- Scientists called it “junk DNA” for decades because they were clueless. Now they know that 80 percent of the genome is transcribed in protein codes. The complexity of the activities in the nucleus of a cell is incredible. A cell nucleus is a dynamic place. There are three major classes of nuclear functions: RNA processing, heterochromatin assembly, and gene regulation.
- All things are triune, with binary interactives.
- Noncoding RNA Importance:
- ncRNAs form processing hubs around genomic DNA regions that are being transcribed.
- ncRNAs and dozens of snoRNAs (small nucleolar RNAs) cluster around genes transcribed for ribosomal RNAs. These ncRNAs form multi-way contact with each other. ncRNAs cluster at splicing sites with a high density of RNA polymerase (the transcription machinery).
- Nucleolus: contains transcribed ribosomal RNAs and associated processing molecules.
- Speckles: contain pre-mRNAs and splicing components.
- Transcriptional condensates: contain RNA polymerase II machines and factors.
- ncRNAs are associated closely with forming small nuclear RNAs (snRNAs). These snRNA transcripts are involved in functional components of the spliceosome at thousands of nascent pre-mRNA targets. ncRNAs concentrate around transcripts where centromeres are forming. These ncRNAs primarily localize over centromere-proximal regions, organizing into higher-order structures containing these ncRNAs. Multiple centromere-proximal areas combine with different chromosomes. Despite being separated by large genomic distances, these DNA regions form long-range contacts.
- Coding RNAs refer to mRNA encoding protein as various components, including enzymes, cell structures, and signal transductors. NNoncodingRNAs act as cellular regulators without encoding proteins.
- Many regions of noncoding DNA play a role in controlling gene activity, meaning they help determine where and when specific genes are switched off and on. Other areas of noncoding DNA are essential for protein assembly.
- Hundreds of ncRNAs build high-concentration areas throughout the nucleus, and specific RNAs recruit various regulators into these areas. These RNAs then shape long-range DNA contacts, heterochromatin assemblies, and gene expressions. (All things are triune, with binary interactives). This binds with diffusible regulators and regulates the requisite functions of the cell. The complexity of the hierarchical organization in the nucleus is off the charts.
- Spatial compartments have a triune function: (1) Nascent RNAs localized near their DNA. (2) This DNA then forms long-range 3D contacts. (3) Diffusible ncRNAs associate with the nascent RNAs and DNA within the compartment. Hundreds of IncRNAs form high-concentration spatial areas throughout the nucleus. Transcripts, formerly thought useless, have risen to the status of essential players.
- If something is working, it didn’t happen accidentally.
- ncRNAs can act as seeds to drive spatial localization of otherwise diffusive ncRNA and protein molecules.
- There is a common mechanism by which RNA can mediate nuclear compartmentalization. Nuclear RNAs can form high-concentration spatial territories close to their transcriptional seed location. Then bind to diffusible regulatory ncRNAs and proteins. Finally, act to change the distribution of diffusible molecules dynamically.
- By recruiting diffusible regulatory factors to multiple DNA sites, these ncRNAs may also drive the coalescence of distinct DNA regions into a shared area.
- Various RNAs are critical for organizing long-range DNA interactions around specific nuclear bodies.
Two differences distinguish DNA from RNA: (a) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (a type of ribose that lacks one oxygen atom), and (b) RNA has the nucleobase uracil while DNA contains thymine.
- Randomness can’t even build a bobsled. Ditto for natural selection.
