Chapter 17 best to study

transcriptional silencing

- siRNAs alter chromatin structure

Define genomic imprinting

-is the process in which genes are silenced depending on which parent transmitted them. The transcriptionally silenced gene is imprinted.

List a few differences between prokaryotic and eukaryotic gene regulation

1. Bacterial and Archaeal genes are organized by an operon and transcribed into a single RNA. Eukaryotes, however, have their own promoter and transcription/translation are separated. 2. Chromatin structure affects gene expression in eukaryotes, the DNA must unwind from histone proteins in order for transcription to take place. 3. The presence of a nuclear membrane is what separates the transcription and translation in time and place. Gene expression is characterized by a greater diversity of mechanisms that act at different points in the transfer of information from DNA to proteins.

What are the 3 different processes that affect gene regulation by altering chromatin structure?

1. Chromatin remodeling 2. Modification of histone proteins 3. DNA methylation

What are the 3 mechanisms of gene regulation by RNAi

1. RNA cleavage 2. inhibition of translation 3. transcriptional silencing

RNA interference (RNAi)

A technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene's messenger RNA. 30% of human genes are regulated by RNAi, widely used as a technique for artificially regulating gene expression in genetically engineered organisms.

How do the transcription factors bind to the DNA if they are wrapped so tight around histone proteins?

Before transcription takes place, the chromatin structure changes so that the DNA is more accessible to the transcription machinery.

General Transcription Factors

Bind to a core promoter and are part of basal transcription apparatus. These factors are required for the initiation of transcription.

What are CpG islands?

DNA regions with many cytosine bases adjacent to guanine bases. Commonly found near transcription start sites. While genes are not being transcribed, the islands are often methylated. However, the methyl group is removed before the initiation of transcription. Also associated with long-term gene repression, such as the X chromosome of female mammals.

What does the enzyme dicer do?

Dicer cleaves and processes double-stranded RNA to produce single-stranded siRNA or miRNA, which is usually 21 to 25 nucleotides long, they then combine with proteins to produce an RNA-induced silencing complex (RISC). It then combines with base sequences in specific mRNA molecules. siRNA base pairs perfectly with mRNA whereas microRNA is less perfect

How is DNA tightly packed and how does transcription occur?

In the nucleus, histone proteins form octamers, which helical DNA tightly coins to create chromatin. For a gene to be transcribed, proteins called, transcribed factors, must bind to the DNA. All other regulatory proteins and RNA polymerase must also bind to the DNA for transcription to take place.

RNA cleavage

RISC containing a siRNA, pairs with the mRNA and cleave the mRNA near the middle of the bound siRNA. Carried out by the protein slicer. After cleavage, the presence of siRNAs increases the rate of mRNA being broken down and decreases the number of proteins produced.

What does RNAi (RNA silencing) lead to?

RNA silencing leads to the degradation of mRNA or to the inhibition of translation or transcription.

What alters chromatin structure?

The Acetylation of histone proteins

how to know which gene is silenced and imprinted

The silenced gene is usually the gene that has DNA methylation. The gene expressed has an unmethylated promoter. DNA methylation blocks the binding of transcription factors to the promotor, leading to a decrease in gene expression.

chromatin remodeling

They bind directly to particular sites on DNA and reposition the nucleosomes. This allows for other transcription factors and RNA polymerase to bind to promoters and initiated transcription.

What do other transcription factors bind to?

They bind to regulatory promoters upstream of the core promoter and enhancers, which may be located some distance from the gene.

Histone modification

They have 2 domains: 1. A globular domain that associates with the other histones in DNA 2. A positively charged histone tail domain interacts with a negatively charged phosphate group. They are modified by the addition or removal of phosphate groups, methyl groups, or acetyl groups.

How is DNA methylation associated with gene expression?

Through the methylation of cytosine bases. Heavily methylated DNA is associated with the repression of transcription in invertebrates and plants, whereas the transcriptionally active DNA is usually not methylated in these organisms. It is most common on cytosine bases adjacent to guanine nucleotides. So 2 methylated cytosines are diagonal from each other on opposite strands. Results in 5-methylcytosine at CpG sequences 5'-CG-3' 3'-GC-5'. (The C is diagonal)

what does an insulator do

also called boundary element, it blocks the effects of enhancers in a position-dependent manner. If the insulator lies between the enhancer and promoter, the insulator blocks the enhancer and blocks the action. If the insulator lies outside the region between the two, it has no effect They create neighborhoods of gene regulation, causing loops

Define epigenetics

alterations to DNA and chromatin structure that affect traits and are passed on to other cells or generations but are not caused by changes in DNA base sequence. These mechanisms include chromatin remodeling, histone modification, and DNA modification.

basal transcription apparatus

binds to a core promoter located upstream of a gene and capable of minimal levels of transcription.

what does the mediator protein do

interacts with RNA polymerase. Transcription factors that bind to sequences in the regulatory promoter (or enhancer) make contact with the mediator and affect the rate at which transcription is initiated.

inhibition of translation

miRNAs block the translation of mRNA many mRNAs have multiple binding sites for miRNA, so translation is efficiently blocked when multiple miRNAs are bound to the mRNA

Eukaryotic genes can be regulated through

the control of mRNA processing

The selection of alternative splice sites leads to

the production of different proteins

DNase1 hypersensitive sites

they are regions around the genes that become more highly sensitive when transcription is active. They develop 1000 nucleotides upstream of the transcription start site. This means that the chromatins in these regions adopt a more configuration during transcription. They also correspond to known regulatory protein binding sites.

How do transcription factors regulate

they regulate by recruiting other proteins called cofactors, which either stimulate or repress transcription.