For the longest time we didn't know what the purpose of the DNA between genes served. More recently, we have been discovering rhat these non-ncoding sections play important regulatory roles by providing binding sites for promoters, repressers, histones, and other proteins that interact with DNA. For a particular gene to function properly, it not only needs the nucleotide sequence to remain intact, but also for its regulatory functionality to remain the same. Altering the non-coding DNA surrounding a gene will almost certainly change its level of transcription.