Chapter 11 Molecular Mechanisms of Gene regulation Jones

Chapter 11 Molecular Mechanisms of Gene regulation Jones and Bartlett Publishers © 2005

Outline of topics • Transcriptional regulation in eukaryotes • Epigenetics • Regulation through RNA processing and decay • Translational control • Programmed DNA rearrangements

Transcriptional Enhancers (Silencers – opposite of enhancers)

Deletion scanning

Transcriptional activation by recruitment (DNA looping)

Basal transcription factors • Transcription factors: TFIIB, TFIID, TFIIE, TFIIF, TFIIH, Pol. II, and TFIIA. • TFIID contains a TATA box-binding protein (TBP) • 10 TAFs- TBP-associated factors • Pol. II RNA polymerase- 12 subunits • Pol. II holoenzyme- Pol. II RNA polymerase plus most basal transcription factors.

Transcriptional activation in Drosophila development

Chromatin remodeling complexes • Purified chromatin + components of transcription don’t result in transcription. • CRCs: SWI-SNF, RSC (remodels the structure of chromatin), NURF (nucleosome remodeling factor), CHRAC (chromatin accessibility complex, and ACF (ATP-dependent chromatin assembly and remodeling factor). • CRCs are part of Pol. II holoenzyme.

Chromatin remodeling complexes

• How are genes regulated during different stages of development in an organism? – Use of alternative promoter

Alternative promoters

Epigenetic methods of transcriptional regulation • CG doublets can be methylated. • 5 -methylcytosine can make up 2 -7% of C in vertebrate DNA and up to 30% of plant DNA. • Both Cs in the CG doublet are methylated. • Maintenance methylase preserves this.

Transcriptional cosuppression • Inserted gene copies can result in transcriptional silencing. • Chalcone synthase gene in petunia. • Methylation is involved here. • Drosophila have no methylation (no DNA methylase), but still have transcriptional silencing.

Genomic Imprinting • • Imprinting occurs in the germ line. Affects a few hundred genes, in clusters. Heavy methylation is involved. Imprinted genes are methylated differently in female and male germ lines. • Once imprinted and methylated, a silenced gene remains transcriptionally inactive during embryogenesis. • Imprints are erased early in germ-line development, then re-established according to sexspecific pattern.

Some human diseases are due to loss of sites involved in genomic imprinting

Alternative splicing of the primary transcript

Regulation through RNA processing and decay • • Alternative splicing m. RNA stability (poly-A tail is trimmed) Posttranscriptional cosuppression RNA interference: a few hundred pairs of double stranded RNA triggers RNA transcript degradation. – RISC (RNA-induced silencing complex) – Plus 21 - or 22 -mer oligonucleotides (chopped ds. RNA) as templates to recognize complementary sequences.

Anti-sense RNA

Structure of an immunoglobulin G (Ig. G) molecule

The distribution of variable, joining and constant sequences which are spliced to create many different light chain proteins

Antibody diversity in humans

Mating type switching during the life cycle of some strains of Saccharomyces

Both mating type genes are located on chromosome III of Saccharomyces. The mating type of the cell is determined by the sequence present at the MAT site

Regulation of a-specific, a-specific and haploid-specific genes in Saccharomyces Three proteins (a 1, a 1 and a 2) are involved in regulating the expression of these 3 classes of genes.