Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

Schmitz, Robert J.; Grotewold, Erich; Stam, Maike

doi:10.1093/plcell/koab281

Cited by 189 publications

(160 citation statements)

References 290 publications

(614 reference statements)

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“…The importance of exclusivity of these transcripts in fiber tissue needs to be explored further; however, tissue-specific variants have been shown to regulate the flowering at different developmental stages in Arabidopsis ( Rosloski et al, 2013 ; Ghelli et al, 2018 ). The tissue-specific expression of variants may be due to the presence of tissue-specific promoter architecture, which requires a tightly regulated transcriptional machinery ( Srivastava et al, 2018 ; Das and Bansal, 2019 ; Schmitz et al, 2021 ). During the domestication of cultivated cotton species, these transcripts might be positively selected in modern cotton for fiber-specific features ( Figures 6A,B ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits

et al. 2022

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Cotton fiber development is still an intriguing question to understand fiber commitment and development. At different fiber developmental stages, many genes change their expression pattern and have a pivotal role in fiber quality and yield. Recently, numerous studies have been conducted for transcriptional regulation of fiber, and raw data were deposited to the public repository for comprehensive integrative analysis. Here, we remapped > 380 cotton RNAseq data with uniform mapping strategies that span ∼400 fold coverage to the genome. We identified stage-specific features related to fiber cell commitment, initiation, elongation, and Secondary Cell Wall (SCW) synthesis and their putative cis-regulatory elements for the specific regulation in fiber development. We also mined Exclusively Expressed Transcripts (EETs) that were positively selected during cotton fiber evolution and domestication. Furthermore, the expression of EETs was validated in 100 cotton genotypes through the nCounter assay and correlated with different fiber-related traits. Thus, our data mining study reveals several important features related to cotton fiber development and improvement, which were consolidated in the “CottonExpress-omics” database.

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Section: Discussionmentioning

confidence: 99%

Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits

et al. 2022

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“…One gene pair ( PtHXK2 and 6 ) was speculated to undergo a segmental duplication combined with the sequence analyses, suggesting notable physiological roles associated with evolved mechanisms to adapt to stress stimuli ( Figure 2 a). The cis -regulatory elements predicted in promoter regions indicated the dynamic regulation and evolution of specific gene expression upon various environmental cues [ 53 ]. Therefore, the deduction of principal diverse cis -regulatory elements related to phytohormone response (ABA, GA, MeJA, and Auxin) and stress factors (e.g., MBS, TC-rich, and LRT), along with TF binding sites, provided a hint that the molecular regulation of PtHXKs depends significantly on the crosstalk between phytohormone and glucose signaling pathways [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Survey and Expression Analyses of Hexokinase Family in Poplar (Populus trichocarpa)

Han

Xiong

et al. 2022

Plants

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Hexokinase (HXK) family proteins exert critical roles in catalyzing hexose phosphorylation, sugar sensing, and modulation of plant growth and stress adaptation. Nevertheless, a large amount remains unknown about the molecular profile of HXK enzymes in Populus trichocarpa, a woody model tree species. A genome-wide survey of HXK-encoding genes, including phylogenies, genomic structures, exon/intron organization, chromosomal distribution, and conserved features, was conducted, identifying six putative HXK isogenes (PtHXK1-6) in the Populus genome. The evolutionary tree demonstrated that 135 homologous HXKs between 17 plant species were categorized into four major subfamilies (type A, B, C, and D), clustering one plastidic (PtHXK3) and five mitochondrial PtHXKs grouped into type A and B, respectively. The in silico deduction prompted the presence of the conserved sugar-binding core (motif 4), phosphorylation sites (motif 2 and 3), and adenosine-binding domains (motif 7). The transcriptomic sequencing (RNA-seq) and the quantitative real-time PCR (qRT-PCR) assays revealed that three isogenes (PtHXK2, 3, and 6) were abundantly expressed in leaves, stems, and roots, while others appeared to be dominantly expressed in the reproductive tissues. Under the stress exposure, PtHXK2 and 6 displayed a significant induction upon the pathogenic fungi (Fusarium solani) infection and marked promotions by glucose feeding in roots. In contrast, the PtHXK3 and 6 are ABA-responsive genes, following a dose-dependent manner. The comprehensive analyses of the genomic patterns and expression profiling provide theoretical clues and lay a foundation for unraveling the physiological and signaling roles underlying the fine-tuned PtHXKs responding to diverse stressors.

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“…This suggests that these cis ‐regulatory elements do not have the same accessibility for CRL1. The accessibility of cis ‐regulatory elements for a transcription factor in planta can be modulated by chromatin structure, DNA methylation, or the interaction with another protein in its near vicinity (Schmitz et al., 2022). Nevertheless, our data revealed that OsROP and OsbHLH044 constitute direct CRL1 target genes in rice stem bases.…”

Section: Discussionmentioning

confidence: 99%

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

et al. 2022

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SUMMARY In cereals, the root system is mainly composed of post‐embryonic shoot‐borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2‐LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD‐box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1‐box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1‐regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1‐box or an LBD‐box in their promoters. In planta, ChIP‐qPCR experiments targeting two of these genes that include both a CRL1‐ and an LBD‐box in their promoter show that CRL1 binds preferentially to the LBD‐box in these promoter contexts. CRISPR/Cas9‐targeted mutation of these two CRL1‐regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix–loop–helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.

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Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

Cited by 189 publications

References 290 publications

Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits

Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits

Genome-Wide Survey and Expression Analyses of Hexokinase Family in Poplar (Populus trichocarpa)

CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice

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