Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana

Nicholas Rutley, Laetitia Poidevin, Tirza Doniger, Richard L. Tillett, Abhishek Rath, Javier Forment, Gilad Luria, Karen A. Schlauch, Alejandro Ferrando, Jeffery F. Harper, Gad Miller

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Key message: Arabidopsis pollen transcriptome analysis revealed new intergenic transcripts of unknown function, many of which are long non-coding RNAs, that may function in pollen-specific processes, including the heat stress response. Abstract: The male gametophyte is the most heat sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison with HS in cauline leaves and other RNAseq experiments indicated that 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed that 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional and play a significant role in pollen biology, including the HS response.

Original languageEnglish
Pages (from-to)61-78
Number of pages18
JournalPlant Reproduction
Issue number1
Early online date18 Jan 2021
StatePublished - Mar 2021

Bibliographical note

Funding Information:
This research was supported by grants to GM and JFH from BARD IS- 4652–13, GM from BSF-2016605, JFH from NSF IOS 1656774, and JFH from UNR Hatch NEV00384. AF was funded by the Spanish Ministry of Science Innovation and Universities [BIO2015-70483-R].

Funding Information:
We thank the Core Facility unit of the Faculty of Life Sciences in Bar Ilan University for providing qRT-PCR services.

Publisher Copyright:
© 2021, The Author(s).


  • Arabidopsis
  • Heat
  • Long noncoding RNA
  • Pollen
  • Transcriptome
  • Translatome


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