Genes whose expression are affected by MESH1 knockdown in H1975
Description
MESH1 is the metazoan homolog of bacterial SpoT involved in the bacterial stringent response. To understand the functional role of MESH1 in cancer cells, we knockdown MESH1 in H1975 cells with independent siRNAs and performed transcriptomic analysis to determine the transcriptional response to MESH1 knockdown [2]. Analysis of the first array set (Table 1) revealed a prominent transcriptional repression of TAZ, but not YAP, upon MESH1 knockdown. to determine the relevant importance of the TAZ repression in the transcriptome response to MESH1 knockdown, we performed a second profiling experiment of MESH1 knockdown in H1975 expressing TAZS89A, a constitutive form of TAZ. The comparison of the transcriptional response to MESH1 knockdown with or without TAZS89A allowed us to separate TAZ-dependent and TAZ-independent effects of the transcriptional changes of MESH1 knockdown (Table 2). Table 1: List of differentially expressed genes in H1975 upon the knockdown of MESH1 by three independent siRNAs targeting MESH1. Table 2: List of differentially expressed genes in MESH1-knockdown H1975 in H1975 with or without TAZS89A restoration
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The microarray data were normalized by the RMA (Robust Multi-Array) algorithm. and zero transformed to the negative control (siNT), where we compared transcript levels for each gene in siMESH1 groups to the siNT group (n = 3 biologically independent replicates in each siRNA group). Data were then filtered with Cluster 3.0 until ~1000 probesets were left and clustered by the genes and shown in tables. For the TAZ-affected genes, the genes were selected by affecting at least 1.5-fold by YAZ.
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Funding
National Institutes of Health
R01GM124062
National Institutes of Health
R21-AG077075
U.S. Department of Defense
W81XWH-17-1-0143