Study Guide: Differential Gene Expression and Mechanisms of Cell Differentiation

Signal V1
- nẞ-TCF: A transcription factor involved in Wnt signaling.
- Hox11/13b: Homeotic genes that play a role in specifying body segments.
- Eve: A gene involved in segmentation.
Signal V2
- Signaling involves the expression of various transcription factors such as:
- Blimp1, Otx, SoxC, Hnf1, Bra, GataE, FoxA, Nrt, GataC, Vegf3, Kri, Myc
- veg1 and veg2: Key genes associated with endodermal and ectodermal differentiation.
- Endo16: A gene linked to endodermal identity.

Protein synthesis: A quick overview of the processes involved in expressing genes into proteins.

Central Dogma of Molecular Biology
- Where in a cell are introns removed from transcripts?
- Where in a cell do codons instruct the formation of polypeptide bonds?

Detecting Transcripts:
- Northern Blot
- (flourescence) In Situ Hybridization
- RT-PCR
- Microarray
- RNA-seq
Detecting Proteins:
- Western Blots
- Immuno-cyto-chemistry
- MALDI-TOF MS
Detecting Promoter Activity:
- Promoter-Probe Fusions
Detecting Epigenetic Modification:
- ChIP-CHIP
- ChIP-Seq
Detecting DNA Sequences:
- Sanger Sequencing
- Next-gen Sequencing

Gene to Phenotype:
- Knockdowns:
- Examples include RNAi and morpholinos.
- Knockouts:
- Examples include CRISPR/Cas9 and homologous recombination.

mRNA: Another name for mRNA is messenger RNA.
Genomic Evidence:
- 1958 Experiment: Frog blastomere nucleus can produce an adult frog.
- 1968 Experiment:
- The nucleus from the intestine of an adult frog can produce a frog.
- This experimentation raises questions about mammalian genomic equivalence.
- Somatic Cell Nuclear Transfer:
- Adult mammalian somatic cell nucleus can generate a cloned adult sheep.

Functional Anatomy of a gene includes various components that regulate gene expression:
- Promoter structure: Contains TATA boxes, transcription initiation sequences, and enhancers.
- Coding sequence: Exons which are translated into proteins, separated by introns that are removed from final mRNA.

Enhancers and Repressors:
- Enhancer: Enhancers bind transcription factors and may be located far from the gene they regulate.
- Cis-regulatory elements: Localized sequences that play roles in gene expression.
Transcription Factors' Role:
- Recruit nucleosome modifying proteins to enhance accessibility for transcription.
- Loop chromatin configurations to bring transcription factors close to promoters.

Includes processes such as transcription, pre-mRNA processing, mRNA translation, and post-translational modification.

Histones as Gatekeepers: Methylation and acetylation dictate chromatin structure and accessibility to transcription machinery.
DNA methylation patterns: Affect gene expression and are heritable.

Proteins may require cleavage or binding to co-factors for functional activity. This is critical in cell signaling and responses during development.

Allows a single pre-mRNA to code for multiple proteins (e.g., Dscam gene in Drosophila can produce 38,016 proteins).
Splicing factors and complexes such as spliceosomes play crucial roles in the regulation of mRNA splicing processes.

MicroRNAs (miRNAs) regulate gene expression by binding to mRNAs, inhibiting their translation or promoting their degradation. Examples include the regulation of lin-14 mRNA by lin-4 RNAs.

Demonstrated by gene regulatory networks exemplified in various organisms (e.g., sea urchin embryos).

Each step of gene expression entails numerous regulatory mechanisms that ensure proper development, including differential splicing and modulations at various levels, from transcription to post-translational modifications. Achieving precise control over these processes is fundamental for normal cellular differentiation and organismal development.