Regulated chloroplast transcription termination

Ji, Daili; Manavski, Nikolay; Meurer, Jörg; Zhang, Lixin; Chi, Wei

doi:10.1016/j.bbabio.2018.11.011

Cited by 9 publications

(11 citation statements)

References 146 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Transcription termination in plastids has recently been reviewed (117). The endosymbiont hypothesis would predict that chloroplast termination would resemble that of bacteria, which use both Rho-dependent and Rho-independent mechanisms.…”

Section: Transcription Termination Analysis With Terminome-seqmentioning

confidence: 99%

“…The 3' end in the PNPase mutant is further downstream, suggesting a model similar to E. coli where Rho factors initiate termination and exoribonucleases like PNPase produce the precise, mature 3' ends directly downstream of stem-loops or RBP sites (120). Similarly, MTERF6, a member of a gene family related to a human mitochondrial transcription termination factor, acts in the trnI and petD-rpoA regions (65,117,121). As additional factors involved in termination are discovered, Terminome-Seq offers a tool to decipher their sites of action.…”

Section: Transcription Termination Analysis With Terminome-seqmentioning

confidence: 99%

See 1 more Smart Citation

Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Castandet

Germain

Hotto³

et al. 2019

Preprint

View full text Add to dashboard Cite

Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-Seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5' ends corresponding to transcription start sites (TSS), as well as 1,628 processed 5' ends and 1,299 3' ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5' and 3' ends, contrasting with the prevailing description of discrete 5' termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-Seq was also implemented for pnp1-1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2,000 termini were altered in pnp1-1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-Seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.

show abstract

Section: Transcription Termination Analysis With Terminome-seqmentioning

confidence: 99%

Section: Transcription Termination Analysis With Terminome-seqmentioning

confidence: 99%

Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Castandet

Germain

Hotto³

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…It has long been known that transcription termination of most plastid genes is inefficient as it results in abundant and diverse read-through transcripts that must be post-transcriptionally processed [26]. In a recent study [27], the mechanism of read-through transcription, which affects the transcription of downstream genes, resulted in extreme accumulation of accD transcripts when transcription termination of the upstream gene, rbcL, was inactivated. Here, we propose that readthrough transcription also helps interpret our finding that plastomic rearrangements influence gene expression.…”

Section: Discussionmentioning

confidence: 99%

Tight association of genome rearrangements with gene expression in conifer plastomes

Sudianto

Chaw

2021

BMC Plant Biol

View full text Add to dashboard Cite

Background Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Conclusions Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

show abstract

“…It has long been known that transcription termination of most plastid genes is ine cient as it results in abundant and diverse read-through transcripts that must be post-transcriptionally processed [26]. In a recent study [27], the mechanism of read-through transcription, which affects the transcription of downstream genes, resulted in extreme accumulation of accD transcripts when transcription termination of the upstream gene, rbcL, was inactivated. Here, we propose that read-through transcription also helps interpret our nding that plastomic rearrangements in uence gene expression.…”

Section: Discussionmentioning

confidence: 99%

Tight Association of Genome Rearrangements With Gene Expression in Conifer Plastomes

Sudianto

Chaw

2020

Preprint

View full text Add to dashboard Cite

Background: Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results: We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data shows a nearly full transcription of both plastomic strands and detects C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.Conclusions: Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

show abstract

Regulated chloroplast transcription termination

Cited by 9 publications

References 146 publications

Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Systematic sequencing of chloroplast transcript termini fromArabidopsis thalianareveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures

Tight association of genome rearrangements with gene expression in conifer plastomes

Tight Association of Genome Rearrangements With Gene Expression in Conifer Plastomes

Contact Info

Product

Resources

About