Aifantis, I. (2022) NUDT21 Limits CD19 Levels through Alternative MRNA Polyadenylation in B Cell Acute Lymphoblastic Leukemia. Nature Immunology, 23, 1424-1432. https://doi.org/10.1038/s41590-022-01314-y
|
[53]
|
Guo, Q., Wang, H., Duan, J., Luo, W., Zhao, R., Shen, Y., Wang, B., Tao, S., Sun, Y., Ye, Q., Bi, X., Yuan, H., Wu, Q., Lobie, P.E., Zhu, T., Tan, S., Huang, X. and Wu, Z. (2022) An Alternatively Spliced P62 Isoform Confers Resistance to Chemotherapy in Breast Cancer. Cancer Research, 82, 4001-4015. https://doi.org/10.1158/0008-5472.CAN-22-0909
|