NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells.

The bidirectional mammalian promoter for mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm) contains an array of four CCAAT boxes separated by 34-49 bp. In mouse, these elements were shown previously to interact with transcription factor NF-Y and to be required for efficient transcription. Here we show that the CCAAT boxes of the human promoter also influence relative transcriptional activities in the two directions, although they are not absolutely required for transcription. By mutating CCAAT boxes in all possible permutations, we demonstrate that their function is combinatorial, although not simply additive. EMSA indicated that NF-Y interacts with the array in two alternate ways related to the directional selectivity of transcription. Inversion and/or exchange of individual CCAAT boxes had minimal effects on directional selectivity. Over-expression of wild-type or dominant-negative NF-Y affected transcription in the Sarsm direction only, but in human cells, concomitant expression of dominant-negative constructs for other factors was needed to reveal such effects. We propose that the array of NF-Y type CCAAT boxes maintains bidirectional transcription with an appropriate directional selectivity. Computational analysis confirmed that NF-Y type CCAAT boxes are found preferentially in bidirectional promoters, but many such promoters lack them and must be regulated in another way.

Modulation of Mrps12/Sarsm promoter activity in response to mitochondrial stress.

Transcription from the bidirectional promoter of two mouse genes encoding components of the mitochondrial translational apparatus, mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm), was shown previously to be dependent upon an array of four CCAAT boxes, interacting with the transcription factor NF-Y. Here we report that the homologous human promoter is governed by a CCAAT box array acting in an essentially similar manner. Analysis of the transcriptional response of both the human and mouse promoters to various mitochondrially acting toxins, including inhibitors of mitochondrial protein synthesis, and agents that bring about uncoupling or respiratory chain inhibition, produced either of two distinct outcomes, depending on the cell type and the conditions used. In mouse C2C12 myoblasts, human HEK293 cells or U2OS osteosarcoma cells, plus HeLa cells at high drug doses or mouse 3T3 fibroblasts subjected to prolonged drug exposure, a dose-dependent, bidirectional suppression of transcription was observed. In 3T3 cells subjected only to pre-treatment with the drugs, bidirectional Mrps12/Sarsm promoter activity was strongly stimulated. A similar, though weaker stimulation was observed at lower drug doses in HeLa cells. Reporter studies using mutated variants of the mouse promoter construct indicated that the stimulation of promoter activity in response to mitochondrial OXPHOS stress in 3T3 cells was independent of the CCAAT box array and of putative binding sites for NRF-2, AP-1 and other transcription factors, whereas transcriptional downregulation under prolonged mitochondrial stress was CCAAT box-dependent. Promoter stimulation was correlated with mitochondrial ROS production, which may be a crucial component in its signalling.

The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y.

The genes for mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm and Sars2) are oppositely transcribed from a conserved promoter region of <200 bp in both human and mouse. Using a dual reporter vector we identified an array of 4 CCAAT box elements required for efficient transcription of the two genes in cultured mouse 3T3 cells, and for enforcing directionality in favour of Mrps12. Electrophoretic mobility shift assay (EMSA) and in vivo footprinting confirmed the importance of these promoter elements as sites of protein-binding, and EMSA supershift and chromatin immunoprecipitation (ChIP) assays identified NF-Y as the key transcription factor involved, revealing a common pattern of protein-DNA interactions in all tissues tested (liver, brain, heart, kidney and 3T3 cells). The inherently bidirectional activity of NF-Y makes it an especially suitable factor to govern promoters of this class, whose expression is linked to cell proliferation.