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Regunath K, Fomin V, Wang P, Liu Z, Hoque M, Tian B, Rabadan R, Prives C. Systematic characterization of p53-regulated long non-coding RNAs across human cancers reveals remarkable heterogeneity among different tumor types. Mol Cancer Res. 2024 Feb 23;. doi: 10.1158/1541-7786.MCR-23-0295. [Epub ahead of print] PubMed PMID: 38393317.
Cui Y, Wang L, Ding Q, Shin J, Cassel J, Liu Q, Salvino JM, Tian B. Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation. Nat Commun. 2023 Aug 1;14(1):4480. doi: 10.1038/s41467-023-39793-8. PubMed PMID: 37528120; PubMed Central PMCID: PMC10394034.
Zhang Q, Tian B. The emerging theme of 3'UTR mRNA isoform regulation in reprogramming of cell metabolism. Biochem Soc Trans. 2023 Jun 28;51(3):1111-1119. doi: 10.1042/BST20221128. Review. PubMed PMID: 37171086; PubMed Central PMCID: PMC10771799.
Ou L, Liu S, Wang H, Guo Y, Guan L, Shen L, Luo R, Elder DE, Huang AC, Karakousis G, Miura J, Mitchell T, Schuchter L, Amaravadi R, Flowers A, Mou H, Yi F, Guo W, Ko J, Chen Q, Tian B, Herlyn M, Xu X. Patient-derived melanoma organoid models facilitate the assessment of immunotherapies. EBioMedicine. 2023 Jun;92:104614. doi: 10.1016/j.ebiom.2023.104614. Epub 2023 May 23. PubMed PMID: 37229906; PubMed Central PMCID: PMC10277922.
Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel). 2023 Mar 24;15(7). doi: 10.3390/cancers15071958. Review. PubMed PMID: 37046619; PubMed Central PMCID: PMC10093138.
Pieraccioli M, Caggiano C, Mignini L, Zhong C, Babini G, Lattanzio R, Di Stasi S, Tian B, Sette C, Bielli P. The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer. Nat Struct Mol Biol. 2022 Nov;29(11):1101-1112. doi: 10.1038/s41594-022-00853-0. Epub 2022 Nov 7. PubMed PMID: 36344846; PubMed Central PMCID: PMC9872553.
Caggiano C, Pieraccioli M, Pitolli C, Babini G, Zheng D, Tian B, Bielli P, Sette C. The androgen receptor couples promoter recruitment of RNA processing factors to regulation of alternative polyadenylation at the 3' end of transcripts. Nucleic Acids Res. 2022 Sep 23;50(17):9780-9796. doi: 10.1093/nar/gkac737. PubMed PMID: 36043441; PubMed Central PMCID: PMC9508809.
Hao X, Shiromoto Y, Sakurai M, Towers M, Zhang Q, Wu S, Havas A, Wang L, Berger S, Adams PD, Tian B, Nishikura K, Kossenkov AV, Liu P, Zhang R. ADAR1 downregulation by autophagy drives senescence independently of RNA editing by enhancing p16(INK4a) levels. Nat Cell Biol. 2022 Aug;24(8):1202-1210. doi: 10.1038/s41556-022-00959-z. Epub 2022 Jul 18. PubMed PMID: 35851616; PubMed Central PMCID: PMC9757154.
Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA. 2022 Jun;28(6):878-894. doi: 10.1261/rna.079104.122. Epub 2022 Mar 29. PubMed PMID: 35351812; PubMed Central PMCID: PMC9074902.
Guvenek A, Shin J, De Filippis L, Zheng D, Wang W, Pang ZP, Tian B. Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs. Front Genet. 2022;13:840369. doi: 10.3389/fgene.2022.840369. eCollection 2022. PubMed PMID: 35664307; PubMed Central PMCID: PMC9159357.
Shin J, Ding Q, Wang L, Cui Y, Baljinnyam E, Guvenek A, Tian B. CRISPRpas: programmable regulation of alternative polyadenylation by dCas9. Nucleic Acids Res. 2022 Mar 21;50(5):e25. doi: 10.1093/nar/gkab519. PubMed PMID: 34244761; PubMed Central PMCID: PMC8934653.
Davis AG, Johnson DT, Zheng D, Wang R, Jayne ND, Liu M, Shin J, Wang L, Stoner SA, Zhou JH, Ball ED, Tian B, Zhang DE. Alternative polyadenylation dysregulation contributes to the differentiation block of acute myeloid leukemia. Blood. 2022 Jan 20;139(3):424-438. doi: 10.1182/blood.2020005693. PubMed PMID: 34482400; PubMed Central PMCID: PMC8777198.
Li WV, Zheng D, Wang R, Tian B. MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads. Genome Biol. 2021 Aug 10;22(1):222. doi: 10.1186/s13059-021-02429-5. PubMed PMID: 34376236; PubMed Central PMCID: PMC8356463.
Li GW, Nan F, Yuan GH, Liu CX, Liu X, Chen LL, Tian B, Yang L. SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells. Genome Biol. 2021 Aug 10;22(1):221. doi: 10.1186/s13059-021-02437-5. PubMed PMID: 34376223; PubMed Central PMCID: PMC8353616.
Richard P, Feng S, Tsai YL, Li W, Rinchetti P, Muhith U, Irizarry-Cole J, Stolz K, Sanz LA, Hartono S, Hoque M, Tadesse S, Seitz H, Lotti F, Hirano M, Chédin F, Tian B, Manley JL. SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation. Autophagy. 2021 Aug;17(8):1889-1906. doi: 10.1080/15548627.2020.1796292. Epub 2020 Aug 7. PubMed PMID: 32686621; PubMed Central PMCID: PMC8386630.
Cheng LC, Zheng D, Zhang Q, Guvenek A, Cheng H, Tian B. Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum. Cell Rep. 2021 Jul 20;36(3):109407. doi: 10.1016/j.celrep.2021.109407. PubMed PMID: 34289366; PubMed Central PMCID: PMC8501909.
Shin J, Wang R, Tian B. Modulation of alternative cleavage and polyadenylation events by dCas9-mediated CRISPRpas. Methods Enzymol. 2021;655:459-482. doi: 10.1016/bs.mie.2021.04.016. Epub 2021 Jun 4. PubMed PMID: 34183133.
Davis AG, Einstein JM, Zheng D, Jayne ND, Fu XD, Tian B, Yeo GW, Zhang DE. A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. Blood Adv. 2021 Mar 9;5(5):1310-1323. doi: 10.1182/bloodadvances.2020002090. PubMed PMID: 33656539; PubMed Central PMCID: PMC7948294.
Tian B. Preface. Methods Enzymol. 2021;655:xix-xx. doi: 10.1016/S0076-6879(21)00309-8. PubMed PMID: 34183136.
Zheng D, Cho H, Wang W, Rambout X, Tian B, Maquat LE. 3'READS + RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association. RNA. 2020 Nov;26(11):1621-1636. doi: 10.1261/rna.076133.120. Epub 2020 Aug 12. PubMed PMID: 32796083; PubMed Central PMCID: PMC7566578.
Oka SI, Chin A, Park JY, Ikeda S, Mizushima W, Ralda G, Zhai P, Tong M, Byun J, Tang F, Einaga Y, Huang CY, Kashihara T, Zhao M, Nah J, Tian B, Hirabayashi Y, Yodoi J, Sadoshima J. Thioredoxin-1 maintains mitochondrial function via mechanistic target of rapamycin signalling in the heart. Cardiovasc Res. 2020 Aug 1;116(10):1742-1755. doi: 10.1093/cvr/cvz251. PubMed PMID: 31584633; PubMed Central PMCID: PMC7825501.
Cheng LC, Zheng D, Baljinnyam E, Sun F, Ogami K, Yeung PL, Hoque M, Lu CW, Manley JL, Tian B. Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation. Nat Commun. 2020 Jun 23;11(1):3182. doi: 10.1038/s41467-020-16959-2. PubMed PMID: 32576858; PubMed Central PMCID: PMC7311474.
Wang R, Tian B. APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms. Bioinformatics. 2020 Jun 1;36(12):3907-3909. doi: 10.1093/bioinformatics/btaa266. PubMed PMID: 32321166; PubMed Central PMCID: PMC7320624.
Tsai YL, Coady TH, Lu L, Zheng D, Alland I, Tian B, Shneider NA, Manley JL. ALS/FTD-associated protein FUS induces mitochondrial dysfunction by preferentially sequestering respiratory chain complex mRNAs. Genes Dev. 2020 Jun 1;34(11-12):785-805. doi: 10.1101/gad.335836.119. Epub 2020 May 7. PubMed PMID: 32381627; PubMed Central PMCID: PMC7263147.
Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, Zhang QC, Shen X. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature. 2020 Apr;580(7801):147-150. doi: 10.1038/s41586-020-2105-3. Epub 2020 Mar 11. PubMed PMID: 32238924.
Dai P, Wang X, Gou LT, Li ZT, Wen Z, Chen ZG, Hua MM, Zhong A, Wang L, Su H, Wan H, Qian K, Liao L, Li J, Tian B, Li D, Fu XD, Shi HJ, Zhou Y, Liu MF. A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis. Cell. 2019 Dec 12;179(7):1566-1581.e16. doi: 10.1016/j.cell.2019.11.022. PubMed PMID: 31835033; PubMed Central PMCID: PMC8139323.
Shin J, Cheng H, Tian B. New means to an end: mRNA export activity impacts alternative polyadenylation. Transcription. 2019 Aug-Oct;10(4-5):207-211. doi: 10.1080/21541264.2019.1658557. Epub 2019 Sep 2. PubMed PMID: 31474181; PubMed Central PMCID: PMC6948955.
Fischl H, Neve J, Wang Z, Patel R, Louey A, Tian B, Furger A. hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles. Nucleic Acids Res. 2019 Aug 22;47(14):7580-7591. doi: 10.1093/nar/gkz461. PubMed PMID: 31147722; PubMed Central PMCID: PMC6698646.
Hou L, Wang Y, Liu Y, Zhang N, Shamovsky I, Nudler E, Tian B, Dynlacht BD. Paf1C regulates RNA polymerase II progression by modulating elongation rate. Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14583-14592. doi: 10.1073/pnas.1904324116. Epub 2019 Jun 27. PubMed PMID: 31249142; PubMed Central PMCID: PMC6642404.
Nakamura M, Liu T, Husain S, Zhai P, Warren JS, Hsu CP, Matsuda T, Phiel CJ, Cox JE, Tian B, Li H, Sadoshima J. Glycogen Synthase Kinase-3α Promotes Fatty Acid Uptake and Lipotoxic Cardiomyopathy. Cell Metab. 2019 May 7;29(5):1119-1134.e12. doi: 10.1016/j.cmet.2019.01.005. Epub 2019 Feb 7. PubMed PMID: 30745182; PubMed Central PMCID: PMC6677269.
Fan J, Wang K, Du X, Wang J, Chen S, Wang Y, Shi M, Zhang L, Wu X, Zheng D, Wang C, Wang L, Tian B, Li G, Zhou Y, Cheng H. ALYREF links 3'-end processing to nuclear export of non-polyadenylated mRNAs. EMBO J. 2019 May 2;38(9). doi: 10.15252/embj.201899910. Epub 2019 Mar 11. PubMed PMID: 30858280; PubMed Central PMCID: PMC6484419.
Chen S, Wang R, Zheng D, Zhang H, Chang X, Wang K, Li W, Fan J, Tian B, Cheng H. The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export. Mol Cell. 2019 Apr 4;74(1):118-131.e7. doi: 10.1016/j.molcel.2019.01.026. Epub 2019 Feb 25. PubMed PMID: 30819645; PubMed Central PMCID: PMC6450743.
Wang R, Zheng D, Wei L, Ding Q, Tian B. Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes. Cell Rep. 2019 Mar 5;26(10):2766-2778.e6. doi: 10.1016/j.celrep.2019.02.049. PubMed PMID: 30840896; PubMed Central PMCID: PMC6428223.
Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Göppinger S, Probst HC, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S. Transcriptome 3'end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma. Nat Commun. 2018 Dec 14;9(1):5331. doi: 10.1038/s41467-018-07580-5. PubMed PMID: 30552333; PubMed Central PMCID: PMC6294251.
Fomin V, Richard P, Hoque M, Li C, Gu Z, Fissore-O'Leary M, Tian B, Prives C, Manley JL. The C9ORF72 Gene, Implicated in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, Encodes a Protein That Functions in Control of Endothelin and Glutamate Signaling. Mol Cell Biol. 2018 Nov 15;38(22). doi: 10.1128/MCB.00155-18. Print 2018 Nov 15. PubMed PMID: 30150298; PubMed Central PMCID: PMC6206455.
Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D, Rodrigue S, Tian B, Jacques PÉ, Bachand F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat Commun. 2018 Oct 19;9(1):4364. doi: 10.1038/s41467-018-06546-x. PubMed PMID: 30341288; PubMed Central PMCID: PMC6195540.
Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res. 2018 Oct;28(10):1427-1441. doi: 10.1101/gr.237826.118. Epub 2018 Aug 24. PubMed PMID: 30143597; PubMed Central PMCID: PMC6169888.
Guvenek A, Tian B. Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data. Quant Biol. 2018 Sep;6(3):253-266. doi: 10.1007/s40484-018-0148-3. Epub 2018 Sep 5. PubMed PMID: 31380142; PubMed Central PMCID: PMC6677405.
Zheng D, Wang R, Ding Q, Wang T, Xie B, Wei L, Zhong Z, Tian B. Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. Nat Commun. 2018 Jun 11;9(1):2268. doi: 10.1038/s41467-018-04730-7. PubMed PMID: 29891946; PubMed Central PMCID: PMC5995920.
Wang R, Nambiar R, Zheng D, Tian B. PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes. Nucleic Acids Res. 2018 Jan 4;46(D1):D315-D319. doi: 10.1093/nar/gkx1000. PubMed PMID: 29069441; PubMed Central PMCID: PMC5753232.
Fontes MM, Guvenek A, Kawaguchi R, Zheng D, Huang A, Ho VM, Chen PB, Liu X, O'Dell TJ, Coppola G, Tian B, Martin KC. Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation. Sci Rep. 2017 Dec 12;7(1):17377. doi: 10.1038/s41598-017-17407-w. PubMed PMID: 29234016; PubMed Central PMCID: PMC5727029.
Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell. 2017 Dec 7;68(5):913-925.e3. doi: 10.1016/j.molcel.2017.11.020. PubMed PMID: 29220656; PubMed Central PMCID: PMC5736309.
Liu X, Freitas J, Zheng D, Oliveira MS, Hoque M, Martins T, Henriques T, Tian B, Moreira A. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA. 2017 Dec;23(12):1807-1816. doi: 10.1261/rna.062661.117. Epub 2017 Aug 29. PubMed PMID: 28851752; PubMed Central PMCID: PMC5689002.
Liu X, Hoque M, Larochelle M, Lemay JF, Yurko N, Manley JL, Bachand F, Tian B. Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe. Genome Res. 2017 Oct;27(10):1685-1695. doi: 10.1101/gr.222331.117. Epub 2017 Sep 15. PubMed PMID: 28916539; PubMed Central PMCID: PMC5630032.
Shi M, Zhang H, Wu X, He Z, Wang L, Yin S, Tian B, Li G, Cheng H. ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo. Nucleic Acids Res. 2017 Sep 19;45(16):9640-9653. doi: 10.1093/nar/gkx597. PubMed PMID: 28934468; PubMed Central PMCID: PMC5766156.
Li W, Li W, Laishram RS, Hoque M, Ji Z, Tian B, Anderson RA. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases. Nucleic Acids Res. 2017 Sep 6;45(15):8930-8942. doi: 10.1093/nar/gkx560. PubMed PMID: 28911096; PubMed Central PMCID: PMC5587728.
Vest KE, Phillips BL, Banerjee A, Apponi LH, Dammer EB, Xu W, Zheng D, Yu J, Tian B, Pavlath GK, Corbett AH. Novel mouse models of oculopharyngeal muscular dystrophy (OPMD) reveal early onset mitochondrial defects and suggest loss of PABPN1 may contribute to pathology. Hum Mol Genet. 2017 Sep 1;26(17):3235-3252. doi: 10.1093/hmg/ddx206. PubMed PMID: 28575395; PubMed Central PMCID: PMC5886286.
Hoque M, Park JY, Chang YJ, Luchessi AD, Cambiaghi TD, Shamanna R, Hanauske-Abel HM, Holland B, Pe'ery T, Tian B, Mathews MB. Regulation of gene expression by translation factor eIF5A: Hypusine-modified eIF5A enhances nonsense-mediated mRNA decay in human cells. Translation (Austin). 2017;5(2):e1366294. doi: 10.1080/21690731.2017.1366294. eCollection 2017. PubMed PMID: 29034140; PubMed Central PMCID: PMC5630042.
Ogami K, Richard P, Chen Y, Hoque M, Li W, Moresco JJ, Yates JR 3rd, Tian B, Manley JL. An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev. 2017 Jun 15;31(12):1257-1271. doi: 10.1101/gad.302604.117. Epub 2017 Jul 21. PubMed PMID: 28733371; PubMed Central PMCID: PMC5558927.
Elbarbary RA, Miyoshi K, Myers JR, Du P, Ashton JM, Tian B, Maquat LE. Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G(1)/S phase transition. Science. 2017 May 26;356(6340):859-862. doi: 10.1126/science.aai9372. PubMed PMID: 28546213; PubMed Central PMCID: PMC5551500.
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