Junk DNA goodbye: the nail in the coffin (Introduction)

by David Turell , Wednesday, November 29, 2023, 18:17 (361 days ago) @ David Turell

The role of RNA:

https://evolutionnews.org/2023/11/the-new-post-junk-dna-paradigm-of-molecular-biology-r...

“'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.” He summarizes the new paradigm this way:

"n simplified Kuhnian terms, the dominant paradigm in molecular biology since its foundation that “genes encode proteins and sequences that do not are mainly junk” should be replaced by “genes encode proteins and regulatory RNAs, the latter required for the epigenetic control of developmental trajectories”. RNA is not simply an intermediate between gene and protein, but a major player in gene regulation and a contributor to inheritance.

"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.”

"Mattick has explained this new paradigm elsewhere as well. In a weighty academic book published earlier this year, RNA: The Epicenter of Genetic Information (Taylor & Francis), Mattick along with bioengineer Paulo Amaral argue that “the genomes of humans and other complex organisms are not full of junk.” They acknowledge that this is “contrary to long-held … dogmas of evolutionary theory.” Here’s the striking quote in full:

"While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory."

JOHN MATTICK AND PAULO AMARAL, RNA: THE EPICENTER OF GENETIC INFORMATION (CRC-TAYLOR & FRANCIS, 2023), P. VII.

Comment: it is not my intent to beat the subject to death. This article teaches us more about RNA's many functions.