ArticlePlant physiology2009
Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis.
Article in Plant physiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 31 citations in OpenAlex.
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- Completion of the cytosolic post-chorismate phenylalanine biosynthetic pathway in plants.Nature communications · 2019Article
- Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing.Frontiers in genetics · 2019Review
- TSSPlant: a new tool for prediction of plant Pol II promoters.Nucleic acids research · 2017Article
- Improvement of barley genome annotations by deciphering the Haruna Nijo genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives.Journal of experimental botany · 2015Article
- Making sense of nuclear localization: a zinc-finger protein encoded by a cytoplasmically replicating plant RNA virus acts a transcription factor: a novel function for a member of large family of viral proteins.Plant signaling & behavior · 2013Article
- Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.Plant & cell physiology · 2013Article
- Catalyzing plant science research with RNA-seq.Frontiers in plant science · 2013Article
- T-DNA insertion mutants reveal complex expression patterns of the aldehyde dehydrogenase 3H1 locus in Arabidopsis thaliana.Journal of experimental botany · 2012Article
- Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.Nucleic acids research · 2011Article
- DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes.Plant physiology · 2011Article
- Induction of vacuolar invertase inhibitor mRNA in potato tubers contributes to cold-induced sweetening resistance and includes spliced hybrid mRNA variants.Journal of experimental botany · 2011Article
- TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.BMC genomics · 2010Article
- Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis.The Plant cell · 2009Article
- A genome-wide characterization of microRNA genes in maize.PLoS genetics · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative usage of transcription start sites (TSSs) is one of the key mechanisms to generate gene variation in eukaryotes. Here, we show diversified molecular evolution of TSSs in remotely related flowering plants, rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), by comprehensive analyses of large collections of full-length cDNAs and genome sequences. We determined 45,917 representative TSSs within 23,445 loci of rice and 35,313 TSSs within 16,964 loci of Arabidopsis, about two TSSs per locus in either species. The nucleotide features around TSSs displayed distinct patterns when the most upstream TSSs were compared with downstream TSSs. We found that CG-skew and AT-skew were clearly different between upstream and downstream TSSs, and that this difference was commonly observed in rice and Arabidopsis. Relative entropy analysis revealed that the most upstream TSSs had retained canonical cis elements, whereas downstream TSSs showed atypical nucleotide features. Expression patterns were distinguishable between upstream and downstream TSSs. These results indicate that plant TSSs were generally diversified in downstream regions, resulting in the development of new gene expression patterns. Furthermore, our comparative analysis of TSS variation between the species showed a positive correlation between TSS number and gene conservation. Rice and Arabidopsis might have evolved novel TSSs in an independent manner, which led to diversification of these two species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.