Regulatory networks of circRNAs related to transcription factors in Populus euphratica Oliv. heteromorphic leaves

Abstract

Circular RNAs (circRNAs) are a novel class of non-coding RNAs that are characterized by a covalently closed circular structure. They have been widely found in Populus euphratica Oliv. heteromorphic leaves (P. hl). To study the role of circRNAs related to transcription factors (TFs) in the morphogenesis of P. hl, the expression profiles of circRNAs in linear, lanceolate, ovate, and broad-ovate leaves of P. euphratica were elucidated by strand-specific sequencing. We identified and characterized 22 circRNAs related to TFs in P. hl at the four developmental stages. Using the competing endogenous RNAs hypothesis as a guide, we constructed circRNA–miRNA–TF mRNA regulatory networks, which indicated that circRNAs antagonized microRNAs (miRNAs), thereby influencing the expression of the miRNA target genes and playing a significant role in transcriptional regulation. Gene ontology annotation of the target TF genes predicted that these circRNAs were associated mainly with the regulation of leaf development, leaf morphogenesis, signal transduction, and response to abiotic stress. These findings implied that the circRNAs affected the size and number of cells in P. hl by regulating the expression of TF mRNAs. Our results provide a basis for further studies of leaf development in poplar trees.

Integrating genome-wide association and transcriptome analysis to provide molecular insights into heterophylly and eco-adaptability in woody plants

“…To adapt to the changeable environment, plants have formed a variety of adaptive strategies; altering leaf morphology is one of the important adaptation mechanisms for heterophyllous plants [ 27 , 28 ]. Although heterophylly has been the subject of a preliminary study in aquatic and amphibian plants [ 6 , 10 ], the genetic basis for eco-adaptability of heterophyllous leaves is still unclear in terrestrial woody plants, and the relevant studies were mainly carried out in Populus euphratica [ 22 , 24 , 29 ]. To further clarify the mechanisms underlying heterophylly in woody plant species, we systematically and comprehensively evaluated the variation of heterophyllous leaves in a natural population of paper mulberry, which exhibits significant heterophylly and eco-adaptability [ 30 ].…”

Identification and regulatory network analysis of SPL family transcription factors in Populus euphratica Oliv. heteromorphic leaves

“…Three biological replicates and three technical replicates were used for each RNA sample. The experiment was carried out according to the method described by Bao 33 .…”

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

“… The numbers represent the total number of circRNAs identified in each study ( Bai et al., 2021 ; Bao et al., 2019 ; Bian et al., 2021 ; Chen et al., 2017 , 2022 ; Darbani et al., 2016 ; Dong et al., 2021 ; Eisenberg and Levanon, 2018 ; Fu et al., 2019 , 2020 ; Ghorbani et al., 2018 ; Han et al., 2021 ; He et al., 2020 ; Hong et al., 2020 ; Jiang et al., 2021 ; Li et al., 2020a , 2020b , 2021a ; Liang et al., 2019 ; Liu et al., 2017 , 2019c , 2020a , 2021a ; Luo et al., 2020 ; Lv et al., 2020 ; Ma et al., 2021a , 2021b ; Medina et al., 2021 ; Meng et al., 2018 ; Pan et al., 2018 ; Qin et al., 2018 ; Ren et al., 2018 ; Salih et al., 2021 ; Shi et al., 2021 , 2022 ; Shu et al., 2021 ; Sun et al., 2016 , 2020 , 2021 , Tang et al., 2018 ; Tong et al., 2018 ; Wang et al., 2017a , 2017b , 2018a , 2018b , 2019c , 2019e , 2020a , 2021a , 2021b , 2021c , 2022a , 2022b , Wu et al., 2020 ; ...…”