Consider this thought from a commentary at Nature:
A great debate pre-dated the start of the HGP: was it worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome? Thanks in large part to the HGP, it is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression.
With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set (1900 to 2017; see SI, Fig. S3a). For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis & Albert-László Barabási, “A wealth of discovery built on the Human Genome Project — by the numbers” at Nature
But wasn’t a vast pile of junk DNA supposed to be one of the Great Proofs of Darwinism in the DNA? Funny, no one suggests that the constant diminution of the pile is evidence against the theory that its presence was supposed to be evidence for. Now why do you think that might be?
See also: Junk DNA regulates regeneration of tissues and organs.