scholarly journals Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways

2020 ◽  
Vol 32 (6) ◽  
pp. 1845-1867 ◽  
Author(s):  
Axel Thieffry ◽  
Maria Louisa Vigh ◽  
Jette Bornholdt ◽  
Maxim Ivanov ◽  
Peter Brodersen ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Decay ◽  
Antisense Rnas ◽  
Nuclear Rna

scholarly journals Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

2019 ◽  
Author(s):  
Axel Thieffry ◽  
Jette Bornholdt ◽  
Maxim Ivanov ◽  
Peter Brodersen ◽  
Albin Sandelin
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Polymerase Ii ◽  
Rna Decay ◽  
Gene Promoters ◽  
Alternative Promoters ◽  
Control Of Gene Expression ◽  
Antisense Rnas ◽  
Nuclear Rna ◽  
Reverse Strand ◽  
Clear Cases

ABSTRACTIn animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Similarly, active enhancer regions in animals initiate transcription of exosome-sensitive enhancer RNAs (eRNAs). Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs. Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs and eRNAs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs and 113 loci producing eRNA-like transcripts were identified. In addition, we found ∼200 transcription start sites within 3’-UTR-encoding regions that produce unspliced exosome-sensitive antisense RNAs covering much of the cognate pre-mRNA. A typical representative of this class of RNAs is the previously characterized non-coding RNA controlling the expression of the key seed dormancy regulator, DELAY OF GERMINATION1. Exosome-sensitive antisense RNAs are overrepresented in transcription factor genes, suggesting a potential for widespread control of gene expression. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

scholarly journals Characterization of two distinct DP-related genes from Arabidopsis thaliana 1

FEBS Letters ◽  
2000 ◽  
Vol 486 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Zoltán Magyar ◽  
Ana Atanassova ◽  
Lieven De Veylder ◽  
Stéphane Rombauts ◽  
Dirk Inzé
Keyword(s):  
Arabidopsis Thaliana

Molecular Cloning and Characterization of a Calmodulin Gene from Arabidopsis thaliana

1994 ◽  
Vol 3 (1) ◽  
pp. 31-35 ◽  
Author(s):  
Amaresh Chandra ◽  
M. Thungapathra ◽  
Kallash C. Upadhyaya
Keyword(s):  
Arabidopsis Thaliana ◽  
Molecular Cloning ◽  
Calmodulin Gene
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