After transcription {post-transcription}, eukaryotic mRNA can change. For example, poly(A) polymerase adds 100 to 300 adenosines as a polyA tail to RNA 3' ends. Methylated guanosine can add to RNA 5' ends.
RNA can alter {adenosine-to-inosine editing} (A-to-I editing), especially in primate Alu repeats.
To regulate gene expression, cell or virus mechanisms can add methyl groups {DNA methylation} {methylation} to cytosines preceding guanines {CG pair}.
virus
Virus can methylate host genes to inactivate them.
cancer
Cancer genes often have demethylated cytosines in promoters.
drugs
Valproic acid tranquilizer and decitabine chemotherapy agent remove methyl groups from DNA or prevent methylation. Procaine affects DNA methylation.
purposes
Researchers methylate nucleotides to prevent cutting by restriction enzymes. Promoter methylation can suppress gene expression.
After translation {post-translation}, proteins can add side groups, go to special locations, and bind to lipids, sugars, and proteins.
Cells, perhaps only neurons, can substitute RNA bases at three-dimensional loops {recoding}.
Enzymes {reverse transcriptase} can make DNA from RNA, typically making mRNA into cDNA. Hundreds of genes code enzymes that can make DNA from RNA.
RNAs can be catalysts {RNA catalyst}.
RNase-P RNA part splits tyrosine-tRNA precursor to make tRNA.
Fungus-mitochondria mRNA and rRNA precursors, and bacteriophage mRNA precursors {Class I self-splicing}, can catalyze themselves to remove introns, using guanosine as cofactor. Introns have further processing to make different RNA catalysts.
Yeast and fungus mitochondria mRNA precursors, and Chlamydomonas chloroplast mRNA precursors {Class II self-splicing}, can catalyze themselves to remove introns, using no cofactors.
Some protozoa edit transcribed RNA to make correct reading frames, possibly using RNA catalysts.
Mammals edit intestine transcribed apolipoprotein B mRNA, possibly using RNA catalyst.
Enzymes {restriction enzyme} can cleave nucleotide sequences at sites. 150 enzymes {endonuclease}, such as FokI and NotI, cut DNA near 4-base to 8-base recognition sequences.
ends
Restriction enzymes can leave ends {blunt end} with paired bases or ends {sticky end} with overlaps. Sticky ends can bind to other sticky ends and then DNA ligase can seal them, allowing splicing with other DNA fragments. Blunt ends can become sticky by terminal transferase, which adds polyA or polyT to one strand. Blunt ends can become sticky by attaching a DNA linker, with recognition sites, to blunt ends and then cleaving with restriction enzyme.
middle
Endonucleases cut nucleic acids at sequence sites not at end. Pancreatic ribonuclease, T1 ribonuclease, and other ribonucleases cut only RNA. Bacterial restriction endonucleases and other deoxyribonucleases cut only double-stranded DNA.
S1 nuclease {exonuclease} pares back RNA and single-stranded DNA ends. Sticky ends can become blunt ends by removing single-stranded DNA using S1 nuclease.
Genes that make mRNA have exon regions for translation and intron regions not for translation.
introns
RNAs typically have several introns. Introns came from bacteria or, if protein folding requires them, have always been in genes. After transcription, mechanisms {RNA splicing}| splice introns out.
exons
Exons typically are functional domains, and proteins have different functional domains. Exons can mix in different ways to make membrane-bound or secretable proteins or to make proteins for different development stages or different tissues.
process
After mRNA leaves cell nucleus, cell processes splice out introns and join exons {mRNA splicing}, to make mRNA for translation. Introns have 5' sequences and 3' sequences.
Large ribonucleotide and protein particles {spliceosome} perform splicing. Spliceosomes have U1 and U2 small nuclear ribonucleoproteins, U1 and U2 small nuclear ribonucleic acids, and SF2, U2AF, and other proteins. Intron 5' ends split first. Intermediate RNAs have lariat shapes, because introns bind to themselves with 2'-5' bonds. Enzymes cut 3' ends, and other enzymes join exon ends. Introns leave as lariats, because introns bind to themselves with 2'-5' bonds to make circles.
Proteins {splicing regulatory protein} (SR protein) can determine which exons to keep, by binding to exonic splicing enhancer (ESE) or exonic splicing suppressor (ESS). SR protein is for fruitfly sex determination.
Protein actions can block RNA 5' sites after transcription, allowing only other splicing sites {alternative splicing}. Alternative splicing results in different-size and different-function proteins.
RNAs can splice pieces together, using mechanisms {self-splicing RNA} different than spliceosomes.
DNA sequences {transposon, DNA} can excise themselves and then insert at other genome locations {transposition, DNA}|. Transposons code for enzymes that recognize DNA splice sites.
methylation
Methylation inactivates transposons.
bacteria
Bacteria have Tn3 and Tn10 transposons with DNA insertion sequences (IS). Tn3 transposons code enzymes that act at transposon-resolvase sites to allow recombination, so they copy themselves, place copies at new sites, and leave originals.
bacteria: Agrobacterium
Agrobacterium infects plants with Ti plasmid.
yeast
Yeast has Ty elements, whose delta-element direct repeats have promoters. Ty elements contain reverse transcriptase.
Yeast MAT genes have mating-type alleles. Yeasts have two mating types, a and alpha. After mating, mating type changes to opposite mating type, as HO endonuclease cuts MAT site. a-gene and alpha-gene copies are far from MAT sites. Copies are templates to reconstruct MAT site as opposite mating type {gene conversion} {replicative transposition}.
Yeast sterile (STE) genes code for a and alpha pheromones, which stop cell growth and change cell shape. Pheromones combine both mating types to form diploids, causing yeast to mate. STE proteins are G-protein subunits (STE4) (STE18), protein kinases, and transcription factors (STE12). STE proteins (STE2) (STE3) can bind factors.
maize
Maize has Ac and Ds transposable elements.
retrovirus
Retroviruses have direct repeats with promoters and contain reverse transcriptase to allow transposition.
trypanosome
Trypanosomes use gene conversion to vary surface glycoproteins (VSG).
fruitfly
Drosophila have P elements. Drosophila have copia elements, which have direct repeats with promoters.
Fruitfly P elements and other transposition elements can code for enzymes that recognize DNA splice sites. By opening and closing splice sites, genes {transposon, genetics} {jumping gene} can excise and insert between any two splice sites.
Reverse transcriptase can make DNA {retrotransposon} {retroposon} from RNA, and DNA can insert back into genome at special sites. Virus-gene fragments can copy themselves and insert in genomes. DNA from retrovirus RNA {human endogenous retrovirus} (Hervs) is 1% of human genome.
All species have 750-base to 5000-base sequences that code for enzymes {transposase} that recognize DNA sites just beyond both transposase-gene ends.
process
Sites have 10-base to 40-base inverted repeats. Transposase enzymes recognize inverted repeats and cut out transposase-gene sequence between sites. Transposases recognize inverted repeat at other locations in genomes, plasmids, or phages and cut sequence to place transposase-gene sequence in those locations. If two transposons are near each other, transposases can cut at the farthest ends and both transposons, and any DNA between them {complex transposon}, can transpose as one sequence to inverted repeats at other locations.
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Date Modified: 2022.0225