CW198 acts as a genetic insulator to block enhancer-promoter interaction in plants

Jiang, Li; Liu, Yue; Wen, Zhi‐Hong; Yang, Yazhou; Singer, Stacy D.; Bennett, Dennis; Xu, Wenying; Yu, Zhifang; Cohn, Josh; Luo, Xi; Liu, Zhongchi; Chae, Hyunsook; Que, Qiudeng; Liu, Zongrang

doi:10.1007/s11248-022-00326-6

Cited by 1 publication

(1 citation statement)

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“…After identifying two new insulator-like sequences, we repeated the earlier motif analysis but limiting our dataset to 12 sequences reported to have insulator-like function in plants: BEAD1c (Zhong and Krangel, 1997), CW198 (Jiang et al, 2022), EXOB (Singer et al, 2010), HIV-LTR (Eggermont and Proudfoot, 1993), RS2-9 (Liu et al, 2022), TBS (Hily et al, 2009), UASrpg (Bi and Broach, 1999), Ugi1, Ugi3, Ugi4 (Illa-Berenguer et al), Ugi21 and Ugi22 (this study). Pairwise local alignments with BLASTn uncovered no evidence of any conserved regions shared between any pair of reported insulators.…”

Section: Conserved Motifs Among Reported Insulator-like Sequencesmentioning

confidence: 99%

Mining the Utricularia gibba genome for insulator-like elements for genetic engineering

Laspisa,

Illa-Berenguer,

Bang

et al. 2023

Front. Plant Sci.

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IntroductionGene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal.MethodsTo identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity.ResultsWe identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller.DiscussionGiven the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.

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