Recent studies that pertain to mRNA 3' end formation in plants

 

Research publications from the Hunt and Li laboratories

Elliott BJ, Dattaroy T, Meeks-Midkiff LR, Forbes KP, Hunt AG. 2003. An interaction between an Arabidopsis poly(A) polymerase and a homologue of the 100 kDa subunit of CPSF. Plant Mol Biol 51:373-84. (request a reprint)

Xu R, Ye X, Quinn Li Q. 2004. AtCPSF73-II gene encoding an Arabidopsis homolog of CPSF 73 kDa subunit is critical for early embryo development. Gene 324: 35-45. (request a reprint)

Addepalli B, Meeks LR, Forbes KP, Hunt AG. 2004. Novel alternative splicing of mRNAs encoding poly(A) polymerases in Arabidopsis. Biochimica Biophysica Acta 1679: 117-128. (request a reprint)

Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ. 2005. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol 138: 1457-1468. (request a reprint)

Forbes KP, Addepalli B, Hunt AG. 2006. An Arabidopsis Fip1 homologue interacts with RNA and provides conceptual links with a number of other polyadenylation factor subunits. J Biol Chem 281: 176-186. (request a reprint)

Delaney KJ, Xu R, Zhang J, Yun K-Y, Li QQ, Falcone DF, Hunt AG. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol 140: 1507-1521. (Open Access article)

Xu R, Zhao H, Dinkins RD, Cheng X, Carberry G, Li QQ. 2006. The 73 kD subunit of the Cleavage and Polyadenylation Specificity Factor (CPSF) Complex affects reproductive development in Arabidopsis. Plant Mol Biol 61: 799-815. (request a reprint)

Ji G, Zheng J, Shen Y, Wu X, Jiang R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ. 2007. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics 8:43. (request a reprint)

Addepalli B, Hunt AG. 2007. A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor. Nucl Acids Res 35: 4453-63. (Open Access article)

Ji G, Wu X, Zheng J, Shen Y, Li QQ. 2007. Modeling Plant mRNA Poly(A) sites: Software Design and Implementation. J Computational Theoretical Nanoscience 4: 1365-1368. (request a reprint)

Addepalli B, Hunt AG. 2008. The interaction between two Arabidopsis polyadenylation factor subunits involves an evolutionarily-conserved motif and has implications for the assembly and function of the polyadenylation complex. Protein Peptide Letters 15: 76-88. (request a reprint)

Xu R, Li QQ. 2008. Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system. Plant Methods 4: 4. (request a reprint)

Xing D, Zhao H, Xu R, Li QQ. 2008. Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time. Plant J 54, 899-910. (request a reprint)

Addepalli B, Hunt AG. 2008. Redox and heavy metal effects on the biochemical activities of an Arabidopsis polyadenylation factor subunit. Arch Biochem Biophys 473, 88-95. (request a reprint)

Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ. 2008. Genome level analysis of rice mRNA 3’-end processing signals and alternative polyadenylation. Nucl Acids Res 36, 3150-3161. (request a reprint)

Liang C, Liu Y, Liu L, Davis AC, Shen Y, Li QQ. 2008. ESTs with cDNA termini – previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics 179, 83093. (request a reprint)

Hunt AG, Xu R, Addepalli B, Rao S, Forbes KP, Meeks LR, Xing D, Mo M, Zhao H, Bandyopadhya A, Dampanaboina L, Marion A, Von Lanken C, Li QQ. 2008. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics 9, 220. (Open Access article)

Shen Y, Liu Y, Liu L, Liang C, Li QQ. 2008. Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii. Genetics 179, 167-76. (request a reprint)

Zhang J, Addepalli B, Yun KY, Hunt AG, Xu R, Rao S, Li QQ, Falcone DF. 2008. A Polyadenylation Factor Subunit Implicated in Regulating Oxidative Signaling in Arabidopsis thaliana. PLoS One 3, e2410. (Open Access Article)

Addepalli B, Hunt AG. 2008. Ribonuclease activity is a common property of Arabidopsis CCCH-containing zinc-finger proteins. FEBS Letters 582, 2577-2582. (request a reprint)

Xing D, Zhao H, Li QQ. 2008. Arabidopsis CLPS3, an Ortholog of Human Polyadenylation Factor CLP1, Functions in Gametophyte, Embryo and Post-Embryonic Development. Plant Physiology 148, 2059-2069. (Open Access Article)

Rao S, Dinkins RD, Hunt AG. 2009. Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biology 10, 51. (Open Access article)

Zhao H, Xing D, Li QQ. 2009. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiol. 151, 1546-1556. (Open Access article)

Meeks LR, Addepalli B, Hunt AG. 2009. Characterization of genes encoding poly(A) polymerases in plants: evidence for duplication and functional specialization. PLoS One 4, e8082. (Open Access article)

Bell SA, Hunt AG. 2010. The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett. 584, 1449-1454. (request a reprint)

Addepalli B, Limbach PA, Hunt AG. 2010. A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Lett. 584, 4408-4412. (request a reprint)

Zheng J, Xing D, Wu X, Shen Y, Kroll DM, Ji G, Li QQ. 2011. Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray. PLoS One 6, e14719. (Open Access article)

Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ, Hunt AG. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A.108, 12533-12538. (Open Access article)

Shen Y, Venu RC, Nobuta K, Wu X, Notibala V, Demirci C, Meyers BC, Wang GL, Ji G, Li QQ. 2011. Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res. 21, 1478-1486. (request a reprint)

Zhao H, Zheng J, Li QQ. 2011. A novel plant in vitro assay system for pre-mRNA cleavage during 3'-end formation. Plant Physiol. 157, 1546-1554. (Open Access article)

Recent reports from other laboratories that are relevant to mRNA 3' end formation in plants

Yao Y, Song L, Katz Y, Galili G. 2002. Cloning and characterization of Arabidopsis homologues of the animal CstF complex that regulates 3' mRNA cleavage and polyadenylation. J Exp Bot 53: 2277-22788.

Hasegawa K, Yukawa Y, Sugiura M. 2003. In vitro analysis of transcription initiation and termination from the Lhcb1 gene family in Nicotiana sylvestris: detection of transcription termination sites. Plant J 33: 1063-1072.

Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C. 2003. FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113: 777-87.

Quesada V, Macknight R, Dean C, Simpson GG. 2003. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J 22: 3142-3152.

Jin Y, Bian T. 2004. Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10: 1695-1697.

Henderson IR, Liu F, Drea S, Simpson GG, Dean C. 2005. An allelic series reveals essential roles for FY in plant development in addition to flowering-time control. Development 132: 3597-607.

Herr AJ, Molnar A, Jones A, Baulcombe DC. 2006. Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis. Proc Natl Acad Sci USA 103: 14994-14501.

Dong H, Deng Y, Chen J, Wang S, Peng S, Dai C, Fang Y, Shao J, Lou Y, Li D. 2007. An exploration of 3'-end processing signals and their tissue distribution in Oryza sativa. Gene 389:107-13.

Havukkala I, Vanderlooy S. 2007. On the reliable identification of plant sequences containing a polyadenylation site. J Comput Biol 14:1229-45. Genome Inform. 19, 73-82.

Koh CH, Wong L. 2007. Recognition of polyadenylation sites from Arabidopsis genomic sequences. GENOME INFORMATICS 2007.
Genome Informatics Series Vol. 19 (pp 73-82).

Manzano D, Marquardt S, Jones AM, Baurle I, Liu F, Dean C. 2009. Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing. Proc Natl Acad Sci U S A 106, 8772-8777.

Yang L, Wakasa Y, Kawakatsu T, Takaiwa F. 2009. The 3'-untranslated region of rice glutelin GluB-1 affects accumulation of heterologous protein in transgenic rice. Biotechnol. Lett. 31, 1625-1631.

Jang YH, Park HY, Kim SK, Lee JH, Suh MC, Chung YS, Paek KH, Kim JK. 2009. Survey for rice proteins interacting with OsFCA and OsFY proteins which are homologous to the Arabidopsis flowering time proteins, FCA and FY. Plant Cell Physiol. 50, 1479-1492.

Lin HH, Huang LF, Su HC, Jeng ST. 2009. Effects of the multiple polyadenylation signal AAUAAA on mRNA 3'-end formation and gene expression. Planta 230, 699-712.

Liu F, Marquardt S, Lister C, Swiezewski S, Dean C. 2010. Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327, 94-97.

Hornyik C, Terzi LC, Simpson GG. 2010. The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell 18, 203-213.

Xing A, Moon BP, Mills KM, Falco SC, Li Z. 2010. Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminators. Plant Biotechnol J. 8, 772-782.

Hornyik C, Duc C, Rataj K, Terzi LC, Simpson GG. 2010. Alternative polyadenylation of antisense RNAs and flowering time control. Biochem Soc Trans. 38, 1077-1081.

Simpson GG, Laurie RE, Dijkwel PP, Quesada V, Stockwell PA, Dean C, Macknight RC. 2010. Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA. Plant Cell 22, 3764-3777.

Mathew LG, Maloney B, Takeda N, Mason HS. 2011. Spurious polyadenylation of Norovirus Narita 104 capsid protein mRNA in transgenic plants. Plant Mol Biol. 75, 263-275.

Feng W, Jacob Y, Veley KM, Ding L, Yu X, Choe G, Michaels SD. 2011. Hypomorphic alleles reveal FCA-independent roles for FY in the regulation of FLOWERING LOCUS C. Plant Physiol. 155, 1425-1434.

Zubko E, Kunova A, Meyer P. 2011. Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region. PLoS One 6, e16769.

Sonmez C, Bäurle I, Magusin A, Dreos R, Laubinger S, Weigel D, Dean C. 2011. RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription. Proc Natl Acad Sci U S A 108, 8508-8513.

Reviews authored by our group

Hunt AG. 1994. Messenger RNA3' End Formation in Plants. Annu Rev Plant Physiol Plant Mol Biol 45: 47-60. (request a reprint)

Li Q, Hunt AG. 1997. The Polyadenylation of RNA in Plants. Plant Physiol 115:321-325.

Hunt AG. 2007. Messenger RNA 3’-end formation and the regulation of gene expression. in Regulation of Gene Expression in Plants - The Role of Transcript Structure and Processing, (C. Bassett, ed., Springer). ISBN: 978-0-387-35449-1. (request a reprint)

Hunt, AG. 2008. Messenger RNA 3’ End Formation in Plants. in Nuclear pre-mRNA Processing in Plants, Current Topics in Microbiology and Immunology 326 (M. Golovkin and ASN Reddy, eds., Springer-Verlag Berlin Heidelberg 2008), pp 151-177. (request a reprint)

Xing D, Li QQ. 2009. Alternative polyadenylation: a mechanism maximizing transcriptome diversity in higher eukaryotes. Plant Signal Behav. 4, 440-442. (request a reprint)

Xing D, Li QQ. 2011. Alternative polyadenylation and gene expression regulation in plants. Wiley Interdiscip Rev RNA 2, 445-458. (Open Access article)

Hunt AG. 2012. RNA regulatory elements and polyadenylation in plants. Front. Plant Sci. 2:109. (Open Access article)

Theses and other publications

Forbes KP, Characterization of plant polyadenylation trans-acting factors that modify poly(A) polymerase activity, Ph.D. Thesis, Plant Physiology, University of Kentucky 2005.

Meeks LR, Isolation and Characterization of the Four Arabidopsis thaliana Poly(A) Polymerase Genes, Ph.D. Thesis, Plant Physiology, University of Kentucky 2005.

Bandyopadhyay A, Analysis of the Arabidopsis Polyadenylation Factors PAP1, CstF64 and CstF77 and their characteristic inter-relationship, M.S. thesis, University of Kentucky 2009.

Dampanaboina L, Functional characterization of WD repeat proteins, AtCSTF50 and AtFY in cleavage and polyadenylation, Ph.D. thesis, Plant Physiology, University of Kentucky 2011.