BIOL1020 Lecture Notes - Lecture 11: Transgenerational Epigenetic Inheritance, Methyl Group, Nucleosome

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blueclam798

18 May 2018

School

Department

Biology

Course

BIOL1020

Professor

Dr Paul Ebert

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Lecture 11- gene regulation in eukaryotes !

Gene structure

•chromatin is double stranded DNA helix !

•DNA is wrapped around histones to form nucleosomes !

•Each nucleosome contains 8 histones (4 pairs)!

Gene regulation

• needed because not all the genes in the cell are needed for that particular cell !

•there are many levels of gene regulation !

Regulation of chromosome structure

There are many ways chromatin can be regulated to make the DNA more or less accessible !

Modification of histones !

•chemical modiﬁcations to histones, found in all eukaryotic organisms, play a direct!

•role in the regulation of gene transcription !

•The N-terminus of each histone protein in a nucleosome protrudes outward from the

nucleosome.!

•These so-called histone tails are accessible to various modifying enzymes that catalyze the

addition or removal of speciﬁc chemical groups !

•histone acetylation—the addition of an acetyl group to an amino acid in a histone tail—promote

transcription by opening up the chromatin structure !

•the addition of methyl groups to histones can lead to the condensation of chromatin and

reduced transcription !

•Often, the addition of a particular chemical group may create a new binding site for enzymes

that further modify chromatin structure in various ways. !

Modification of DNA (DNA Methylation)!

•usually happens on cytosine!

•Happens in plants, animals and fungi !

•Methylation is removing the methyl group !

•This can turn oﬀ the gene !

•Even after replication and cell division, enzymes will methylate the new daughter DNA !

•This preservation of methylation, keeps the gene expression from a young age to adulthood !

•#!

Epigenetic inheritance !

•inheritance of traits transmitted by mechanisms not including the nucleotide sequence itself

(example is methylation) !

•Epigenetic variations might help explain why one identical twin acquires a genetically based

disease despite identical genome !

After chromatin regulation, the initiation of transcription is the next stage where expression can

be regulated. !

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Document Summary

Gene structure: chromatin is double stranded dna helix, dna is wrapped around histones to form nucleosomes, each nucleosome contains 8 histones (4 pairs) Gene regulation: needed because not all the genes in the cell are needed for that particular cell, there are many levels of gene regulation. There are many ways chromatin can be regulated to make the dna more or less accessible. Epigenetic inheritance: inheritance of traits transmitted by mechanisms not including the nucleotide sequence itself (example is methylation, epigenetic variations might help explain why one identical twin acquires a genetically based disease despite identical genome. After chromatin regulation, the initiation of transcription is the next stage where expression can be regulated. Basal promoters: required for the binding of general transcription factors, examples of transcription factors tbp (tata box binding protein), tfiia (transcription factor 2 a), The roman numeral stands of the type of rna polymerase that will be attaching for the transcription of that gene.

Related Questions

Synergism in transcriptional regulation occurs when two transcription factors have a much greater effect when they are both active than would be predicted if one added their individual effects.
A. True
B. False

The N-terminal region of histones extends from nucleosomes. These histone tails can be covalently modified to signal that a gene in the region should be transcribed. What is the covalent modification?
A. Adding a poly A tail
B. Adding acetyl groups
C. Removing acetyl groups
D. Removing a poly A tail

You are studying how the estrogen receptor regulates expression of a particular gene in breast cancer cells grown in a test tube. You examine cells grown in the presence of estrogenic hormones. Using various biochemical techniques, you find that the activated estrogen receptor [i.e., with hormone(s) bound] binds to cis regulatory sequences in the gene of interest and recruits (physically interacts with) a protein that has histone deacetylase activity. Based on this information, do you predict that estrogen hormones induce transcription, have no effect on transcription, or suppress transcription of the target gene?
A. No effect
B. Induce
C. Suppress

A. True or false. Support your answer

a. RNA differs from DNA in that is single-stranded and cannot base pair.

b. The fetal Î²-globins arose from a gene duplication that occurred 200 million years ago, which gave rise to a different forms of b-gobins expressed in the fetus and in the adult.

c. A total genomic library will be larger than a cDNA library for a given cell.

d. Histone acetyltransferases affect transcription by both altering chromatin structure to allow accessibility to the DNA and by adding acetyl groups to histones that can bind proteins that promote transcription.

e. The proteins in neurons and white blood cells are completely different.

f. Maternally âcoded transcription factors determine segmentation in Drosophila melanogaster larvae.

greentermite580

The bacterium E. coli, which is a major model system for the study of genes and DNA, has a singular circular chromosome of about 4x106 bp. In contrast, human diploid cells have __1__ chromosomes, of __2__ different types (donât forget that the X Â¹ Y!). The total amount of DNA found in a haploid cell such as a sperm or egg is called the organismâs âC-valueâ; the human C-value is __3__.

Also in contrast to the E. coli circular chromosome is the fact that eukaryotic chromosomes are not circular, but instead are __4__. Eukaryotic chromosomes are complexed heavily with protein to form a DNA-protein complex generically called __5__. The proteins found can be considered to fall into two general classes: __6__ and __7__. The first class is made up of 5 major proteins called __8__, __9__, __10__, __11__, and __12__. On a weight to weight basis, these proteins make up about __13__% of the total mass of a chromosome. Since these proteins must associate relatively non-specifically with DNA, they are rich in the basic amino acids __13__ and __14__, which gives the proteins a net __15__ charge.

One goal of packaging the DNA into chromatin is to compact the genome so it will fit into a nucleus. The basic unit of chromatin structure is the __16__, which has __17__ base pairs of DNA wrapped around a âcore particleâ composed of __18__ copies each of the core histones. Each nucleosome is separated by a stretch of âlinkerâ DNA so that the repeating unit is approximately 200 bp. Lets do a little arithmetic: If we consider that the nucleosome is approximately __19__ nm in diameter, that there is about 200 bp in this structure, and that 200 bp of DNA would normally occupy __20__ nm if stretched out straight (recall that each base is spaced about 0.34 nm from the next), we can see that the nucleosome alone allows for a __21__-fold compaction ratio.

The nucleosome structure is further compacted by histone __22__, which is not a part of the core particle. Instead, this histone __23__ (does what?) to cause the nucleosomal 10 nm fiber to condense into a higher-order structure referred to as the __24__ nm fiber. In the nucleus, chromosomes do not just float around freely: they are tethered to a proteinaceous structure called the __25__ at specific DNA regions called âSARsâ, which stands for __26__. SARs are rich in topoisomerases, to allow the winding and unwinding of the DNA that accompanies replication and transcription to occur, despite this constraint.

The 30 nm fiber discussed above is the form in which transcriptionally active DNA is believed to exist in the nucleus; however, further condensation leads to a highly condensed inactive form called __27__; in this terminology, the active form is referred to as __28__. The inactive condensed form can be divided into two types: one type is essentially invariant between cell types, and since it is âon all t timeâ, it is referred to as __29__. The other type comes and goes, depending on the expression of the genes present in that region of the chromosome; it is referred to as __30__.

Eukaryotic chromosomes carry the genes, of course, but also have other functional regions. One such region is the place where the spindle apparatus attaches during mitosis and meiosis; this region of the chromosome is called the __31__. Another important part of the linear eukaryotic chromosome is the ends; these are called __32__. In humans, the end of each chromosome is composed of many repeats of the short sequence __33__. One more type of functional region on each chromosome is the place where DNA replication starts; in humans, each chromosome has several of these __34__. Thus, eukaryotic chromosomes carry several different types of functional sequences, which together allow for their __35__ during S phase, __36__ during mitosis and meiosis, and the __37__ of their genes

BIOL1020 Lecture Notes - Lecture 11: Transgenerational Epigenetic Inheritance, Methyl Group, Nucleosome

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