We've known for more than half-a-century that a lot of noncoding DNA is functional. Why are some people still surprised? It's a puzzlement.
A paper in Trends in Genetics caught my eye as I was looking for somethng else. The authors review the various functions of noncoding DNA such as regulatory sequences and noncoding genes. There's nothing wrong with that but the context is a bit shocking for a paper that was published in 2021 in a highly respected journal.
Leypold, N.A. and Speicher, M.R. (2021) Evolutionary conservation in noncoding genomic regions. TRENDS in Genetics 37:903-918. [doi: 10.1016/j.tig.2021.06.007]
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.