> See also: > - Reference # Transcriptional Regulation One of the most common mechanisms of gene The process of transcription cannot occur if the DNA is tightly compacted in its chromosomal form.**Chromatin accessibility**, or the is neccessary ## Transcription Factors **Transcription Factors** - TFIIF is a general transcription factor bound to RNA Polymerase II before it is recruited to the promoter - TFIIH is a type of DNA helicase - TBP is a transcription factor utilized by all three eukaryotics RNA polymerases https://en.wikipedia.org/wiki/Transcription_factor - The general transcription factor TFIIH can: - assist in formation of the closed complex - unwind the DNA near the transcriptional start site - directly interact with RNA polymerase II - recruit nucleotide excision repair proteins to the site of a DNA lesion ### Sigma Factors (Bacteria) | Subunit Class | Function of Genes Activated | -35 | -10 | | -------------------- | -------------------------------------------------- | --- | --- | | $\sigma^{70}$ (RpoD) | “Housekeeping” gene expressed in all growing cells | | | | $\sigma^{38}$ (RpoS) | Starvation/stationary growth phase | | | | $\sigma^{28}$ (RpoF) | Flagellar structure and movement | | | | $\sigma^{32}$ (RpoH) | Heat Shock | | | | $\sigma^{54}$ (RpoN) | Nitrogen uptake and metabolism | | | ## RNA & The Transcriptome *5’ Untranslated Region (UTR)* - aa *3’ Untranslated Region (UTR)* - Stagbility elements ![[Pasted image 20240329175314.png|300]] - By mass, the majority in cells is rRNA - By molecules, the majority in cells is tRNA - Long noncoding RNAs that can act as scaffolding guides, effectors/enhancers that regulate genes, and a signal for viral infection - may be byproducts or junk, and just happen to serve a valuable purpose - also involved in chromatin regulation, imprinting, X inactivation, telomere replication and transposon repression ![[Pasted image 20240329180153.png|400]] **RNA Polymerase Mediated Inhibition** - Anti-sense RNA can be generated along the sense DNA strand (inverse of normal process) that can then bind to the sense RNA due to their complimentary nature - Remember that the “sense” strand *correlates* to the DNA sequence that will actually be used during translation, but in order to actually make a “copy” of that, RNA Polymerase will use the “anti-sense” DNA strand and generate its complementary “sense” mRNA **MicroRNA (miRNA) and RNA Interference (RNAi)** - MicroRNA is initially a ssRNA that forms a secondary hairpin structure - MicroRNA → Dicer → RISC - Analogous to: - CRISPR/Cas9 System - *Small Interfering RNA* - Functionally similar to miRNA, but originates from dsRNA (viruses, transposons) - Cells take dsRNA and transform it into a miRNA-like complex using Dicer and RISC - Unlike miRNA, siRNA must have perfectly complementary base pairings - Argonaute (protein & siRNA) RISC system - MicroRNAs are tissue specific, involved in setting up the body plan, DNA repair, etc - miRNAs has been shown to be heritable - Potential evidence of Lamarckism, which counters the Mendelian belief that all heredity is from DNA - a ![[Pasted image 20240329190716.png|300]]