atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes

Lopato, Sergiy; Kalyna, Maria; Dorner, Silke; Kobayashi, Ryûji; Krainer, Adrian R.; Barta, Andrea

doi:10.1101/gad.13.8.987

Cited by 149 publications

(221 citation statements)

References 81 publications

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“…Finally, in the inflorescence stems, SR1 is expressed at extremely high levels throughout the stem, whereas SR33 and atSRp30 are expressed at progressively lower levels. Tissue-specific promoter activities of SR proteins were also observed by histochemical analyses with lower resolution and sensitivity (Lopato et al, 1999b(Lopato et al, , 2002. It has been proposed that the ratio of various splicing factors in the spliceosome may regulate splice site choice (for review, see Smith and Valcarcel, 2000).…”

Section: Spatially and Temporally Regulated Splicing Factor Expressiomentioning

confidence: 99%

“…Upstream regulatory sequence of atSRp30 (At1g09140) (Lopato et al, 1999b), SR1/atSRp34 (At1g02840) (Lazar et al, 1995;Lopato et al, 1999b), and SR33 (At1g55310) (Golovkin and Reddy, 1999) plus their complete 5Ј untranslated regions was amplified by polymerase chain reaction (PCR) from genomic DNA of A. thaliana (ecotype, Columbia); primers for SR33 promoter were 5Ј-NNNAAGCTTCATTATAAGATAAACCTTCTAG-3Ј and 5Ј-NNNGGAT-CCTGAGTCAAGCTTCAATCTCTC-3Ј; primers for SR1/atSRp34 promoter were 5Ј-NNNAAGCTTAAATATTGAACCGGCCTCGGTTC-3Ј and 5Ј-NNNGGATCCTCTTCCTTTATCAAATCC-3Ј; and primers for atSRp30 promoter were 5Ј-NNNAAGCTTTAATTCTTAGATTCTACAATC-3Ј and 5Ј-NNNGGATCCCTGATACCTCAGAGCAGAAA-3Ј. The amplified promoter fragments containing a HindIII site at their 5Ј end and a BamHI site at their 3Ј end were digested with HindIII and BamHI.…”

Section: Constructsmentioning

confidence: 99%

“…For the SR33 promoter region with an extra HindIII site, partial HindIII digestion and complete BamHI digestion were applied to clone the intact promoter sequence. SR33 coding sequence was amplified from a SR33 cDNA clone (Golovkin and Reddy, 1999) by using primers 5Ј-NNNGGATCCATGAGGGGAAG-GAGCTACACT-3Ј and 5Ј-NNNACCGGTCGCTGGCTTGGTGAACGGTC-TTC-3Ј; SR1/atSRp34 coding sequence was amplified from pUC35S-SR1nos (Lazar et al, 1995) by using primers 5Ј-NNNGGATCCATGAGCA GTCG-TTCGAGTAGA-3Ј and 5Ј-NNNACCGGTCGCCTCGATGGACTCATAGT-GTG-3Ј; atSRp30 coding sequence was amplified from pC30 (Lopato et al, 1999b) by using primers 5Ј-NNNGGATCCATGAGTAGCCGATGGA-ATCGT-3Ј and 5Ј-NNNACCGGTCGACCAGATATCACAGGTGAAAC-3Ј. The amplified coding sequences containing a BamHI site at their 5Ј end and an AgeI site at their 3Ј end were digested with BamHI and AgeI.…”

mentioning

confidence: 99%

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Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Fang

Hearn

Spector

2004

MBoC

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The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism. INTRODUCTIONPre-mRNA (pre-mRNA) splicing, a process of excision of introns and ligation of exons, is essential for generating mature transcripts and enhancing mRNA export from the nucleus to the cytoplasm. Splicing occurs within a large macromolecular complex called the spliceosome, which is composed of U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles and a large number of non-small nuclear ribonucleoprotein particle proteins (Zhou et al., 2002). The latter include members of the SR (Ser-Arg) family of pre-mRNA splicing factors characterized by one or two N-terminal RNA recognition motifs that interact with the pre-mRNAs and a C-terminal variable-length Arg/Ser(RS)-rich domain that influences its subcellular localization and splicing activity depending upon its phosphorylation levels (for review, see Graveley, 2000).In mammalian cells, pre-mRNA splicing factors are concentrated in 20 -50 distinct nuclear domains called speckles as well as being diffusely distributed throughout the nucleoplasm, and this distribution corresponds to interchromatin granule clusters (IGCs) and perichromatin fibrils (PFs). PFs often extend from the periphery of IGCs or are present in the nucleoplasm at some distance from an IGCs (for review, see Lamond and Spector, 2003). It has been proposed that IGCs are storage and/or modification/reassembly sites for premRNA splicing factors and that splicing factors are recruited from these compartments to the sites of active transcription (PFs) (Jiménez-García and Spector, 1993). Disassembly of IGCs by overexpression of an SR protein kinase Clk/STY disrupts the coo...

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Section: Spatially and Temporally Regulated Splicing Factor Expressiomentioning

confidence: 99%

Section: Constructsmentioning

confidence: 99%

mentioning

confidence: 99%

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Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Fang

Hearn

Spector

2004

MBoC

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“…Examples include AtSRp30, a serine/arginine-rich (SR) protein [49], poly(A)-binding proteins [50,51], the U1-70K protein and its interacting SR proteins [52,53], and an exonuclease AtRrp41p [54] from Arabidopsis. Several Nicotiana plumbaginifolia proteins, such as UBP1, a novel hnRNP-like protein [55], the UBP1-interacting proteins UBA1 and UBA2 [56], and RBP45 and RBP47, two oligouridylatespecific hnRNP-like proteins [57], have also been characterized.…”

Section: Developmental Roles Of Rna-binding Proteins Explored Using Rmentioning

confidence: 99%

“…Although most studies have focused on the expression patterns of genes that encode RNA-binding proteins or on the biochemical activities of the proteins, the developmental roles of some RNA-binding proteins have been explored. For example, the overexpression of AtSRp30 in Arabidopsis leads to alternative RNA processing and delays developmental transitions [49].…”

Section: Developmental Roles Of Rna-binding Proteins Explored Using Rmentioning

confidence: 99%

Posttranscriptional control of plant development

Cheng¹

2004

Current Opinion in Plant Biology

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Genetic studies have provided increasing evidence that proteins involved in all aspects of RNA metabolism, such as RNA processing, transport, stability, and translation, are required for plant development and for plants' responses to the environment. Such proteins act in floral transition, floral patterning, and signaling by abscisic acid, low temperature and circadian rhythms. Although some of these proteins belong to core RNA metabolic machineries, others may have more specialized cellular functions. Despite the limited knowledge of the underlying molecular mechanisms, posttranscriptional regulation is known to play a key role in the control of plant development.

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Challenges in Plant Alternative Splicing

Barta

Márquez

Brown

2012

Alternative Pre‐mRNA Splicing

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This chapter highlights the unique and common features of plant splicing compared to the better understood mammalian and yeast systems (see Chapter 5 L€ uhrmann and 6 Rymond for further discussion). In the past, experiments aimed at elucidating splicing mechanisms have been conducted mainly in mammalian and yeast systems, as these are more amenable to in vitro and genetic analyses. In fact, plant intron splicing began to attract more attention only when experiments conducted in planta indicated that plants were unable to splice out animal introns, or to recognize animal poly A signals correctly [1]. On the other hand, plant-derived introns were in most cases accurately and efficiently spliced in HeLa cells, using in vitro splicing extracts [2,3]. This prompted many lines of research to identify the mechanistic differences between splicing in plants, and splicing in animals. Consequently, although several laboratory groups embarked on the enterprise to develop an in vitro cell-based splicing extract, they invariably failed despite valiant attempts. Whilst plant cell extracts have been instrumental in elucidating the principles of translation, by using in vitro wheat germ system, it has not been possible to acquire a stable mRNA in vitro transcription or splicing system from plants. Hence, the detailed analysis of plant splicing has relied instead on the development of in vivo splicing analysis systems, that use transient transfection assays of splicing constructs and splicing factors (as discussed in Chapter 42, Simpson). The availability of the whole genome sequence of Arabidopsis has indicated that most of the important splicing components are also present in the plant genome [4]. Together with results from the in vivo analysis of splicing events in different plants, which indicated the requirement for U-rich sequences in plant introns, these data have indicated that the basic splicing mechanisms are comparable. However, there are clear differences in the size of plant introns compared to those of vertebrates, and also in the sequence composition of plant introns (U-rich). This, in turn, implies that there are differences in the definition of introns or exons, and thereby also differences in the RNA-binding properties of splicing regulatory proteins. Consequently, differences in intron composition and binding specificity, and the strength of splicing factors between different plant species as well as between plants and animals, might account for the variability in splicing efficiency.The past five years have witnessed a growing interest in alternative splicing in plants such that, today, high-throughput genomic and transcriptomic sequencing data are beginning to address the hitherto underdeveloped sequencing effort for expressed plant sequences [5] (see Chapter 23, Brown). Similar to mammalian systems (Chapter 3 Hertel), it has become very clear that alternative splicing is much more prevalent than was originally thought, rising from 7% to more than 35% in only three years as additional sequence data have become...

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atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes

Cited by 149 publications

References 81 publications

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Posttranscriptional control of plant development

Challenges in Plant Alternative Splicing

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