Abstract
Recently, a large number of non-coding RNAs (ncRNAs) have been found in a wide variety of organisms, but their biological functions are poorly understood, except for several tiny RNAs. To identify novel ncRNAs with essential functions in flowering plants, we focused attention on RNA polymerase III (Pol III) and its transcriptional activity, because most Pol III-transcribed RNAs contribute to key processes relating to cell activities, and have highly conserved promoter elements: upstream sequence elements, a TATA-like sequence, and a poly(T) stretch as a transcription terminator. After in silico prediction from the Arabidopsis genome, 20 novel ncRNAs candidates were obtained. AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts. AtR8 RNA was conserved among six additional taxa of Brassicaceae, and the secondary structure of the RNA was also conserved among the orthologs. Abundant accumulation of AtR8 RNA was observed in the plant roots and cytosol of cultured cells. The RNA was not processed into a smaller fragment and no short open reading frame was included. Remarkably, expression of the AtR8 RNA responded negatively to hypoxic stress, and this regulation evidently differed from that of U6 snRNA.
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Claims 9
Claim · model-written summary
Genome prediction yielded 20 new ncRNA candidates.
- Taxon
- Arabidopsis
Arabidopsise0 - Outcome
- novel ncRNAs candidatese0
- Value
- 20e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“After in silico prediction from the Arabidopsis genome, 20 novel ncRNAs candidates were obtained”
Claim · model-written summary
AtR8 RNA of approximately 260 nt was identified by Pol III transcription.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AtR8 RNAe0
- Outcome
- identified by efficient in vitro transcription by Pol IIIe0
- Value
- approx. 260 nte0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
Claim · model-written summary
AtR18 RNA of approximately 160 nt was identified by Pol III transcription.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AtR18 RNAe0
- Outcome
- identified by efficient in vitro transcription by Pol IIIe0
- Value
- approx. 160 nte0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
Claim · model-written summary
AtR8 RNA sequence and secondary structure were conserved across Brassicaceae taxa.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AtR8 RNAe0
- Outcome
- conserved among six additional taxa of Brassicaceaee0
- Value
- six additional taxae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“AtR8 RNA was conserved among six additional taxa of Brassicaceae, and the secondary structure of the RNA was also conserved among the orthologs”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
Claim · model-written summary
AtR8 RNA accumulated abundantly in roots and cultured-cell cytosol.
- Taxon
- ArabidopsisArabidopsist0
- Organ / stage
- plant roots and cytosol of cultured cellse0
- Gene
- AtR8 RNAe0
- Outcome
- Abundant accumulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Abundant accumulation of AtR8 RNA was observed in the plant roots and cytosol of cultured cells”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
Claim · model-written summary
AtR8 RNA was not processed into a smaller fragment.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AtR8 RNAe1
- Outcome
- not processed into a smaller fragmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The RNA was not processed into a smaller fragment and no short open reading frame was included”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
e1“AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts”
Claim · model-written summary
AtR8 RNA contained no short open reading frame.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AtR8 RNAe1
- Outcome
- no short open reading frame was includede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The RNA was not processed into a smaller fragment and no short open reading frame was included”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
e1“AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts”
Claim · model-written summary
Hypoxic stress negatively regulated AtR8 RNA expression.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- hypoxic stresse0
- Gene
- AtR8 RNAe0
- Outcome
- expression of the AtR8 RNAe0
- Direction
- negativelye0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“expression of the AtR8 RNA responded negatively to hypoxic stress”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
Claim · model-written summary
AtR8 hypoxia regulation differed from U6 snRNA regulation.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- U6 snRNAe0
- Outcome
- regulation evidently differede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“this regulation evidently differed from that of U6 snRNA”
t0“A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis”
The same questions in other papers
flooding · molecular: expression · ArabidopsisPositive and negative results
4 papers in the same direction as this paper · 6 in the opposite direction
- positive
- positive
- positive
7 papers more in this group
See all 11 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.