Junk DNA goodbye!: even pseudogenes have functions (Introduction)

by David Turell , Thursday, January 09, 2020, 05:03 (1781 days ago) @ David Turell

The evidence keeps piling up:

https://www.nature.com/articles/s41576-019-0196-1

"Abstract
Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution."

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"Many pseudogenes contain a frequency of mutations that render them unlikely to be (or incapable of being) translated into proteins. However, such mutations do not necessarily preclude pseudogenes from performing a biological function.

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"Another mechanism through which pseudogenes can function is by influencing chromatin or genomic architecture. HBBP1, a pseudogene residing within the haemoglobin locus, enables the dynamic chromatin changes that regulate expression of fetal and adult globin genes during development. Notably, although inhibiting HBBP1 transcription has no effect, deletion of the genomic locus reactivates fetal globin expression. HBBP1 DNA contacts, but not transcription, are required for suppressing the expression of fetal globin genes in adult erythroid cells.

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"The examples of pseudogene function elaborated on here should not imply that pseudogene functionality is likely to be confined to isolated instances. At least 15% of pseudogenes are transcriptionally active across three phyla, many of which are proximal to conserved regulatory regions. It is estimated that at least 63 new human-specific protein-coding genes were formed by retrotransposition since the divergence from other primates. Numerous ‘retrogenes’ continue to be recognized as functional protein-coding genes rather than pseudogenes across species. High-throughput mass spectrometry and ribosomal profiling approaches have identified hundreds of pseudogenes that are translated into peptides. Although the functions of these peptides remain to be experimentally determined, such examples illustrate the challenge in substantiating a gene–pseudogene dichotomy.

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"In addition to the demotivation into exploring pseudogene function by the a priori assumption that they are functionless, their systematic study has also been hindered by a lack of robust methodologies capable of distinguishing the biological activities of pseudogenes from the functions of the genes from which they are derived."

Comment: More evidence that even Darwinist scientist are recognizing their mistake in not looking carefully at genes and portions of the genome that do not simply code for protein. Most of DNA is not junk (about 80%) and removes a 'proof' for random discarded mutations and other stretches of DNA as the backbone of Darwinian style of evolution. If not by chance, then design is required.