genetics: chapter 17

1) chromatin remodeling 2) the modification of histone proteins 3) DNA methylation

3 different processes affect gene regulation by altering chromatin structure, which are?

operons

In prokaryotic cells, a cluster of genes under control of a promoter.

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Know this picture

cleavage of mRNA

a mechanism that regulates gene expression by siRNA and miRNA -*RISCs that contain an siRNA (and some that contain an miRNA) pair with an mRNA molecule and cleave the mRNA near the middle of the bound siRNA* -This cleavage is carried out by a protein that is sometimes referred to as *Slicer*. After cleavage, the mRNA is further degraded.

true

true or false: And finally, numerous studies have demonstrated that abnormal expression of miRNAs plays a role in many cancers; miRNAs are now being used for cancer prognosis and experimental treatment.

transcriptional activator proteins

"this" stimulates and stabilizes the basal transcription apparatus at the core promoter. -"these" may interact directly with the basal transcription apparatus or act on it indirectly through *coactivator proteins* -Some activators and coactivators, as well as general transcription factors, also have acetyltransferase activity and so further stimulate transcription by altering chromatin structure.

enhancers

*"these" are regulatory elements that affect the transcription of distant genes.* - For example, an enhancer that regulates the gene encoding the alpha chain of the T-cell receptor is located 69,000 bp downstream of the gene's promoter; some vertebrate enhancers act over distances of millions of base pairs

DNA Methylation

*Another change in chromatin structure associated with transcription is the methylation of cytosine bases, which yields 5-methylcytosine* - Heavily methylated DNA is associated with the repression of transcription in vertebrates and plants, whereas transcriptionally active DNA is usually unmethylated in these organisms.

response element

*Genes that are coordinately expressed in eukaryotic cells are able to respond to the same stimulus because they share short regulatory sequences in their promoters or enhancers called "this"* -*they are short stretches of DNA that typically contain the same consensus sequences at varying distances from the genes being regulated.* -For example, different eukaryotic heat-shock genes possess a common regulatory sequence upstream of their transcription start sites.

Dnase 1

*an enzyme that digests DNA* - The ability of this enzyme to digest DNA depends on chromatin structure: when DNA is tightly bound to histone proteins, it is less sensitive to "this", whereas unbound DNA is more sensitive to "this"

DNase I hypersensitive site

*regions around the genes become highly sensitive to the action of DNase I* -these regions frequently *develop about 1000 nucleotides upstream of the transcription start site*, suggesting that the chromatin in these regions adopts a more open configuration during transcription -This relaxation of the chromatin structure allows regulatory proteins access to binding sites on the DNA. Indeed, many of "these" correspond to known binding sites for regulatory protein

initiation factors

A class of proteins that assist ribosomes in binding to a messenger RNA molecule to begin translation -This increase in "these" leads to more translation of the existing mRNA molecules, increasing the overall amount of protein synthesized.

native ChIP (nChIP)

Another version of ChIP, called "this", *does not use crosslinking.* -*It is often used for finding the locations of modified histone proteins.* -. In this case, crosslinking is not required because the DNA and the histones are naturally linked by the nucleosome structure.

ribonucleases

Cellular RNA is degraded by "this" -*enzymes that specifically break down RNA* -Most eukaryotic cells contain 10 or more types of "these", and there are several different pathways of mRNA degradation.

DNA methylation is most common on cytosine bases adjacent to guanine nucleotides (CpG, where p represents the phosphate group in the DNA backbone), so two methylated cytosines sit diagonally across from each other on opposite strands:

DNA methylation is most common on cytosine bases adjacent to what?

CpG islands

DNA regions with many CpG sequences are called "this" and are commonly found near transcription start sites

As discussed in Chapter 13, *transcription factors* are proteins that bind to DNA and facilitate or repress the synthesis of RNA, the first step in the process of information transfer from genotype to phenotype. *Each transcription factor may affect the expression of multiple genes, so a small genetic change affecting the expression of a single transcription factor can influence many additional genes*. The differences that Nowick and her colleagues found in the expression of transcription factors were particularly pronounced in brain tissue, where they may account for the large differences in neural and cognitive function between humans and chimpanzees. -Many of the transcription factors that Nowick and her colleagues identified were *Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs)*, transcription factors that bind to specific DNA sequences and bring about changes in chromatin structure -*changes in a relatively small number of regulatory sequences affect the expression of numerous genes in humans and chimpanzees and help produce the large differences we see in their anatomy, brain size, cognition, and behavior.*

Explain how organisms with highly similar DNA sequences can display drastic phenotypic differences

heat-shock proteins

For example, *stalling is observed at genes that encode "these" in Drosophila—proteins that help to prevent damage by stressors such as extreme heat* -*During times of environmental stress, transcription of all the heat-shock genes is greatly elevated. In the absence of stress, RNA polymerase initiates transcription at heat-shock genes in Drosophila, but stalls downstream of the transcription start site* -Stalled polymerases are released when stress is encountered, allowing rapid transcription of the genes and the production of heat-shock proteins that facilitate adaptation to the stressful environment.

For example, the activation of T lymphocytes (T cells) is critical to the development of immune responses to viruses (see Chapter 22). T cells are normally in the G0 stage of the cell cycle and not actively dividing. Upon exposure to viral antigens, however, specific T cells become activated and undergo rapid proliferation (Figure 17.14). Activation begins with a 7- to 10-fold increase in protein synthesis that causes the cells to enter the cell cycle and proliferate. This global burst of protein synthesis does not require an increase in mRNA synthesis. Instead, *it is due to the increased availability of initiation factors, which allow ribosomes to bind to mRNA and begin translation.* - In a similar way, insulin stimulates protein synthesis by increasing the availability of initiation factors.

Give two examples of how translational control can regulate the overall amount of protein synthesized

P bodies

Much of RNA degradation takes place in specialized complexes called "this" -However, "this" appear to be more than simply destruction sites for RNA. Evidence suggests that "this" can temporarily store mRNA molecules, which may later be released and translated. Thus, "this" helps control the expression of genes by regulating which RNA molecules are degraded and which are sequestered for later release

SR proteins

One group of proteins involved in splice-site selection consists of "this" -*which have two protein domains: one domain is an RNA-binding region and the other contains alternating serine and arginine amino acids* - The precise mechanism by which SR proteins influence the choice of splice sites is poorly understood. One model suggests that SR proteins bind to splicing enhancers on the pre-mRNA and stimulate the attachment of small nuclear ribonucleoproteins (snRNPs), which then commit the site to splicing.

1) In this procedure (Figure 17.4), the protein and associated DNA are temporarily crosslinked, which means that they are treated with formaldehyde or UV light to create covalent bonds between the DNA and protein -The crosslinking holds the DNA and protein together so that the DNA to which the protein is bound can be isolated along with the protein 2) After crosslinking, the cell is lysed, and the chromatin is broken into pieces by digestion with an enzyme or by mechanical shearing. Antibodies specific for a particular protein—such as a specific transcription factor—are then applied 3) The antibodies attach to the protein-DNA complexes as well as to a solid substrate (usually small beads). These beads can then be used to precipitate the protein-DNA complex 3) After the protein-DNA complex is precipitated, the crosslinking is reversed, separating the DNA and the protein 4) The protein is removed by an enzyme that digests protein but not DNA, leaving fragments of the DNA to which the protein was bound 5) The location of the resulting DNA fragments within the genome can then be determined by several different methods. One method, termed *ChIP-Seq*, determines the base sequences of the fragments using next-generation sequencing technologies 6) When the chromatin is broken into pieces and subjected to immunoprecipitation (see Figure 17.4), many short overlapping fragments of DNA are precipitated. Some of the sequences within each fragment are those that were covered by the protein; others are DNA on either side of the binding site. When the overlapping fragments are sequenced, the base pairs that were covered by the protein will be present in more copies and will be sequenced more often (resulting in more sequence reads) than base pairs that were not covered by the protein, producing peaks of sequence reads at those sites where the protein was bound. The locations of these peaks within the genome can be determined by comparing the sequences within the peaks with a reference genome sequence. The results provide information about the genomic locations of binding sites for the specific protein.

One version of ChIP, called crosslinked ChIP (XChIP), occurs how?

chromatin immunization

Our understanding of how changes in chromatin structure are associated with gene expression, and of how DNA-binding proteins affect transcription, has been greatly advanced by the use of a technique called "this' -*This technique allows researchers to determine the locations within the genome where a specific protein interacts with DNA* -ChIP has been used to determine the locations of histones that have undergone modifications as well as where transcription factors and other proteins bind to promoters and enhancers

miR-1

Overexpression of another miRNA, called "this", in the hearts of adult mice causes cardiac arrhythmia—irregular electrical activity of the heart that can be life-threatening in humans

microRNAs (miRNAs) and small interfering RNAs (siRNAs)

RNA interference is triggered by very small RNA molecules known as "this" and "this", depending on their origin and mode of action

siRNAs or miRNAs 21-25 nucleotides long and proteins

RNA-induced silencing complex (RISC) is made up of?

(1) cleavage of mRNA, (2) inhibition of translation, (3) transcriptional silencing, and (4) degradation of mRNA.

Small interfering RNAs and microRNAs regulate gene expression through at least four distinct mechanisms, which are?

AU-rich element

Some short-lived eukaryotic mRNAs have one or more copies of the consensus sequence 5′-AUUUAUAA-3′, referred to as "this" , in the 3′ UTR. -Messenger RNAs containing AU-rich elements are degraded by a mechanism in which microRNAs take part

transcriptional repressors

Some transcriptional regulator proteins in eukaryotic cells act as "this", inhibiting transcription.

histone code

The tails of histone proteins are often modified by the addition or removal of *phosphate groups, methyl groups, or acetyl groups*. Another modification of histones is *ubiquitination*, in which a small molecule called ubiquitin is added to or removed from the histones. -*These modifications have sometimes been collectively called "this" because they encode information that affects how genes are expressed*

silencers

These repressors bind to sequences in the regulatory promoter or to distant sequences called "this", which, like enhancers, are position and orientation independent

inhibition of translation

a mechanism that regulates gene expression by siRNA and miRNA - *Some miRNAs regulate genes by inhibiting the translation of complementary mRNAs*

degradation of mRNA

a mechanism that regulates gene expression by siRNA and miRNA -*A final mechanism by which miRNAs regulate gene expression is by triggering the decay of mRNA through a process that does not require Slicer activity* -This mechanism plays a role in the degradation of short-lived mRNAs that contain an AU-rich element in their 3′ UTR. -This miRNA binds to the AU-rich element and, in a way that is not yet fully understood, brings about the degradation of the mRNA in a process that requires Dicer and RISC.

transcriptional silencing

a mechanism that regulates gene expression by siRNA and miRNA -Some siRNAs silence transcription by altering chromatin structure. These siRNAs combine with proteins to form a complex called *RITS (for RNA- induced transcriptional silencing)*, which is analogous to RISC. -*The siRNA component of RITS then binds to a complementary sequence in DNA or in an RNA molecule in the process of being transcribed, where it represses transcription by attracting enzymes that methylate the tails of histone proteins.* The addition of methyl groups to the histones causes them to bind DNA more tightly, restricting the access of the proteins and enzymes necessary to carry out transcription

nucleosome

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

ubiquitination

a type of modification of histones -*a small molecule called ubiquitin is added to or removed from the histones.*

dicer

an enzyme called "this" cleaves and processes double-stranded RNA to produce single-stranded siRNAs or miRNAs 21-25 nucleotides long (Figure 17.13), which combine with proteins to form an *RNA-induced silencing complex (RISC)*

Acetyl groups are added to histone proteins by *acetyltransferase enzymes*; other enzymes called *deacetylases* strip acetyl groups from histones and restore chromatin structure, which represses transcription. Certain transcription factors (see Chapter 13) and other proteins that regulate transcription either have acetyltransferase activity themselves or attract acetyltransferases to DNA.

how does Acetylation of histones occur?

1) In XX embryos, the activated *sex-lethal gene (Sxl)* produces a protein 2) That causes the *transfer (tra)* pre-mRNA to be spliced at a downstream 3' site 3) Which produces a tra protein 4) Together, tra and tra-2 proteins direct the female specific splicing of another gene called *doublesex (dsx)* 4) This produces a protein that causes the embryo to develop into a female

how does alternative splicing result in a female Drosophila fly?

1) In XY embryos, the Sxl gene is not activated, and the Sxl protein is not produced 2) Thus, tra pre-mRNA is spliced at an upstream site 3) Producing a non-functional tra protein 4) Without tra, this results in the male specific splicing of dsx pre-mRNA 5) This produces a male dsx protein that causes the embryo to develop into a male

how does alternative splicing result in a male Drosophila fly?

*The basic idea of ChIP is that a particular protein and the DNA to which it is bound are isolated, the protein and DNA are then separated, and the DNA sequence to which the protein was formerly bound is identified.* The technique has provided a powerful means of determining the genome-wide locations of modified histones and the binding sites for transcription factors and other proteins that affect transcription.

how does chromatin immunization occur?

-Enzymes called *histone methyltransferases* add methyl groups to specific amino acids (usually lysine) of histones. Other enzymes, called *histone demethylases*, remove methyl groups from histones. -Many of the enzymes and proteins that modify histones, such as histone methyltransferases and demethylases, do not bind to specific DNA sequences and must be recruited to specific chromatin sites. *Sequence-specific binding proteins, preexisting histone modifications, and RNA molecules* serve to recruit histone-modifying enzymes to specific sites.

how does methylation of histones occur?

Messenger RNA degradation from the 5′ end is most common and *begins with the removal of the 5′ cap.* This pathway is *usually preceded by the shortening of the poly(A) tail.* Poly(A)-binding proteins (PABPs) normally bind to the poly(A) tail and contribute to its stability-enhancing effect. The presence of these proteins at the 3′ end of the mRNA protects the 5′ cap. *When the poly(A) tail has been shortened below a critical limit, the 5′ cap is removed, and nucleases then degrade the mRNA by removing nucleotides from the 5′ end.* These observations suggest that the 5′ cap and the 3′ poly(A) tail of eukaryotic mRNA physically interact with each other, most likely by the poly(A) tail bending around so that the PABPs make contact with the 5′ cap

how does the degradation of mRNA take place when the 5' end is removed first, followed by 5′→3′ removal of nucleotides?

micro RNA (miRNA)

is a type of RNA Cell type: Eukaryotic Location: nucleus and cytoplasm Function: inhibits translation of mRNA

small interfering RNA (siRNA)

is a type of RNA Cell type: Eukaryotic Location: nucleus and cytoplasm Function: triggers degradation of other RNA molecules

miR-1-2

one miRNA, called "this", is highly expressed in heart muscle. Mice genetically engineered to express only 50% of the normal amount of miR-1-2 frequently have holes in the wall that separates the left and right ventricles, a common congenital heart defect seen in newborn humans

methylation of histones

one type of histone modification -*is the addition of methyl groups (CH3) to the tails of histone proteins* -These modifications can bring about either the activation or the repression of transcription, depending on which histone is modified and which particular amino acids in the histone tail are methylated

Acetylation of histones

one type of histone modification -*the addition of acetyl groups (CH3CO) to histones, which usually stimulates transcription* -In general, acetyl groups destabilize chromatin structure, allowing transcription to take place

chromatin remodeling

the 1st process that affects gene regulation by altering chromatin structure -Some transcription factors and other regulatory proteins alter chromatin structure without altering the chemical structure of the histones directly. These proteins are called *chromatin-remodeling complexes*. They bind directly to particular sites on DNA and reposition the nucleosomes, allowing other transcription factors and RNA polymerase to bind to promoters and initiate transcription

histone modification

the 2nd process that affects gene regulation by altering chromatin structure -The histones in the octamer core of a nucleosome have two domains: (1) a globular domain that associates with the other histones and the DNA, and (2) a positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA. -The tails of histone proteins are often modified by the addition or removal of phosphate groups, methyl groups, or acetyl groups. Another modification of histones is ubiquitination, in which a small molecule called ubiquitin is added to or removed from the histones. -These modifications have sometimes been collectively called the *histone code* because they encode information that affects how genes are expressed. The histone code affects gene expression by altering chromatin structure directly or, in some cases, by providing recognition sites for proteins that bind to DNA and regulate transcription.

mediator

the binding of transcriptional activator proteins to the consensus sequences in the regulatory promoter affects the assembly or stability of the basal transcription apparatus at the core promoter -*One of the components of the basal transcription apparatus is a complex of proteins called "this"* -*which interacts with RNA polymerase. Transcriptional regulator proteins that bind to sequences in the regulatory promoter (or enhancer) make contact with the mediator and affect the rate at which transcription is initiated*

miR-1-1

the vertebrate heart develops through the programmed differentiation and proliferation of cardiac muscle cells, which are controlled by a specific miRNA termed "this"

1) they are capable of binding DNA at a specific base sequence, usually a consensus sequence in a regulatory promoter or enhancer 2) Their second function is to interact with other components of the basal transcription apparatus and influence the rate of transcription.

transcriptional activator proteins have 2 distinct functions, which are?

true

true or false: "As genes become transcriptionally active", regions around the genes become highly sensitive to the action of *DNase I*

true

true or false: *Enhancers are often a few hundred base pairs in length and contain multiple binding sites for transcriptional activator proteins*; a typical enhancer contains about 10 binding sites for proteins that regulate transcription. -Enhancers often regulate genes in a cell type-specific manner, meaning that they turn on different sets of genes in different cell types and help to establish the traits that characterize cells of different tissues.

true

true or false: *Regulatory promoters typically contain several different consensus sequences to which different transcriptional activators can bind.* On different promoters, activator binding sites are mixed and matched in different combinations, so each promoter is regulated by a unique combination of transcriptional activator proteins.

true

true or false: Abnormal patterns of methylation are also associated with some types of cancer.

true

true or false: Although most eukaryotic cells do not possess operons, several eukaryotic genes may be activated by the same stimulus -Groups of bacterial genes are often coordinately expressed (turned on and off together) because they are physically clustered in an operon and share a promoter, but coordinately expressed genes in eukaryotic cells are not clustered.

true

true or false: As we saw in Section 14.2, proper splicing is dependent on the presence of consensus sequences at the 5′ splice site, the 3′ splice site, and the branch point. These consensus sequences determine the precise locations of introns and exons. Additional sequences called *exonic/intronic splicing enhancers and splicing silencers* help to promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes. *Proteins and ribonucleoprotein particles bind to these sequences and promote or repress splice-site selection.*

true

true or false: As we saw in Section 17.3, the presence of extreme heat or other stressors induces the synthesis of heat-shock proteins, which reduce cellular damage resulting from those stressors. Transcription of heat-shock genes is rapidly increased by the release of stalled RNA polymerases when stress is encountered. Translational control also plays a role in the induction of heat-shock proteins. -*In response to heat shock, adenosine nucleotides in the 5′ UTRs of mRNAs transcribed from heat-shock genes are preferentially methylated to form N6-methyladenosine. The presence of N6-methyladenosine then promotes cap-independent initiation of translation (see p. 444 in Chapter 15), leading to the synthesis of heat-shock proteins.*

true

true or false: Chromatin immunoprecipitation (ChIP) can be used to identify the DNA binding sites of a specific protein and the locations of modified histone proteins. Shown here is the method for crosslinked chromatin immunoprecipitation (XChIP).

true

true or false: CpG methylation is also associated with long-term gene repression, such as that of the inactivated X chromosome of female mammals

true

true or false: Evidence indicates that an association exists between DNA methylation and the deacetylation of histones, both of which repress transcription. Certain proteins that bind tightly to methylated CpG sequences form complexes with other proteins that act as histone deacetylases. In other words, methylation appears to attract deacetylases, which remove acetyl groups from the histone tails, stabilizing the nucleosome structure and repressing transcription. -Demethylation of DNA allows acetyltransferases to add acetyl groups, disrupting nucleosome structure and permitting transcription.

true

true or false: For example, a genetic form of hearing loss has been associated with a mutation in the gene that encodes an miRNA. Other miRNAs are associated with heart disease

true

true or false: For example, research has demonstrated that *eukaryotic initiation factor 3 (eIF3)*, which functions generally to initiate eukaryotic translation, can also bind to secondary structures in the 5′ untranslated regions of specific mRNAs and either stimulate or repress their translation, depending on the particular sequence to which it binds.

true

true or false: In addition to increasing overall protein synthesis, translational control can also target the synthesis of specific proteins

true

true or false: In general, acetyl groups destabilize chromatin structure, allowing transcription to take place

true

true or false: Other parts of eukaryotic mRNA, including sequences in the 5′ untranslated region (5′ UTR), the coding region, and the 3′ UTR, also affect mRNA stability

true

true or false: Recent research has demonstrated that miRNA molecules are key factors in controlling development in animals, including humans, and plants

true

true or false: Sensitivity to DNase I in regions around transcriptionally active genes indicates that the chromatin in these regions assumes an open configuration before transcription.

true

true or false: Some regulatory promoters contain sequences that are bound by transcriptional repressor proteins, which lower the rate of transcription through inhibitory interactions with the mediator.

`true

true or false: Stalling was formerly thought to take place at only a small number of genes, but research now indicates that stalling is widespread throughout eukaryotic genomes, occurring at 30%-50% of genes. Several factors that promote stalling have been identified. One of these factors is a protein called *negative elongation factor (NELF)*, which binds to RNA polymerase and causes it to stall after initiation. Another protein, called *positive transcription elongation factor b (P-TEFb)*, relieves stalling and promotes elongation by phosphorylating NELF and RNA polymerase, perhaps by causing NELF to dissociate from the polymerase.

true

true or false: The RNA component of RISC then pairs with complementary base sequences in specific mRNA molecules, *most often with sequences in the 3′ UTR of the mRNA*. Small interfering RNAs tend to base pair perfectly with mRNAs, whereas microRNAs often form less-than-perfect pairings.

true

true or false: The exact position and orientation of an enhancer relative to the promoter it regulates are not critical to its function---- the *enhancer* is thousands of base pairs away from the promoter

true

true or false: The expression of a number of eukaryotic genes is controlled through *RNA interference* -Research suggests that as many as 30% of human genes are regulated by RNA interference. RNA interference is widespread in eukaryotes, existing in fungi, plants, and animals. This mechanism is also widely used as a technique for artificially regulating gene expression in genetically engineered organisms

true

true or false: The initiation of eukaryotic transcription was discussed in detail in Chapter 13. Recall that general transcription factors are part of the basal transcription apparatus. The basal transcription apparatus binds to a core promoter located immediately upstream of a gene and is capable of minimal levels of transcription, but transcriptional regulator proteins are required to bring about normal levels of transcription. These proteins bind to a regulatory promoter, which is located upstream of the core promoter (Figure 17.5), and to enhancers, which may be located some distance from the gene. Some transcriptional regulator proteins are activators, stimulating transcription; others are repressors, inhibiting transcription.

true

true or false: The initiation of translation in some mRNAs is regulated by proteins that bind to the 5′ UTR of certain mRNAs and inhibit the binding of ribosomes, in a manner similar to the binding of repressor proteins to operators that prevents the transcription of structural genes in prokaryotes. The translation of other mRNAs is affected by the binding of proteins to sequences in the 3′ UTR.

true

true or false: The response elements are binding sites for transcriptional activator proteins, which bind to the response elements and elevate transcription. If the same response element is present at multiple genes, it allows all of those genes to be activated by the same stimulus.

true

true or false: This increase in initiation factors leads to more translation of the existing mRNA molecules, increasing the overall amount of protein synthesized.

true

true or false: Thus, the presence of siRNAs and miRNAs increases the rate at which mRNAs are broken down and decreases the amount of protein produced.

true

true or false: Unlike repressors in bacteria, most eukaryotic repressors do not directly block RNA polymerase.

true

true or false: We have just considered one level at which gene expression is controlled: the alteration of chromatin and DNA structure. -We now turn to another important level of control: control through the binding of proteins to DNA sequences that affect transcription.

true

true or false: When the initiation of transcription has taken place, RNA polymerase moves downstream, transcribing the structural gene and producing an RNA product. At some genes, RNA polymerase initiates transcription and transcribes 24 to 50 nucleotides of RNA, but then *pauses or stalls.*

true

true or false: While genes are not being transcribed, these *CpG islands* are often methylated, but the methyl groups are removed before the initiation of transcription

1) many bacterial and archaeal genes are organized into operons and are transcribed into a single RNA molecule. Although some operon-like gene clusters have been found in worms and even in some primitive chordates, most eukaryotic genes have their own promoters and are transcribed separately 2) chromatin structure affects gene expression in eukaryotic cells; DNA must unwind from the histone proteins before transcription can take place 3) the presence of the nuclear membrane in eukaryotic cells separates transcription and translation in time and space. Therefore, the regulation of gene expression in eukaryotic cells is characterized by a greater diversity of mechanisms that act at different points in the transfer of information from DNA to protein.

what are some general differences that between eukaryotic and prokaryotic gene regulation?

in both types of cells, DNA-binding proteins influence the ability of RNA polymerase to initiate transcription

what are some general similarities between eukaryotic and prokaryotic gene regulation?

1) some complexes cause the nucleosome to slide along the DNA, allowing DNA that was wrapped around the nucleosome to occupy a position in between nucleosomes, where it is more accessible to proteins affecting gene expression (shown in the picture of chromatin remodeling) 2) Second, some complexes cause conformational changes in the DNA, in nucleosomes, or in both so that DNA that is bound to the nucleosome assumes a more exposed configuration.

what are the 2 ways that chromatin-remodeling complexes reposition nucleosomes?

1) These repressors may compete with transcriptional activators for binding sites on the DNA: when a site is occupied by an activator, transcription is activated, but if a repressor occupies that site, there is no activation 2) Alternatively, a repressor may bind to sites near an activator binding site and prevent the activator from contacting the basal transcription apparatus 3) A third possible mechanism of repressor action is direct interference with the assembly of the basal transcription apparatus, thereby blocking the initiation of transcription

what are the 3 mechanisms by which transcriptional repressors inhibit transcription initiation?

In one pathway, the 5′ cap is first removed, followed by 5′→3′ removal of nucleotides. A second pathway begins at the 3′ end of the mRNA and removes nucleotides in the 3′→5′ direction. In a third pathway, the mRNA is cleaved at internal sites.

what are the 3 ways mRNA is degraded?

slicer

what enzyme is involved in cleavage of mRNA?

-*A common modification is the addition of three methyl groups to lysine 4 in the tail of the H3 histone protein, abbreviated H3K4me3 (K is the abbreviation for lysine).* -Histones containing the H3K4me3 modification are frequently found near promoters of transcriptionally active genes -Studies have identified proteins that recognize and bind to H3K4me3, including nucleosome remodeling factor (NURF). NURF and other proteins that recognize H3K4me3 have a common protein-binding domain that binds to the H3 histone tail and then alters chromatin packing, allowing transcription to take place. -Research has also demonstrated that some transcription factors that are necessary for the initiation of transcription (see Chapter 13 and Section 17.3) bind directly to H3K4me3.

what is an example of *methylation of histones*?

-For example, the addition of a single acetyl group to lysine 16 in the tail of the H4 histone prevents the formation of the 30-nm chromatin fiber (see Figure 11.4), causing the chromatin to be in an open configuration that makes the DNA available for transcription

what is an example of Acetylation of histones?

One of the best-studied examples of a chromatin-remodeling complex is *SWI-SNF* -This complex uses energy derived from the hydrolysis of ATP to reposition nucleosomes, exposing promoters in the DNA to the action of other regulatory proteins and RNA polymerase.

what is an example of chromatin remodeling?

A single eukaryotic gene may be regulated by several different response elements. For example, the metallothionein gene encodes a protein that protects cells from the toxicity of heavy metals by binding to those metals and removing them from cells. Under normal conditions, the basal transcription apparatus assembles around the TATA box just upstream of the transcription start site for the metallothionein gene, but the apparatus alone is capable of only low rates of transcription. Other response elements found upstream of the metallothionein gene contribute to increasing its rate of transcription. For example, several copies of a metal response element (MRE) lie upstream of the metallothionein gene (Figure 17.9). The presence of heavy metals stimulates the binding of transcriptional activator proteins to the MRE, which elevates the rate of transcription of the metallothionein gene. Because there are multiple copies of the MRE, high rates of transcription are induced by metals

what is an example of how *response elements* are used?

"this" is used for identifying the binding sites of transcription factors and other proteins that bind to DNA

what is the function of crosslinked ChIP (XChIP)

-histones are in the *octamer core of the nucleosome* -*histones contain 2 domains:* 1) a globular domain that associates with the other histones and the DNA 2) a positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA

what is the structure of a *histone* like?

tails of histone proteins

what region of the histones is is heavily post-translationally modified?