Phosphate deficiency alters transcript isoforms via alternative transcription start sites.
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State: Public
Version: Final published version
License: CC BY-NC-ND 4.0
State: Public
Version: Final published version
License: CC BY-NC-ND 4.0
Serval ID
serval:BIB_DFA16258AAE3
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Phosphate deficiency alters transcript isoforms via alternative transcription start sites.
Journal
The Plant journal
ISSN
1365-313X (Electronic)
ISSN-L
0960-7412
Publication state
Published
Issued date
10/2024
Peer-reviewed
Oui
Volume
120
Number
1
Pages
218-233
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Publication Status: ppublish
Abstract
Alternative transcription start sites (TSS) are widespread in eukaryotes and can alter the 5' UTR length and coding potential of transcripts. Here we show that inorganic phosphate (Pi) availability regulates the usage of several alternative TSS in Arabidopsis (Arabidopsis thaliana). In comparison to phytohormone treatment, Pi had a pronounced and specific effect on the usage of many alternative TSS. By combining short-read RNA sequencing with long-read sequencing of full-length mRNAs, we identified a set of 45 genes showing alternative TSS under Pi deficiency. Alternative TSS affected several processes, such as translation via the exclusion of upstream open reading frames present in the 5' UTR of RETICULAN LIKE PROTEIN B1 mRNA, and subcellular localization via removal of the plastid transit peptide coding region from the mRNAs of HEME OXYGENASE 1 and SULFOQUINOVOSYLDIACYLGLYCEROL 2. Several alternative TSS also generated shorter transcripts lacking the coding potential for important domains. For example, the EVOLUTIONARILY CONSERVED C-TERMINAL REGION 4 (ECT4) locus, which encodes an N <sup>6</sup> -methyladenosine (m <sup>6</sup> A) reader, strongly expressed under Pi deficiency a short noncoding transcript (named ALT <sub>ECT4</sub> ) ~550 nt long with a TSS in the penultimate intron. The specific and robust induction of ALT <sub>ECT4</sub> production by Pi deficiency led to the identification of a role for m <sup>6</sup> A readers in primary root growth in response to low phosphate that is dependent on iron and is involved in modulating cell division in the root meristem. Our results identify alternative TSS usage as an important process in the plant response to Pi deficiency.
Keywords
Arabidopsis/genetics, Arabidopsis/metabolism, Transcription Initiation Site, Phosphates/deficiency, Phosphates/metabolism, 5' Untranslated Regions/genetics, Gene Expression Regulation, Plant, RNA, Messenger/genetics, RNA, Messenger/metabolism, Arabidopsis Proteins/genetics, Arabidopsis Proteins/metabolism, ECT4, noncoding RNA, phosphate deficiency, transcription start sites, upstream open reading frame
Pubmed
Web of science
Open Access
Yes
Create date
26/08/2024 10:48
Last modification date
01/10/2024 6:21