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. 2017 Aug 30;45(20):11658–11672. doi: 10.1093/nar/gkx762

Figure 4.

Figure 4.

The LZA element can be used to predict genes regulated by zinc deficiency in Caenorhabditis elegans. (A) An overview of the strategy used to identify candidate genes regulated by zinc deficiency. The Regulatory Sequence Analysis Tools database was used to obtain the predicted promoters of all C. elegans genes (C. elegans promoterome). MEME was used to generate the LZA weight matrix. The Find Individual Motif Occurrences program was used to search the promoterome for matches to the LZA weight matrix, generating a list of candidate genes. (B) Sequence alignments of the LZA elements in the promoter regions of C. elegans genes zipt-7.1, zipt-2.1 and zipt-2.3, which were used to generate the LZA weight matrix, and D2024.10, F44E7.5, R08F11.4 and srw-7, which were identified in the genome-wide LZA element search. Identical residues are highlighted in black. (C) A population of mixed-stage, wild-type animals were cultured with 0 or 40 μM TPEN for 16 h. RNA was analyzed by qRT-PCR. Values are the ratio of mRNA levels at 40 μM TPEN/ 0 μM TPEN, an indication of transcriptional activation, and are the average of three biological replicates; error bars display standard deviation. Each gene displayed significantly increased mRNA levels at 40 μM TPEN (*P < 0.01).