Nuclear pre-mRNA splicing in plants

Critical Reviews in Plant Sciences

Volumn 20, Issue 6, 2001, Pages 523-571

  Reddy, A S N ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

Alternative splicing; Arabidopsis; Exon; Gene expression; Intron; RNA helicase; RNA processing; Serine arginine rich proteins; snRNP; Spliceosome

Indexed keywords

ANIMALIA; ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA; METAZOA;

EID: 0035212996     PISSN: 07352689     EISSN: None     Source Type: Journal    
DOI: 10.1080/20013591099272     Document Type: Review

References (285)

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13. A coactivator of pre-mRNA splicing
14. Intron sequences are involved in the plastid- and light-dependent expression of the spinach PsaD gene
15. Coiled body numbers in the Arabidopsis root epidermis are regulated by cell type, developmental stage and cell cycle parameters
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33. A combinatorial role for exon, intron and splice site sequences in splicing in maize
34. In vivo analysis of intron processing using splicing-dependent reporter gene assays
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37. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA
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39. The question remains: Is the spliceosome a ribozyme?
40. SRPK1 and Clk/Sty protein kinases show distinct substrate specificities for serine/arginine-rich splicing factors
41. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution
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43. Initial sequencing and analysis of the human genome
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45. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP
46. Cis-acting elements distinct from the 5′ splice site promote U1-independent pre-mRNA splicing
47. Characterization of Gmhsp26-A, a stress gene encoding a divergent heat shock protein of soybean: Heavy-metal-induced inhibition of intron processing
48. Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean
49. Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns
50. Alternatively spliced N resistance gene transcripts: Their possible role in tobacco mosaic virus resistance
51. Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants
52. Progress and variations in two-hybrid and three-hybrid technologies
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54. The Clk2 and Clk3 dual-specificity protein kinases regulate the intranuclear distribution of SR proteins and influence pre-mRNA splicing
55. Why do genes have introns? Recombination might add a new piece to the puzzle
56. Sequencing the rice genome
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59. Structure and expression of a Xenopus gene encoding an snRNP protein (U1 70K)
60. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction
61. The superfamily of arginine/serine-rich splicing factors
62. Isolation of a complementary DNA that encodes the mammalian splicing factor SC35
63. Gene discovery using the maize genome database ZmDB
64. Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes
65. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro
66. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro
67. Origin of genes
68. Characterization of intronic uridine-rich sequence elements acting as possible targets for nuclear proteins during pre-mRNA splicing in Nicotiana plumbaginifolia
69. The plant U1 small nuclear ribonucleoprotein particle 70K protein interacts with two novel serine/arginine-rich proteins
70. An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein
71. Structure and expression of a plant U1 snRNP 70K gene: Alternative splicing of U1 snRNP 70K pre-mRNAs produces two different transcripts
72. The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing
73. Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants
74. Nuclear RNA splicing and small nuclear RNAs and their genes in higher plants
75. Organ-specific differences in the ratio of alternatively spliced chorismate synthase (LeCS2) transcripts in tomato
76. A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins
77. Sorting out the complexity of SR protein functions
78. SR proteins are 'locators' of the RNA splicing machinery
79. Arginine/Serine-rich domains of SR proteins can function as activators of pre-mRNA splicing
80. Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors
81. A serine kinase regulates intracellular localization of splicing factors in the cell cycle
82. Purification and characterization of a kinase specific for the serine- and arginine-rich pre-mRNA splicing factors
83. Messenger RNA splicing in yeast: Clues to why the spliceosome is a ribonucleoprotein
84. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites
85. Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns
86. Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins
87. Isolation of a novel RNA-binding protein and its association with a large ribonucleoprotein particle present in the nucleoplasm of tobacco cells
88. Alternative splicing of human genes: More the rule than the exception?
89. cDNA cloning of U1, U2, U4 and U5 snRNA families expressed in pea nuclei
90. Developmental expression of plant snRNAs
91. In vitro processing of a plant pre-mRNA in HeLa cell nuclear extract
92. In vitro processing of the human growth hormone primary transcript
93. Molecular characterisation of two paralogous SPO11 homologues in Arabidopsis thaliana
94. Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly
95. A survey on intron and exon lengths
96. U1-specific protein C needed for efficient complex formation of U1 snRNP with a 5′ splice site
97. Molecular cloning and characterization of the Arabidopsis thaliana alpha-subunit of elongation factor 1B
98. snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions
99. Characterization of the major transcripts encoded by the regulatory MuDR transposable element of maize
100. The amino-terminal domain of yeast U1-70K is necessary and sufficient for function
101. cDNA structure, expression and nucleic acid-binding properties of three RNA-binding proteins in tobacco: Occurrence of tissue specific alternative splicing
102. Characterization of the genes encoding U4 small nuclear RNAs in Arabidopsis thaliana
103. The heat shock response of pollen and other tissues of maize
104. Analysis of genomic clones of the murine U1RNA-associated 70-kDa protein reveals a high evolutionary conservation of the protein between human and mouse
105. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
106. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron
107. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron
108. Dull: Rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA
109. A reappraisal of non-consensus mRNA splice sites
110. Tissue-preferential expression of a rice alpha-tubulin gene, OsTubA1, mediated by the first intron
111. The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation
112. Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA
113. Regulation of adenovirus alternative RNA splicing by dephosphorylation of SR proteins
114. U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize
115. Protein-protein interactions and 5′-splice-site recognition in mammalian mRNA precursors
116. H-protein of the glycine cleavage system in Flaveria: Alternative splicing of the pre-mRNA occurs exclusively in advanced C4 species of the genus
117. Alternative splicing results in two different transcripts for H-protein of the glycine cleavage system in the C4 species Flaveria trinervia
118. Using the yeast three-hybrid system to detect and analyze RNA-protein interactions
119. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa Cells
120. hnRNP complexes: Composition, structure, and function
121. A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: Common use of the same mitochondrial targeting signal for different proteins
122. Control of alternative splicing by differential binding of U1 small nuclear ribonucleoprotein particle
123. Novel SR-protein-specific kinase, SRPK2, disassembles nuclear speckles
124. A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation
125. UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation
126. Transcript accumulation and utilization of alternate and non-consensus splice sites in rice granule-bound starch synthase are temperature-sensitive and controlled by a single-nucleotide polymorphism
127. pEmu: An improved promoter for gene expression in cereal cells
128. Test of the combinatorial model of intron recognition in a native maize gene
129. A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding
130. The Arabidopsis splicing factor SR1 is regulated by alternative splicing
131. Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF
132. Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato
133. Like attracts like: Getting RNA processing together in the nucleus
134. Mapping of branchpoint nucleotides in mutant pre-mRNAs expressed in plant cells
135. Ligand-dependent interactions of coactivators steroid receptor coactivator-1 and peroxisome proliferator-activated receptor binding protein with nuclear hormone receptors can be imaged in live cells and are required for transcription
136. A novel family of plant splicing factors with a Zn knuckle motif: Examination of RNA binding and splicing activities
137. atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes
138. Pre-mRNA splicing in plants: Characterization of Ser/Arg splicing factors
139. Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis
140. RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells
141. Pre-mRNA splicing in higher plants
142. 3′ Splice site selection in dicot plant nuclei is position dependent
143. Expression of maize Adh1 intron mutants in tobacco nuclei
144. Nuclear pre-mRNA processing in higher plants
145. Intron enhancement of gene expression and the splicing efficiency of introns in maize cells
146. Addition of A- and U-rich sequences increases the splicing efficiency of a deleted form of a maize intron
147. Intron creation and polyadenylation in maize are directed by AU-rich RNA
148. A novel DNA-binding domain in the Shrunken initiator-binding protein (IBP1)
149. snRNP proteins
150. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing
151. The combination of a novel stimulatory element in the first exon of the maize Shrunken-1 gene with the following intron 1 enhances reporter gene expression up to 1000-fold
152. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains
153. SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract
154. Structure and expression of the Drosophila melanogaster gene for the U1 small nuclear ribonucleoprotein particle 70K protein
155. SR proteins and splicing control
156. Hydroxypyruvate reductase with a carboxy-terminal targeting signal to microbodies is expressed in Arabidopsis
157. Light regulates alternative splicing of hydroxypyruvate reductase in pumpkin
158. Expression and RNA splicing of the maize glutathione-S-transferase Bronze2 gene is regulated by cadmium and other stresses
159. Essential large transcripts of the maize Spm transposable element are generated by alternative splicing
160. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2
161. 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II
162. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription
163. Interactions across exons can influence splice site recognition in plant nuclei
164. Factors affecting authentic 5′ splice site selection in plant nuclei
165. AU-rich intronic elements affect pre-mRNA 5′ splice site selection in Drosophila melanogaster
166. Intronic and exonic sequences modulate 5′ splice site selection in plant nuclei
167. Isolation of an efficient actin promoter for use in rice transformation
168. Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism
169. Internal AU-rich elements modulate activity of two competing 3′ splice sites in plant nuclei
170. Developmentally and transgene regulated nuclear processing of primary transcripts of chalcone synthase A in petunia
171. Posttranscriptional silencing of pectin methylesterase gene in transgenic tomato fruits results from impaired pre-mRNA processing
172. RNA splicing: What has phosphorylation got to do with it?
173. Protein dynamics: Implications for nuclear architecture and gene expression
174. The dynamics of a pre-mRNA splicing factor in living cells
175. Protein phosphoprotein and the nuclear organization of pre-mRNA splicing
176. RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo
177. ZEMa, a member of a novel group of MADS box genes, is alternatively spliced in maize endosperm
178. Intron recognition comes of AGe
179. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing
180. The U1 small nuclear RNA-protein complex selectively binds a 5′ splice site in vitro
181. The type 2C Ser/Thr phosphotase PP2cγ is a pre-mRNA splicing factor
182. Molecular comparison of monocot and dicot U1 and U2 snRNAs
183. Molecular comparison of monocot and dicot U1 and U2 snRNAs
184. Bronze-2 gene of maize: Reconstruction of a wild-type allele and analysis of transcription and splicing
185. The association of the U1-specific 70K and C proteins with U1 snRNPs is mediated in part by common U snRNP proteins
186. The intron of Arabidopsis thaliana polyubiquitin genes is conserved in location and is a quantitative determinant of chimeric gene expression
187. Purification of the major UsnRNPs from broad bean nuclear extracts and characterization of their protein constituents
188. Expression of a mouse metallothionein gene in transgenic plant tissues
189. High mobility of proteins in the mammalian cell nucleus
190. Shuttling of pre-mRNA binding proteins between nucleus and cytoplasm
191. The gene encoding human splicing factor 9G8: Structure, chromosomal localization, and expression of alternatively processed transcripts
192. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection
193. A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein
194. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer
195. Exon definition may facilitate splice site selection in RNAs with multiple exons
196. Overexpression of the arginine-rich carboxy-terminal region of U1 snRNP 70K inhibits both splicing and nucleocytoplasmic transport of mRNA
197. The U1 small nuclear ribonucleoprotein (snRNP) 70K protein is transported independently of U1 snRNP particles via a nuclear localization signal in the RNA-binding domain
198. Who's on first? The U1 snRNP-5′splice site interaction and splicing
199. SR proteins escort U4/6.U5 tri-snRNP to the spliceosome
200. Introns act post-transcriptionally to increase expression of the Arabidopsis thaliana tryptophan pathway gene PAT1
201. A monoclonal antibody that recognizes a phosphorylated epitope stains lampbrush chromosome loops and small granules in the amphibian germinal vesicle
202. International rice genome sequencing project: The effort to completely sequence the rice genome
203. The ethylene-inducible PK12 kinase mediates the phosphorylation of SR splicing factors
204. Cloning, mapping and expression analysis of barley MADS-box genes
205. Plant pre-mRNA splicing
206. A new twist on RNA helicases: DExH/D box proteins as RNPases
207. RNA helicase dynamics in pre-mRNA splicing
208. Exon mutations uncouple 5′ splice site selection from U1 snRNA pairing
209. PK12, a plant dual-specificity protein kinase of the Lammer family, is regulated by the hormone ethylene
210. Split genes and RNA splicing
211. Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes
212. Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants
213. Efficient splicing of an AU-rich antisense intron sequence
214. Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency
215. Requirements for mini-exon inclusion in potato invertase mRNAs provides evidence for exon-scanning interactions in plants
216. Characterization of exon skipping mutants of the COP1 gene from Arabidopsis
217. Molecular characterization of spliceosomal proteins U1A and U2B″ from higher plants
218. Splicing of precursors to mRNA in higher plants: Mechanism, regulation, and sub-nuclear organisation of the spliceosomal machinery
219. Evolutionary conservation of the spliceosomal protein, U2B″
220. Alternative pre-mRNA splicing: The logic of combinatorial control
221. Alternative splicing in the control of gene expression
222. Cloning of a yeast U1 snRNP 70K protein homologue: Functional conservation of an RNA-binding domain between humans and yeast
223. Alternative splicing of a novel diacylglycerol kinase in tomato leads to a calmodulin-binding isoform
224. Uridylate-rich small nuclear RNAs (UsnRNAs), their genes and pseudogenes, and UsnRNPs in plants: Structure and function. A comparative approach
225. Nuclear organization and gene expression
226. The human U1-70K snRNP protein: cDNA cloning, chromosomal localization, expression, alternative splicing and RNA-binding
227. Mechanical devices of the spliceosome: Motors, clocks, springs, and things
228. SR proteins are sufficient for exon bridging across an intron
229. Architectural limits on split genes
230. General splicing factor SF2/ASF promotes alternative splicing by binding to an exonic splicing enhancer
231. Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: Creation of an SRp40-specific splicing enhancer
232. Determinants of SR protein specificity
233. Intron definition in splicing of small Drosophila introns
234. Alternative RNA products from a rice homeobox
235. Enhancement of foreign gene expression by a dicot intron in rice but not in tobacco is correlated with an increased level of mRNA and an efficient splicing of the intron
236. Polypurine sequences within a downstream exon function as a splicing enhancer
237. SR proteins can compensate for the loss of U1 snRNP functions in vitro
238. Modulation of 5′ splice site choice in pre-messenger RNA by two distinct steps
239. A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro
240. Thiophosphorylation of U1-70K protein inhibits pre-mRNA splicing
241. Cloning of the human cDNA for the U1 RNA-associated 70K protein
242. Positive control of pre-mRNA splicing in vitro
243. Molecular characterization of ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice leaves
244. Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs
245. Calcium channels, stores, and oscillations
246. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
247. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA
248. The SR protein family: Pleiotropic functions in pre-mRNA splicing
249. The MKK(3/6)-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation
250. Nucleotide sequence of a bean (Phaseolus vulgaris) U1 small nuclear RNA gene: Implications for plant pre-mRNA splicing
251. Splicing of plant pre-mRNAs in animal systems and vice versa
252. Structure and expression of the U5 snRNA gene of Arabidopsis thaliana. Conserved upstream sequence elements in plant U-RNA genes
253. Structure of U2 snRNA genes of Arabidopsis thaliana and their expression in electroporated plant protoplasts
254. Increased gene expression by the first intron of maize shrunken-1 locus in grass species
255. Characterization and expression of U1 snRNA genes from potato
256. The sequence of the human genome
257. SRPK2: A differentially expressed SR protein-specific kinase involved in mediating the interaction and localization of pre-mRNA splicing factors in mammalian cells
258. Genetic analysis of the SR protein ASF/SF2: Interchangeability of RS domains and negative control of splicing
259. The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene
260. Nuclear pre-mRNA processing in plants: Distinct modes of 3′ splice site selection in plants and animals
261. Alternative mRNA splicing generates the two ribulosebisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis
262. The product of the tobacco mosaic virus resistance gene N: Similarity to toll and the interleukin-1 receptor
263. Protein functions in pre-mRNA splicing
264. Identification of an snRNP-associated kinase activity that phosphorylates arginine/serine rice domains typical of splicing factors
265. Non-canonical introns are at least 10(9) years old
266. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing
267. Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs
268. AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes
269. Phosphorylation-dephosphorylation differentially affects activities of splicing factor ASF/SF2
270. Phosphorylation of the ASF/SF2 RS domain affects both protein-protein and protein-RNA interactions and is necessary for splicing
271. An RNA-dependent ATPase associated with U2/U6 snRNAs in pre-mRNA splicing
272. Phosphorylation regulates in vivo interaction and molecular targeting of serine/arginine-rich pre-mRNA splicing factors
273. An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3-1 functions by suppressing defects in splicing
274. Alternatively spliced mRNA variants of chloroplast ascorbate peroxidase isoenzymes in spinach leaves
275. RNA metabolism: Strategies for regulation in the heat shock response
276. The growing world of small nuclear ribonucleoproteins
277. Genetic analysis of the role of human U1 snRNA in mRNA splicing. I. Effect of mutations in the highly conserved stem-loop I of U1
278. SR proteins: A conserved family of pre-mRNA splicing factors
279. Distinct functions of SR proteins in alternative pre-mRNA splicing
280. Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5′ splice sites
281. Yeast three-hybrid system to detect and analyze RNA-protein interactions
282. Identification and characterization of yUAP/Sub2p, a yeast homolog of the essential human pre-mRNA splicing factor hUAP56
283. Mechanism of light regulation of Rubisco: A specific role for the larger Rubisco activase isoform involving reductive activation by thioredoxin-f
284. Sipl, a novel RS domaincontaining protein essential for pre-mRNA splicing
285. Molecular cloning and characterization of cDNAs encoding two isoforms of ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice (Oryza sativa L.)