Like much of the rest of the world that follows science news, we have been overwhelmed by the implications of ENCODE 2.0. From reading through the papers and looking at the data, it is quite clear that the unit “gene” is no more. That is to say, the “gene” is to morphogenesis what “phlogiston” is to chemistry and physics….an obsolete concept. And with the former void of content, the framework of evolutionary/population genetics is, well, gone. That’s right: Gone. What do we inherit, then? A phenotype (= RNA sequences; transcripts).
Note well:

…three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
This supports and is consistent with earlier observations of a highly interleaved transcribed genome, but more importantly, prompts the reconsideration of the definition of a gene. As this is a consistent characteristic of annotated genomes, we would propose that the TRANSCRIPT be considered as THE BASIC ATOMIC UNIT OF INHERITANCE. Concomitantly, the term gene would then denote a higher-order concept intended to capture all those transcripts (eventually divorced from their genomic locations) that contribute to a given phenotypic trait. (Landscape of transcription in human cells. Sarah Djebali et al. Nature 2012 489: 101-108.)

And:

Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order framework around which individual transcripts coalesce, creating a poly-functional entity that assumes different forms under different cellular states, guided by differential utilization of regulatory DNA. (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.)