Publications from Bin Tian Laboratory

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2013
Tian B, Manley JL.(2013). Alternative Cleavage and Polyadenylation: the long and short of it. Trends Biochem Sci. In press. PubMed Devany E, Zhang X, Park JY, Tian B, Kleiman FE. (2013). Positive and negative feedback loops in the p53 and mRNA 3' processing pathways.(2013). Proc Natl Acad Sci USA. 110:3351-6. Matsushima S, Kuroda J, Ago T, Zhai P, Park JY, Xie LH, Tian B, Sadoshima J. (2013). Increased Oxidative Stress in the Nucleus Caused by Nox4 Mediates Oxidation of HDAC4 and Cardiac Hypertrophy. Circ Res. 112:651-63. Hoque M*, Ji Z*, Zheng D, Luo W, Li W, You B, Park JY, Yehia G, Tian B. (2013). Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat Methods. 10:133-9. PubMed, Data.
2012
Larsson O, Tian B, Sonenberg N. (2012). Toward a Genome-Wide Landscape of Translational Control. Cold Spring Harb Perspect Biol. doi: 10.1101/cshperspect.a012302. Bravo C, Kudej RK, Yuan C, Yoon S, Ge H, Park JY, Tian B, Stanley WC, Vatner SF, Vatner DE, Yan L. (2012). Metabolomic Analysis of Two Different Models of Delayed Preconditioning. J Mol Cell Cardiol. In press. Li W*, Yeh HJ*, Shankarling GS, Ji Z, Tian B, Macdonald CC. (2012). The tCstF-64 Polyadenylation Protein Controls Genome Expression in Testis. PLoS ONE. 7:e48373. Yan L, Park JY, Dillinger JG, De Lorenzo MS, Yuan C, Lai L, Wang C, Ho D, Tian B, Stanley WC, Auwerx J, Vatner DE, Vatner SF. (2012). Common Mechanisms for Calorie Restriction and AC5 Knockout Models of Longevity. Aging Cell. 11:1110-20. Henriques T, Ji Z, Tan-Wong SM, Carmo AM, Tian B, Proudfoot NJ, Moreira A. (2012). Transcription termination between polo and snap, two closely spaced tandem genes of D. melanogaster. Transcription. 3:198-212. Yin J, Liang Y, Park JY, Chen D, Xiao Y, Xiao Q, Liu Z, Jiang B, Fu Y, Huang Y, Liu Y, Yan J, Zhu M, Yang Z, Gao P, Tian B, Li D, Wang G. (2012). The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation. Genes Dev. 26:2192-205. Lee JE, Lee JY, Trembly J, Wilusz J, Tian B, Wilusz CJ. (2012). The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts. PLoS Genetics. 8:e1002901. Neff AT, Lee JY, Wilusz J, Tian B, Wilusz CJ. (2012). Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res. 22:1457-67. Xie LH, Shanmugam M, Park JY, Zhao Z, Wen H, Tian B, Periasamy M, Babu GJ. (2012). Ablation of sarcolipin results in atrial remodeling. Am J Physiol Cell Physiol. 302:C1762-71. Haenni S*, Ji Z*, Hoque M, Rust N, Sharpe H, Eberhard R, Browne C, Hengartner MO, Mellor J, Tian B, Furger A. (2012). Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. Nucleic Acids Res. 40:6304-18. PubMed. Oka SI, Zhai P, Alcendor R, Park JY, Tian B, Sadoshima J. (2012). Suppression of ERR targets by a PPARalpha/Sirt1 complex in the failing heart. Cell Cycle. 11:856-64. Zhao X, Park J, Ho D, Gao S, Yan L, Ge H, Ilsmaa S, Lin L, Tian B, Vatner DE, Graham RM, Vatner SF. (2012). Cardiomyocyte Overexpression of the alpha1A-Adrenergic Receptor in the Rat Phenocopies Second But Not First Window Preconditioning. Am J Physiol Heart Circ Physiol. 302:H1614-24. Huang Y, Li W, Yao X, Lin Q, Yin J, Heiner M, Tian B, Hui J, Wang G. (2012). Mediator Complex Regulates Alternative mRNA Processing via the Med23 Subunit. Mol Cell. 45:459-469. Freed-Pastor WA, Mizuno H, Zhao X, Langerød A, Chicas A, Li W, Polotskaia A, Bissell MJ, Tian B, Lowe SW, Dale AB, Levine AJ, Bargonetti J, Prives C. (2012). Mutant p53 Disrupts Mammary Acinar Morphogenesis via the Sterol Biosynthesis Pathway. Cell. 148:244-58. Li W, Laishram RS, Ji Z, Barlow CA, Tian B, Anderson RA. (2012). Star-PAP Control of BIK Expression and Apoptosis is Regulated by Nuclear PIPKI-alpha and PKC-delta Signaling. Mol Cell. 45:25-37.
2011
Oka S, Alcendor R, Zhai P, Park JY, Shao D, Cho J, Yamamoto T, Tian B, Sadoshima J. (2011). PPARalpha-Sirt1 complex mediates cardiac hypertrophy and failure through suppression of the ERR transcriptional pathway. Cell Metab. 14:598-611. Ji Z*, Luo W*, Li W, Hoque M, Pan Z, Zhao Y, Tian B. (2011). Transcriptional activity regulates alternative cleavage and polyadenylation. Mol Syst Biol. 7:534. Featured Article. Tian B, Graber JH. (2011). Signals for Pre-mRNA Cleavage and Polyadenylation. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna.116. WIRES RNA. Park JY, Li W, Zheng D, Zhai P, Zhao Y, Matsuda T, Vatner SF, Sadoshima J, Tian B. (2011). Comparative analysis of mRNA isoform expression in cardiac hypertrophy and development reveals multiple post-transcriptional regulatory modules. PLoS ONE 6(7): e22391. Open Access. Qiu H, Lizano P, Laure L, Sui X, Rashed E, Park JY, Hong C, Gao S, Holle E, Morin D, Dhar SK, Wagner T, Berdeaux A, Tian B, Vatner SF, Depre C. (2011). H11 Kinase/Heat Shock Protein 22 Deletion Impairs Both Nuclear and Mitochondrial Functions of STAT3 and Accelerates the Transition Into Heart Failure on Cardiac Overload. Circulation. 124:406-15. Usui S, Maejima Y, Pain J, Hong C, Cho J, Park JY, Zablocki D, Tian B, Glass DJ, Sadoshima J. (2011). Endogenous Muscle Atrophy F-Box Mediates Pressure Overload-Induced Cardiac Hypertrophy Through Regulation of Nuclear Factor-{kappa}B. Circ Res. 109:161-71. Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB. (2011). The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res. 39:1485-1500. Zhao Q, Beck AJ, Vitale JM, Schneider JS, Gao S, Chang C, Elson G, Leibovich SJ, Park JY, Tian B, Nam HS, Fraidenraich D. (2011). Developmental ablation of Id1 and Id3 genes in the vasculature leads to postnatal cardiac phenotypes. Dev Biol. 349:53-64.
2010
Depre C, Park JY, Shen YT, Zhao X, Qiu H, Yan L, Tian B, Vatner SF, Vatner DE. (2010). Molecular Mechanisms Mediating Preconditioning Following Chronic Ischemia Differ from those in Classical Second Window. Am J Physiol Heart Circ Physiol. 299:H752-62. Lee JE*, Lee JY*, Wilusz J, Tian B, Wilusz CJ. (2010). Systematic Analysis of Cis-Elements in Unstable mRNAs Demonstrates that CUGBP1 Is a Key Regulator of mRNA Decay in Muscle Cells. PLoS One. 5:e11201. Open Access. Newnham CM, Hall-Pogar T, Liang S, Wu J, Tian B, Hu J, Lutz CS. (2010). Alternative polyadenylation of MeCP2: Influence of cis-acting elements and trans-acting factors. RNA Biol. 7:3. Nunes NM, Li W, Tian B, Furger A. (2010). A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence. EMBO J. 29:1523-36.
2009
Ji Z, Tian B. (2009). Reprogramming of 3' Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types. PLoS ONE 4(12): e8419. Open Access. Ji Z*, Lee JY*, Pan Z*, Jiang B, Tian B. (2009). Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl. Acad. Sci. U. S. A. 106:7028-33. PubMed, Highlighted by Nature Review Genetics, Comments by Nature Journal Club. *Equal contribution.
2008
Matsuda T, Zhai P, Maejima Y, Hong C, Gao S, Tian B, Goto K, Takagi H, Tamamori-Adachi M, Kitajima S, Sadoshima J. (2008). Distinct roles of GSK-3{alpha} and GSK-3{beta} phosphorylation in the heart under pressure overload. Proc. Natl. Acad. Sci. U. S. A. 105:20900-5. Shen Y-T, Depre C, Yan L, Park JY, Tian B, Jain K, Chen L, Zhang Y, Kudej RK, Zhao X, Sadoshima J, Vatner DE, Vatner SF. (2008). Repetitive Ischemia Induces a Novel Window of Ischemic Preconditioning. Circulation. 118:1961-9. Lee JY, Ji Z, Tian B. (2008). Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3' end of genes. Nucleic Acids Res. 36:5581-90. PubMed. Tian B. (2008). Alternative Polyadenylation in the Human Genome: Evolution. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd. DOI: 10.1002/9780470015902.a0020768. http://www.els.net. Qiu H, Dai H, Jain K, Shah R, Hong C, Pain J, Tian B, Vatner DE, Vatner SF, Depre C. (2008). Characterization of a novel cardiac isoform of the cell cycle-related kinase that is regulated during heart failure. J. Biol. Chem. 283:22157-65. Khaladkar M, Liu J, Wen D, Wang JTL, Tian B. (2008). Mining Structural Elements in Human and Mouse Untranslated Regions of mRNAs using Structure-based Alignment. BMC Genomics 9:189. PubMed. Lee JY, Park JY, Tian B. (2008). Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags and Trace. Methods Mol. Biol. 419:23-37. PubMed.
2007
Dass B, Tardif S, Park JY, Tian B, Weitlauf HM, Hess RA, Carnes K, Griswold MD, Small CL, Macdonald CC. (2007) Loss of polyadenylation protein tCstF-64 causes spermatogenic defects and male infertility. Proc. Natl. Acad. Sci. U.S.A. 104:20374-9 Terskiy A, Wannemacher KM, Yadav PN, Tsai M, Tian B, Howells RD. (2007). Search of the human proteome for endomorphin-1 and endomorphin-2 precursor proteins. Life Sciences. 81:1593-601. Young TM, Tsai M, Tian B, Mathews MB, Pe'ery T. (2007). Cellular mRNA Activates Transcription Elongation by Displacing 7SK RNA. PLoS ONE. 2(10):e1010. Kirchner S, McDaniel NK, Sugiura SH, Soteropoulos P, Tian B, Fletcher JW, Ferraris RP. (2007). Salmonid microarrays identify intestinal genes that reliably monitor P-deficiency in rainbow trout aquaculture. Anim. Genet. 38:319-31. Khaladkar M, Bellofatto V, Wang JTL, Tian B, Shapiro BA. (2007). RADAR: A Web Server for RNA Data Analysis and Research. Nucleic Acids Res. 35 (Web Server issue): W300-4. Alcendor RR, Gao S, Zhai P, Zablocki D, Holle E, Yu X, Tian B, Wagner T, Vatner SF, Sadoshima J. (2007). Sirt1 Regulates Aging and Resistance to Oxidative Stress in the Heart. Circ. Res. 100:1512-21. Qiu H, Tian B, Resuello RG, Natividad FF, Peppas A, Shen Y-T, Vatner DE, Vatner SF, Depre C. (2007). Gender-specific regulation of gene expression in the aging monkey aorta. Physiol. Genomics. 29:169-80. Lu B, Yadav S, Shah PG, Liu T, Tian B, Pukszta S, Villaluna N, Kutejova E, Newlon CS, Herzog JH, Suzuki CK. (2007). Roles for the human ATP-dependent Lon protease in mitochondrial DNA maintenance. J. Biol. Chem. 282:17363-74. Tian B, Pan Z, Lee JY (2007). Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res. 17:156-65. PubMed, Rated "Must Read" by Faculty of 1000. Lee JY, Yeh I, Park JY, Tian B. (2007). PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. D116-20. PubMed.
2006
D'mello V, Lee JY, Macdonald CC, Tian B. (2006). Alternative mRNA Polyadenylation Can Potentially Affect Detection of Gene Expression by Affymetrix GeneChip((R)) Arrays. Appl. Bioinformatics 5:249-53. PubMed, Rated "Must Read" by Faculty of 1000. Ago T, Yeh I, Yamamoto M, Schinke-Braun M, Brown JA, Tian B, Sadoshima J. (2006). Thioredoxin1 Upregulates Mitochondrial Proteins Related to Oxidative Phosphorylation and TCA Cycle in the Heart. Antioxid. Redox. Signal. 8:1635-50. Cheng Y, Miura RM, Tian B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5. PubMed. Usui S, Yeh I, Tian B, Sadoshima J. (2006). Global changes in gene expression during cardiac hypertrophy: A new direction of cardiac signaling research. J. Mol. Cell. Cardiol. 41:219-22. Lasfar A, Lewis-Antes A, Smirnov SV, Anantha S, Abushahba W, Tian B, Reuhl K, Dickensheets H, Sheikh F, Donnelly RP, Raveche E, Kotenko SV. (2006). Characterization of the Mouse IFN-lambda Ligand-Receptor System: IFN-lambdas Exhibit Antitumor Activity against B16 Melanoma. Cancer Res. 66:4468-77. Pan Z, Zhang H, Hague LK, Lee JY, Lutz CS, and Tian B. (2006). An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene 366:325-334. PubMed.
2005
Tian B, Mukhopadhyay R, Mathews MB. (2005). Polymorphic CUG repeats in human mRNAs and their effects on gene expression. RNA Biol. 2:149-156. PubMed. Zhang H, Lee JY, Tian B. (2005). Biased alternative polyadenylation in human tissues. Genome Biol. 6:R100. PubMed. Hu J, Lutz CS, Wilusz J, Tian B. (2005). Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11:1485-1493. PubMed. Duttagupta1 R, Tian B, Wilusz CJ, Khounh DT, Soteropoulos P, Ouyang M, Dougherty JP, Peltz SW. (2005). Global Analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol. Cell. Biol. 25:5499-5513. Ondrovicova G, Liu T, Singh K, Tian B, Li H, Gakh O, Perecko D, Janata J, Granoti Z, Orlyi J, Kutejova E, Suzuki CK. (2005). Cleavage site selection within a folded substrate by the ATP-dependent LON protease. J. Biol. Chem. 280:25103-25110. Hall-Pogar T, Zhang H, Tian B, Lutz CS. (2005). Alternative polyadenylation of COX-2: a mechanism for gene regulation. Nucleic Acids Res. 33:2565-2579. Liu J, Wang TL, Hu J, Tian B. (2005). A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 6:89. PubMed. Hoque M, Tian B, Mathews MB, Pe'ery T. (2005). Granulin and granulin repeats interact with the Tat:P-TEFb complexand inhibit tat transactivation. J. Biol. Chem. 280:13648-13657. Netterwald J, Yang S, Wang W, Ghanny S, Cody M, Soteropoulos P, Tian B, Dunn W, Liu F, Zhu H. (2005). Two VRS Elements in the Human Cytomegalovirus Major Immediate-Early Promoter/Enhancer Are Important for Viral Replication. J. Virol. 79:5035-5046. Tian B, Hu J, Zhang H, Lutz CS. (2005). A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33:201-212. PubMed, Rated "Must Read" by Faculty of 1000. Zhang H, Hu J, Recce M, Tian B. (2005). PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. D116-20. PubMed.
2004
Tian B, Bevilacqua PC, Diegelman-Parente A, Mathews MB. (2004). The double-stranded RNA-binding motif: Interference and much more. Nat. Rev. Mol. Cell Biol. 5:1013-1023. PubMed. Toruner GA, Ulger C, Alkan M, Galante AT, Rinaggio J, Wilk R, Tian B, Soteropoulos P, Hameed MR, Schwalb MN, Dermody JJ. (2004). Association between gene expression profile and tumor invasion in oral squamous cell carcinoma. Cancer Genet. and Cytogenet. 154:27-35. Lo JF, Hayashi M, Kim SW, Tian B, Huang JF, Fearns C, Takayama S, Zapata JM, Yang Y, Lee JD. (2004). Tid1, a cochaperone of the heat shock 70 protein and the mammalian counterpart of the Drosophila tumor suppressor l(2)tid, is critical for early embryonic development and cell survival. Mol. Cell. Biol. 24:2226-2236. Dai H, Tian B, Zhao D, Leung A, Smith S, Wan J, Yao X. (2004). Dynamic integration of gene annotation and its application to microarray analysis. J. Bioinform. Comput. Biol. 1:627-645.
Bin Tian's earlier papers
Tian B, Mathews MB. (2003). Phylogenetics and functions of the double-stranded RNA-binding motif: a genomic survey. Prog. Nucleic Acid Res. Mol. Biol. 74:123-158. PubMed. Bonaventure P, Guo H, Tian B, Liu X, Bittner A, Roland B, Salunga R, Ma XJ, Kamme F, Meurers B, Bakker M, Jurzak M, Leysen JE, Erlander MG. (2002). Nuclei and subnuclei gene expression profiling in mammalian brain. Brain Res. 943:38-47. Zhang F, Romano PR, Nagamura-Inoue T, Tian B, Dever TE, Mathews MB, Ozato K, Hinnebusch AG. (2001). Binding of double-stranded RNA to protein kinase PKR is required for dimerization and promotes critical autophosphorylation events in the activation loop. J. Biol. Chem. 276:24946-24958. Tian B, Mathews MB. (2001). Functional characterization of and cooperation between the double-stranded RNA-binding motifs of the protein kinase PKR. J. Biol. Chem. 276:9936-9944. PubMed. Taylor DR, Tian B, Romano PR, Hinnebusch AG, Lai MMC, Mathews MB. (2001). Hepatitis C virus envelope protein E2 does not inhibit PKR by simple competition with autophosphorylation sites in the RNA-binding domain. J. Virol. 75:1265-1273. Tian B, White RJ, Xia T, Welle S, Turner DH, Mathews MB, Thornton CA. (2000). Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR. RNA 6:79-87. PubMed.
*Equal contribution.

Last updated: 5/5/2013

Tian Lab @ UMDNJ/Rutgers - New Jersey Medical School