An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length

Jia, Jinbu; Lu, Wenqin; Liu, Bo; Yu, Yimin; Jin, Xianhao; Shu, Yi; Long, Yanping; Zhai, Jixian

doi:10.1101/2022.01.21.477033

Cited by 3 publications

(2 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Poly(A) tail length ranges between 10 to 104 nt long with a primary peak at 21 nt and a shorter secondary peak at 50 nt. The bimodal poly(A) tail length distribution is also observed in Arabidopsis seeding transcriptomes 35 . We also investigated alternative splicing events in the assembled transcripts.…”

Section: Reference-free Assembly Of a Sitka Spruce Transcriptomementioning

confidence: 72%

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Nip

Hafezqorani

Gagalova

et al. 2022

Preprint

View full text Add to dashboard Cite

Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. Using simulated datasets and spike-in control data, we show that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods. Furthermore, RNA-Bloom2 requires 27.0 to 80.6% of the peak memory and 3.6 to 10.8% of the total wall-clock runtime of a competing reference-free method. Finally, we showcase RNA-Bloom2 in assembling a transcriptome sample of Picea sitchensis (Sitka spruce). Since our method does not rely on a reference, it sets up the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.

show abstract

Section: Reference-free Assembly Of a Sitka Spruce Transcriptomementioning

confidence: 72%

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Nip

Hafezqorani

Gagalova

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…This may be attributed to some overall unique features of expressed genes at the early stage of rice development, such as the shorter poly(A) tail length that represses translation, as observed in animals ( Subtelny et al., 2014 ). A study using a more accurate poly(A) enrichment-free and nanopore-based method found that, in Arabidopsis , poly(A) tail length was much shorter in the root ( Jia et al., 2022 ). However, comparison of the dispersion of expression across genes at the translational level led to the finding that the panicle showed increased variance ( Figure 2 B).…”

Section: Discussionmentioning

confidence: 99%

Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

Zhu

Zhou

Che

et al. 2023

Plant Communications

View full text Add to dashboard Cite

Epitranscriptome insights into Riccia fluitans L. (Marchantiophyta) aquatic transition using nanopore direct RNA sequencing

Maździarz,

Krawczyk,

Kurzyński

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

Background Riccia fluitans, an amphibious liverwort, exhibits a fascinating adaptation mechanism to transition between terrestrial and aquatic environments. Utilizing nanopore direct RNA sequencing, we try to capture the complex epitranscriptomic changes undergone in response to land-water transition. Results A significant finding is the identification of 45 differentially expressed genes (DEGs), with a split of 33 downregulated in terrestrial forms and 12 upregulated in aquatic forms, indicating a robust transcriptional response to environmental changes. Analysis of N6-methyladenosine (m6A) modifications revealed 173 m6A sites in aquatic and only 27 sites in the terrestrial forms, indicating a significant increase in methylation in the former, which could facilitate rapid adaptation to changing environments. The aquatic form showed a global elongation bias in poly(A) tails, which is associated with increased mRNA stability and efficient translation, enhancing the plant’s resilience to water stress. Significant differences in polyadenylation signals were observed between the two forms, with nine transcripts showing notable changes in tail length, suggesting an adaptive mechanism to modulate mRNA stability and translational efficiency in response to environmental conditions. This differential methylation and polyadenylation underline a sophisticated layer of post-transcriptional regulation, enabling Riccia fluitans to fine-tune gene expression in response to its living conditions. Conclusions These insights into transcriptome dynamics offer a deeper understanding of plant adaptation strategies at the molecular level, contributing to the broader knowledge of plant biology and evolution. These findings underscore the sophisticated post-transcriptional regulatory strategies Riccia fluitans employs to navigate the challenges of aquatic versus terrestrial living, highlighting the plant’s dynamic adaptation to environmental stresses and its utility as a model for studying adaptation mechanisms in amphibious plants.

show abstract

An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length

Cited by 3 publications

References 44 publications

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

Epitranscriptome insights into Riccia fluitans L. (Marchantiophyta) aquatic transition using nanopore direct RNA sequencing

Contact Info

Product

Resources

About