Imagine discovering a loss-of-function mutation in a eukaryotic gene. You determine the gene's nucleotide sequence from the start site for transcription to the termination point of transcription and find no differences from the wild-type sequence. Explain where you think the mutation might be and how the mutation might be acting.

Verified step by step guidance

1. First, consider that the mutation might be located in regulatory regions of the gene, such as the promoter, enhancers, or silencers, which are not typically included in the transcribed region. These regions are crucial for the control of gene expression.
2. Next, think about the possibility of a mutation in the splice sites of the pre-mRNA. Incorrect splicing can lead to a non-functional protein, even if the sequence of the exons remains unchanged.
3. Consider the impact of mutations in the 5' untranslated region (UTR) or 3' UTR of the mRNA. These regions can influence mRNA stability, translation efficiency, or localization, all of which can affect gene function without altering the protein-coding sequence.
4. Evaluate the possibility of epigenetic changes, such as DNA methylation or histone modification, which can affect gene expression without altering the nucleotide sequence. These changes can lead to a loss of function by preventing transcription.
5. Finally, explore the potential for a mutation in a non-coding RNA that interacts with the gene of interest. Non-coding RNAs can regulate gene expression at various levels, including chromatin remodeling, transcription, and post-transcriptional modifications.