Pre-mRNA splicing in higher plants

Lorković, Zdravko J.; Kirk, Dominika A. Wieczorek; Lambermon, Mark H. L.; Filipowicz, Witold

doi:10.1016/s1360-1385(00)01595-8

Cited by 280 publications

(237 citation statements)

References 46 publications

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“…Similar to vertebrate introns, most plant introns have canonical GU and AG dinucleotides at their 5Ј and 3Ј ends, suggesting the presence of a conserved splicing mechanism. However, plant cells have special requirements for intron recognition; for example, the necessity of AU-rich sequences in the intron, a relaxed criteria for branch site selection and the unessential requirement for a polypyrimidine tract (for reviews, see Lorkovic et al, 2000;Reddy, 2001). Given that SR proteins play important roles in both constitutive and alternative pre-mRNA splicing, the larger number of SR proteins in Arabidopsis may be a reflection of specific roles in both constitutive and alternative pre-mRNA splicing among different cell types and developmental stages.…”

Section: Spatially and Temporally Regulated Splicing Factor Expressiomentioning

confidence: 99%

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%

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

Fang

Hearn

Spector

2004

MBoC

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“…Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al, 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products.…”

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confidence: 99%

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

et al. 2015

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Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage-or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.After transcription, the majority of eukaryotic premRNA is subjected to a series of posttranscriptional modifications, including the removal of introns to form a mature mRNA (Stamm et al., 2005). Although some introns are removed constitutively, many can be processed in a variety of alternative ways, including exon skipping, intron retention, alternative acceptor, alternative donor, and alternative position (change in both acceptor and donor positions; Lorkovic et al., 2000). These alternative splicing events form a crucial regulatory level and have the ability to alter an mRNA's stability, localization, and protein products. Alternative splicing events are controlled by a variety of cis-elements, including the presence of consensus splice sequences at the intron-exon border and intronic and exonic splicing enhancer sequences (Pertea et al., 2007). Trans-acting factors also exert a strong effect on splicing and are mostly composed of Ser/Arg-rich proteins, which typically promote intron removal, and heterogenous nuclear ribonucleoproteins, which typically inhibit it (Erkelenz et al., 2013). A host of other indirect factors can affect splicing, including transcription rate, methylation status, and any cellular conditions that alter RNA secondary structure (Kornblihtt et al

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“…The removal of introns from intron-containing genes through the splicing of pre-mRNAs is emerging as a key step in gene expression 21,22 . Alternative splicing (AS) regulates not only transcript levels but also transcript isoforms, giving rise to proteins that differ in subcellular localization, stability and function [23][24][25] .…”

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confidence: 99%

ABA signalling is fine-tuned by antagonistic HAB1 variants

et al. 2015

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Group A protein type 2C phosphatases (PP2Cs) are negative regulators of abscisic acid (ABA) signalling and plant adaptation to stress. However, our knowledge of the regulation of PP2C activity is limited. Here we report that the PP2C HAB1 undergoes alternative splicing to produce two splice variants, which encode HAB1.1 and HAB1.2, that play opposing roles in ABA-mediated seed germination and ABA-mediated post-germination developmental arrest. HAB1.2 is predominately formed in the presence of ABA and prevents seed germination and post-germinative growth. HAB1.2 interacts with OST1, but cannot inhibit OST1 kinase activity; thus, it functions as a positive regulator of ABA signalling. We also identified an RNA-recognition motif-containing protein, RBM25, as a potential regulator of HAB1 alternative splicing and molecular diversity. Our results reveal a mechanism for turning ABA signalling on and off and for plant adaptation to abiotic stress.

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Pre-mRNA splicing in higher plants

Cited by 280 publications

References 46 publications

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

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

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

ABA signalling is fine-tuned by antagonistic HAB1 variants

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