Transcription Regulation in Eukaryotes

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Questions and Answers

What role do the +Arg side chains of histones H3 and H4 play in DNA interaction?

They destabilize the nucleosome structure.

They deter transcription factor invasions.

They prevent DNA from wrapping around histones.

They facilitate the attachment of the minor grooves to histones. (correct)

How can the nucleosome core particle (NCP) be characterized?

It is fragile and exhibits incipient instability. (correct)

It has a substantial capacity to withstand mechanical stress.

It is a compact structure that is completely stable.

It remains unchanged during transcription regulation.

What is the function of the H1 histone in relation to chromatin structure?

It is responsible for unwrapping all chromatin structures.

It interacts with linker DNA and contributes to dynamic chromatin changes. (correct)

It prevents the interaction of protein motifs with histones.

It serves as a stabilizer for the DNA within the nucleosome.

Which of the following describes the structural models of chromatin?

Two established models include zigzag and a helical structure. Signup and view all the answers

What happens to the chromatin volume during mitosis?

It increases before returning to normal levels. Signup and view all the answers

What is the function of transcription factors in gene regulation?

They regulate specific genes based on sequence logos. Signup and view all the answers

What characterizes super-enhancers?

They are clustered regions that regulate pluripotency genes and oncogenes. Signup and view all the answers

Which statement about nucleosomes is incorrect?

They are traditional components of active enhancers. Signup and view all the answers

What is the relationship between transcription factors and nucleosomes?

Transcription factors usually destabilize DNA wrapped around nucleosomes. Signup and view all the answers

What defines a pioneer transcription factor?

It binds with high affinity, increasing nucleosome accessibility for other transcription factors. Signup and view all the answers

What does cohesion ring looping facilitate in transcription regulation?

It allows for the physical interaction between distant regulatory elements. Signup and view all the answers

Which technique is implied to study TF invasion regarding nucleosomes?

Cy3 DNA/Cy5 Histones for measuring unwrapping and sliding. Signup and view all the answers

What role do coregulators play in the transcription initiation complex?

They assist sequence specific transcription factors by linking them to RNA polymerase. Signup and view all the answers

Study Notes

Transcription Regulation (Eukaryotic)

Physical interactions occur between promoters (near genes) and enhancers (far from genes).
Cis regulatory interactions are encouraged by cohesion ring looping.
Enhancers and promoters are linked by sequence-specific transcription factors (TFs), co-regulators, mediator complex, and polymerase. The process culminates in a complex involving ~56 polypeptides, general TFs, TFIID TAFs, and mediator.
The Polymerase CTD may interact with the mediator complex.

Transcription Factors (TFs)

Sequence-specific TFs regulate specific genes based on their sequence.
Different binding domains include Zinc-Finger (e.g., CTCF), Leucine zipper, Helix-turn-helix.
Master developmental regulators and reprogramming factors (e.g., fibroblast to muscle/neuron) are TFs.
TFs bind nucleosomes, but often destabilize DNA structure.
Pioneer TFs bind with high affinity, increasing nucleosome accessibility for other TFs.

Enhancers

Enhancers typically range from 1 kb to 1 Mb away from target genes.
Located upstream or downstream of genes.
Orientation of enhancers is independent.
Super-enhancers are clusters of enhancers that regulate pluripotency genes/oncogenes.
Epigenetic signatures (e.g., H3K27ac) and lack of nucleosomes can identify enhancers.

Nucleosomes

Nucleosomes are the fundamental units of chromatin. DNA wraps around histone octamers (2 each of H2A, H2B, H3, and H4).
Organization proceeds from 10nm beads-on-a-string, to 30nm fibers (zigzag or solenoid), to 300-700 nm chromatids and ultimately to 1400 nm chromosomes.
Nucleosomes are absent at active promoters and enhancers, which are therefore nucleosome-depleted regions (NDRs).
Histone octamers are comprised of two H2A-H2B dimers and two H3-H4 dimers.
DNA wraps around the histone core in a left-handed manner, forming nucleosome core particles (NCPs). Histone tails are unstructured and are often modified.

Chromatin Remodeling

Chromatin remodeling can involve spontaneous unwrapping/sliding.
Or be ATP-driven, using factors from families like SNF2, CHD1, ISWI, and INO80 (distinct activities termed pushers (SWI/SNF), pullers (ISW2), and spacers (ISW1)).
Histone modification (acetylation, methylation) is a mechanism of transcription regulation.

Chromatin Structure

Two models for chromatin configuration exist: a zigzag model and a two-start helix model.
Various post-translational modifications (PTMs) on histone tails can influence DNA binding and consequently the chromatin state.

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Description

Explore the complex mechanisms of transcription regulation in eukaryotic cells. This quiz covers the interactions between promoters and enhancers, the role of transcription factors, and the composition of regulatory complexes. Test your knowledge on the various elements that contribute to gene expression.