Advanced biochemistry

• Posttranscriptional regulation of eukaryotic gene expression involves mRNA degradation, protein degradation, and protein synthesis.
• Prokaryotes (P) have different mechanisms of mRNA degradation and protein degradation compared to Eukaryotes (E).
• Posttranscriptional controls in prokaryotes include possible start transcription, possible attenuation, capping, splicing +3’ end cleavage, and possible RNA editing.
• We suggest that splice variants with nonenzymatic functions may be more general, as evidenced by recent findings of other catalytically inactive splice-variant enzymes.
• If a protein has multiple domains, but the cell only needs one, it would be a lot of energy to transcribe all the domains via alternative splicing.
• Splicing events retain noncatalytic domains while ablating the catalytic domain to create C Ns with diverse functions.
• Each synthetase is converted into several new signaling proteins with biological activities “orthogonal” to that of the catalytic parent.
• Posttranscriptional controls in eukaryotes include possible start transcription, spatial localization, start translation, possible translational recoding, and possible RNA (de)stabilization.
• Transcription to be initiated, the polymerase must first gain access to the promoter region at the beginning of a gene.
• Promoter access is impaired by chromatin, which can inhibit transcription and must be removed or shifted for transcription to occur.
• Active promoters are found in nucleosome-depleted regions, which are flanked by specialized +1 and −1 nucleosomes on the downstream and upstream side of these regions, respectively.
• Chromatin opening is regulated differently for distinct classes of promoters.
• In the case of Pol II, one class of human promoters contains CpG islands that can impair the assembly of inhibitory nucleosomes and facilitate polymerase access.
• Promoters such as these are often found at housekeeping genes that encode for proteins that are required in all the cell types of an organism.
• Translational regulation in the cytosol involves 5’ mRNA, 7 G (A) n, 3’ ORF, uORF, eIF, modification, sequestration, masking, blocking, cap-independent initiation, re-initiation, frameshifting, readthrough, recoding, breakdown, localization, cytoplasmic polyadenylation, mature mRNA, RNA interference.
• Translational recoding includes frameshifting, +1 frameshifting, nonsense suppression, stop codon recoding, and others.
• Posttranscriptional regulation in the nucleus involves elongation pause/termination, TATA box, alternative splicing, nuclear export, transcript cleavage, and others.
• The activity of promoters that contain CpG islands can be altered by DNA methylation.
• Only a fraction of Pol II promoters is active in a particular cell.
• These promoters are activated by transcription factors that are available in the nucleus.
• In males, the absence of TRA protein results in the default splice of dsx transcripts and the loss of exon 4.
• Most somatic sexual characters are differentially determined by the 16 two dsx proteins.
• In males, the absence of SXL results in mRNAs that retain the stop codons in exon 2, leading to premature termination of translation and absence of any functional TRA protein.
• Sxl codes for an RNA-binding protein that regulates production of not only its own transcripts but also those of transformer (tra), the next gene in the sex-determination pathway.
• Hence male dsx mRNA contains exons 1–3 and 5–6, producing the male-specific DSXM isoform.
• This creates an open reading frame, which now allows the production of active TRA protein.
• These act as transcription factors that sex-specifically enhance or repress a number of downstream male- and female-specific genes, which implement the two different routes of sexual differentiation.
• Female dsx mRNA contains exons 1–4 and produces the female-specific DSXF isoform.
• Tra codes for another RNA-binding protein that causes alternative splicing of doublesex (dsx), the next downstream element in the pathway.
• In females, SXL protein blocks the canonical splice site and forces use of a cryptic splice site just downstream of the stop codons.
• Like Sxl, tra produces transcripts that contain several stop codons at the beginning of exon 2.
• In females, the presence of TRA protein, together with the cofactor TRA2, initiates an alternative splicing pattern, which includes and terminates with exon 4.
• Male Sxl transcripts produced from the late Pm promoter retain exon 3, resulting in premature termination of translation and absence of functional SXL protein.
• Transcription factors bind, in a sequence-specific manner, to DNA elements and can guide polymerase s to their target promoters.
• Transcription factors use intrinsically disordered ‘transaction’ regions that have amino acid sequences of low complexity to recruit proteins that regulate promoter accessibility and transcription initiation.
• About 1,600 human transcription factors are known.
• Artificial tethering can be used to regulate gene expression by linking a DNA-binding protein to a transcription factor.
• Promoter-proximal pausing can limit the frequency of transcription initiation, and thereby regulate a gene by changing the amount of RNA synthesized per unit of time.
• Co-activators can regulate gene expression by enhancing the activity of transcription factors.
• The importance of gene regulatory variation in morphological evolution has been extensively studied.