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Encoding specificity in plant calcium signalling: hot-spotting the ups and downs and waves.

ABSTRACT: Calcium ions function as intracellular second messengers in regulating a plethora of cellular processes from acclimative stress responses to survival and programmed cell death. The generation of specificity in Ca2+ signals is dependent on influx and efflux from the extracellular milieu, cytosol and intracellular organelles. One aspect of plant Ca2+ signalling that is currently attracting a great deal of interest is how 'Ca2+-signatures', specific spatio-temporal changes in cytosolic-free Ca2+, encode the necessary information to bring about this range of physiological responses. Here, current information is reviewed on how Ca2+-signatures are generated in plant cells and how stimulus-specific information can be encoded in the form of Ca2+-signatures.

SUBMITTER: Ng CK

PROVIDER: S-EPMC4243675 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

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Encoding specificity in plant calcium signalling: hot-spotting the ups and downs and waves.

Ng Carl K-Y CK McAinsh Martin R MR

Annals of botany 20030821 4

Calcium ions function as intracellular second messengers in regulating a plethora of cellular processes from acclimative stress responses to survival and programmed cell death. The generation of specificity in Ca2+ signals is dependent on influx and efflux from the extracellular milieu, cytosol and intracellular organelles. One aspect of plant Ca2+ signalling that is currently attracting a great deal of interest is how 'Ca2+-signatures', specific spatio-temporal changes in cytosolic-free Ca2+, e ...[more]

PMID: 12933365

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Project description:Recent genome-wide analyses have uncovered a high accumulation of RNA polymerase II (Pol II) at the 5' end of genes. This elevated Pol II presence at promoters, referred to here as Poll II poising, is mainly (but not exclusively) attributed to temporal pausing of transcription during early elongation which, in turn, has been proposed to be a regulatory step for processes that need to be activated "on demand". Yet, the full genome-wide regulatory role of Pol II poising is yet to be delineated. To elucidate the role of Pol II poising in B cell activation, we compared Pol II profiles in resting and activated B cells. We found that while Pol II poised genes generally overlap functionally among different B cell states and correspond to the functional groups previously identified for other cell types, non-poised genes are B cell state specific. Focusing on the changes in transcription activity upon B cell activation, we found that the majority of such changes were from poised to non-poised state. The genes showing this type of transition were functionally enriched in translation, RNA processing and mRNA metabolic process. Interestingly, we also observed a transition from non-poised to poised state. Within this set of genes we identified several Immediate Early Genes (IEG), which were highly expressed in resting B cell and shifted from non-poised to poised state after B cell activation. Thus Pol II poising does not only mark genes for rapid expression in the future, but it is also associated with genes that are silenced after a burst of their expression. Finally, we performed comparative analysis of the presence of G4 motifs in the context of poised versus non-poised but active genes. Interestingly we observed a differential enrichment of these motifs upstream versus downstream of TSS depending on poising status. The enrichment of G4 sequence motifs upstream of TSS of non-poised active genes suggests a potential role of quadruplexes in expression regulation.

Dataset Information

Encoding specificity in plant calcium signalling: hot-spotting the ups and downs and waves.

Publications

Encoding specificity in plant calcium signalling: hot-spotting the ups and downs and waves.

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