The New Post-Junk-DNA Paradigm of Molecular Biology: RNA Genes
As I wrote here yesterday, molecular biologist John Mattick’s new Bio Essays paper reviews many “anomalies” in the evidence that contradict the “junk DNA” paradigm that has reigned in biology over the past few decades. If there are so many problems with the paradigm, why do so many biologists still adhere to it? Mattick believes it’s because “many molecular biologists are invested in the current paradigm and a coherent alternative synthesis has not been offered.” His BioEssays paper thus turns to the task of offering a new paradigm that accepts the importance of non-coding DNA. But he notes that according to the famous historian of scientist Thomas Kuhn, a new paradigm won’t be accepted “unless it is both credible and consistent with the established body of knowledge.”
“Another Class of Genes That Produce RNAs”
The main point of Mattick’s new paradigm is that in addition to protein-coding genes, there’s “another class of genes that produce RNAs.” These “RNA genes” perform many diverse functions, but primarily they “act as regulatory molecules to control gene expression and organise nuclear territories and cytoplasmic domains during ontogeny.
These RNA genes have many functions but a large proportion entail gene regulation-related functions that fall within the category of epigenetics. Mattick identifies multiple types of RNAs that perform these important functions:
Small regulatory RNAs (e.g., microRNAs) which regulate translation of proteins, regulate epigenetic process, and are also involved in alternative splicing.Long non-coding RNAs (called “lncRNAs”) which also influence gene expression by controlling transcription factors and transcription-splicing and also modulate many genetically variable traits. Some may even encode peptides.
Transposable elements are important for gene structure and function, and gene regulatory networks.
Overall these types of functional RNAs undergo much post-transcriptional editing and are important for brain function, and also can foster “transgenerational epigenetic inheritance.”
As Mattick and Amaral note in their book, for many years it was strongly resisted by biologists who followed “the dogmas of evolutionary theory.” According to the dogmas, DNA that doesn’t code for proteins is largely junk. There’s one simple reason why this junk DNA paradigm is falling apart: the evidence shows that non-protein-coding DNA is functional. Rather than being junk, non-protein-coding-DNA is full of RNA genes that produce RNA molecules with a myriad of functions, perhaps the most prominent of which is regulating the expression of protein-coding genes. This new RNA gene paradigm is replacing the junk DNA paradigm.
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