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Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives.

Castaings L, Bergonzi S, Albani MC, Kemi U, Savolainen O, Coupland G - Nat Commun (2014)

Bottom Line: Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle.Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors.Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.

View Article: PubMed Central - PubMed

Affiliation: 1] Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D-50829 Cologne, Germany [2].

ABSTRACT
Antisense RNA (asRNA) COOLAIR is expressed at A. thaliana FLOWERING LOCUS C (FLC) in response to winter temperatures. Its contribution to cold-induced silencing of FLC was proposed but its functional and evolutionary significance remain unclear. Here we identify a highly conserved block containing the COOLAIR first exon and core promoter at the 3' end of several FLC orthologues. Furthermore, asRNAs related to COOLAIR are expressed at FLC loci in the perennials A. alpina and A. lyrata, although some splicing variants differ from A. thaliana. Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle. Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors. Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.

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Conservation and divergence of non-coding regulatory cis-elements among FLC orthologues.(a) mVista pair-wise alignments of the 5′ intergenic regions of FLC orthologues. From top to bottom, A. lyrata FLC1, A. lyrata FLC2, C. rubella FLC, T. halophila FLC and A. alpina PEP1a aligned to A. thaliana FLC. Alignment of PEP1b and A. thaliana FLC is presented in Supplementary Fig. 1f. (b) GATA pair-wise alignment of A. thaliana VRE to the first intron of each of the FLC orthologues mentioned in a. Regions showing homology to the VRE are annotated as VRE-like. For A. alpina PEP1, VRE-like sequences were detected only in the region spanning exon 1b and exon 2 (intron 1 of PEP1b). Scale bar, 1 kb. (c) mVista pair-wise alignment of the 3′ regions of FLC orthologues. PEP1 3′ end was aligned to the 3′ intergenic regions of A. thaliana FLC, A. lyrata FLC1, A. lyrata FLC2, C. rubella and T. halophila FLC orthologues. Coloured areas in mVista graphs illustrate stretches of homology greater than 75% identity at the nucleotide level. Pink, regions of homology in the promoter region (a) or at the 3′ end (c); dark blue, exonic sequences; light blue, untranslated region. Grey and pink boxes in GATA plots are homologous regions and inverted homologous regions respectively (the darker the box, the higher the similarity).
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f1: Conservation and divergence of non-coding regulatory cis-elements among FLC orthologues.(a) mVista pair-wise alignments of the 5′ intergenic regions of FLC orthologues. From top to bottom, A. lyrata FLC1, A. lyrata FLC2, C. rubella FLC, T. halophila FLC and A. alpina PEP1a aligned to A. thaliana FLC. Alignment of PEP1b and A. thaliana FLC is presented in Supplementary Fig. 1f. (b) GATA pair-wise alignment of A. thaliana VRE to the first intron of each of the FLC orthologues mentioned in a. Regions showing homology to the VRE are annotated as VRE-like. For A. alpina PEP1, VRE-like sequences were detected only in the region spanning exon 1b and exon 2 (intron 1 of PEP1b). Scale bar, 1 kb. (c) mVista pair-wise alignment of the 3′ regions of FLC orthologues. PEP1 3′ end was aligned to the 3′ intergenic regions of A. thaliana FLC, A. lyrata FLC1, A. lyrata FLC2, C. rubella and T. halophila FLC orthologues. Coloured areas in mVista graphs illustrate stretches of homology greater than 75% identity at the nucleotide level. Pink, regions of homology in the promoter region (a) or at the 3′ end (c); dark blue, exonic sequences; light blue, untranslated region. Grey and pink boxes in GATA plots are homologous regions and inverted homologous regions respectively (the darker the box, the higher the similarity).

Mentions: In A. thaliana cold-induced repression of FLC mRNA requires cis-regulatory sequences in the promoter and first intron1314. Whether these cis-regulatory elements are evolutionarily conserved was tested by comparing genomic sequences of FLC orthologues from a range of Brassicaceae species (Methods; Fig. 1; Supplementary Figs 1–3).With the exception of PEP1 in A. alpina, FLC orthologues from A. lyrata, Capsella rubella and Thellungiella halophila exhibit the same gene structure as A. thaliana FLC. A. alpina PEP1 harbours a tandem duplication (PEP1a and PEP1b) containing part of the promoter, the first exon and part of intron 1 (Fig. 2a; ref. 21). The two copies of exon 1 have individual transcriptional start sites and each is spliced to the unique exon 2 giving rise to two overlapping transcripts37. Two tandemly arranged full-length copies of FLC, called AlFLC1 and AlFLC2, are present in A. lyrata, and both are transcriptionally active2638. Promoter sequences between the translational start site (ATG) of FLC and the end of the next upstream gene were compared revealing two main blocks of homology (Fig. 1a and Supplementary Fig. 1). The first block was ~400 bp long and included the proximal promoter as well as the 5′ untranslated leader. In A. alpina, homology in this region was reduced and mainly restricted to the untranslated leaders of PEP1a and PEP1b (Supplementary Fig. 1g). The second region was ~2 kb further upstream, and in A. alpina was found only in PEP1a. Apart from these two conserved blocks, the FLC promoter has diverged rapidly during evolution, even between the closely related species A. thaliana and A. lyrata, as observed previously38.


Evolutionary conservation of cold-induced antisense RNAs of FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives.

Castaings L, Bergonzi S, Albani MC, Kemi U, Savolainen O, Coupland G - Nat Commun (2014)

Conservation and divergence of non-coding regulatory cis-elements among FLC orthologues.(a) mVista pair-wise alignments of the 5′ intergenic regions of FLC orthologues. From top to bottom, A. lyrata FLC1, A. lyrata FLC2, C. rubella FLC, T. halophila FLC and A. alpina PEP1a aligned to A. thaliana FLC. Alignment of PEP1b and A. thaliana FLC is presented in Supplementary Fig. 1f. (b) GATA pair-wise alignment of A. thaliana VRE to the first intron of each of the FLC orthologues mentioned in a. Regions showing homology to the VRE are annotated as VRE-like. For A. alpina PEP1, VRE-like sequences were detected only in the region spanning exon 1b and exon 2 (intron 1 of PEP1b). Scale bar, 1 kb. (c) mVista pair-wise alignment of the 3′ regions of FLC orthologues. PEP1 3′ end was aligned to the 3′ intergenic regions of A. thaliana FLC, A. lyrata FLC1, A. lyrata FLC2, C. rubella and T. halophila FLC orthologues. Coloured areas in mVista graphs illustrate stretches of homology greater than 75% identity at the nucleotide level. Pink, regions of homology in the promoter region (a) or at the 3′ end (c); dark blue, exonic sequences; light blue, untranslated region. Grey and pink boxes in GATA plots are homologous regions and inverted homologous regions respectively (the darker the box, the higher the similarity).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4109010&req=5

f1: Conservation and divergence of non-coding regulatory cis-elements among FLC orthologues.(a) mVista pair-wise alignments of the 5′ intergenic regions of FLC orthologues. From top to bottom, A. lyrata FLC1, A. lyrata FLC2, C. rubella FLC, T. halophila FLC and A. alpina PEP1a aligned to A. thaliana FLC. Alignment of PEP1b and A. thaliana FLC is presented in Supplementary Fig. 1f. (b) GATA pair-wise alignment of A. thaliana VRE to the first intron of each of the FLC orthologues mentioned in a. Regions showing homology to the VRE are annotated as VRE-like. For A. alpina PEP1, VRE-like sequences were detected only in the region spanning exon 1b and exon 2 (intron 1 of PEP1b). Scale bar, 1 kb. (c) mVista pair-wise alignment of the 3′ regions of FLC orthologues. PEP1 3′ end was aligned to the 3′ intergenic regions of A. thaliana FLC, A. lyrata FLC1, A. lyrata FLC2, C. rubella and T. halophila FLC orthologues. Coloured areas in mVista graphs illustrate stretches of homology greater than 75% identity at the nucleotide level. Pink, regions of homology in the promoter region (a) or at the 3′ end (c); dark blue, exonic sequences; light blue, untranslated region. Grey and pink boxes in GATA plots are homologous regions and inverted homologous regions respectively (the darker the box, the higher the similarity).
Mentions: In A. thaliana cold-induced repression of FLC mRNA requires cis-regulatory sequences in the promoter and first intron1314. Whether these cis-regulatory elements are evolutionarily conserved was tested by comparing genomic sequences of FLC orthologues from a range of Brassicaceae species (Methods; Fig. 1; Supplementary Figs 1–3).With the exception of PEP1 in A. alpina, FLC orthologues from A. lyrata, Capsella rubella and Thellungiella halophila exhibit the same gene structure as A. thaliana FLC. A. alpina PEP1 harbours a tandem duplication (PEP1a and PEP1b) containing part of the promoter, the first exon and part of intron 1 (Fig. 2a; ref. 21). The two copies of exon 1 have individual transcriptional start sites and each is spliced to the unique exon 2 giving rise to two overlapping transcripts37. Two tandemly arranged full-length copies of FLC, called AlFLC1 and AlFLC2, are present in A. lyrata, and both are transcriptionally active2638. Promoter sequences between the translational start site (ATG) of FLC and the end of the next upstream gene were compared revealing two main blocks of homology (Fig. 1a and Supplementary Fig. 1). The first block was ~400 bp long and included the proximal promoter as well as the 5′ untranslated leader. In A. alpina, homology in this region was reduced and mainly restricted to the untranslated leaders of PEP1a and PEP1b (Supplementary Fig. 1g). The second region was ~2 kb further upstream, and in A. alpina was found only in PEP1a. Apart from these two conserved blocks, the FLC promoter has diverged rapidly during evolution, even between the closely related species A. thaliana and A. lyrata, as observed previously38.

Bottom Line: Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle.Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors.Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.

View Article: PubMed Central - PubMed

Affiliation: 1] Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, D-50829 Cologne, Germany [2].

ABSTRACT
Antisense RNA (asRNA) COOLAIR is expressed at A. thaliana FLOWERING LOCUS C (FLC) in response to winter temperatures. Its contribution to cold-induced silencing of FLC was proposed but its functional and evolutionary significance remain unclear. Here we identify a highly conserved block containing the COOLAIR first exon and core promoter at the 3' end of several FLC orthologues. Furthermore, asRNAs related to COOLAIR are expressed at FLC loci in the perennials A. alpina and A. lyrata, although some splicing variants differ from A. thaliana. Study of the A. alpina orthologue, PERPETUAL FLOWERING 1 (PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle. Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA patterns depends on both cis-elements and species-specific trans-acting factors. Thus, expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.

Show MeSH
Related in: MedlinePlus