Exam 4

Chromodomain

A 60-amino acid domain that can recognize methylated lysines in histones; some chromodomains have different functions such as RNA binding.

Zinc Finger

A DNA-binding motif that typifies a class of transcription factor that contains one or more zinc ions to help stabilize the protein.

bZIP (Basic Zipper)

A bZIP protein has a basic DNA-binding region adjacent to a leucine zipper dimerization motif

Homeodomain

A class of DNA-binding motifs that contain the helix-turn-helix structure, with an additional third helix, that typifies a class of transcription factors often found in developmentally regulated genes.

Leucine Zipper

A dimerization motif that is found in a class of transcription factors

Kuru

A human neurological disease caused by prions. It can be caused by eating infected brains.

Mediator

A large protein complex associated with RNA polymerase II. It contains factors that are necessary for transcription from many or most promoters.

Antirepressor

A positive regulator that functions in opening chromatin

True Activator

A positive transcription factor that functions by making contact, direct or indirect, with the basal apparatus to activate transcription

Repressor

A protein that inhibits expression of a gene, typically by binding to a silencer

Architectural Protein

A protein that, when bound to DNA, can alter its structure (e.g., introduce a bend)

Prion

A proteinaceous infectious agent that behaves as an inheritable trait, although it contains no nucleic acid. Examples are PrPSc, the agent of scrapie in sheep and bovine spongiform encephalopathy, and [PSI+], which confers an inherited state in yeast.

Nucleosome Organization or Content May Be Changed

A remodeling complex does not itself have specificity for any particular target site, but must be recruited by a component of the transcription apparatus. Remodeling complexes are recruited to promoters by sequence-specific activators (or repressors). The factor may be released once the remodeling complex has bound. Transcription activation often involves nucleosome repositioning and/or displacement at the promoter. The MMTV promoter requires correct positioning of a nucleosome, and not a nucleosome-free region, to allow a complete set of activators to bind to DNA on the nucleosome.

There Are Many Types of DNA-Binding Domains

Activators are classified according to the type of DNA-binding domain. Members of the same group have sequence variations of a specific motif that confer specificity for individual DNA target sites.

Lysine (K) Acetyltransferase (KAT)

An enzyme (typically present in large complexes) that acetylates lysine residues in proteins. Also known as histone acetyltransferase (HAT) when it acetylates a histone target.

Methyltransferase

An enzyme that adds a methyl group to a substrate, which can be a small molecule, a protein, or a nucleic acid

Dosage Compensation

Any mechanisms employed to compensate for the discrepancy between the presence of two X chromosomes in one sex but only one X chromosome in the other sex.

Epigenetic

Changes that influence the phenotype without altering the genotype. They consist of changes in the properties of a cell that are inherited but that do not represent a change in genetic information. Epigenetic effects can result from modification of a nucleic acid after it has been synthesized or by the perpetuation of protein structures.

Independent Domains Bind DNA and Activate Transcription

DNA-binding and transcription-activation activities are carried by independent domains of an activator. The role of the DNA-binding domain is to bring the transcription-activation domain into the vicinity of the promoter.

CpG Islands Are Subject to Methylation

Demethylation of a gene promoter is necessary, but not sufficient, for transcription. CGIs can be found in gene promoters, gene bodies, intergenic regions, and repetitive sequences. CGI methylation in a promoter leads to gene silencing, but CGI methylation in the gene body is activating. CpG shores are found within 2 kb of CGIs and are important in tissue-specific gene regulation. *De novo methyltransferases* can act on fully unmethylated sites. Replication converts a *fully methylated* site to a *hemimethylated site.* Hemimethylated sites are converted to fully methylated sites by a *maintenance methyltransferase.* DNA and histone methylation are mutually reinforcing.

Activators

Determine the frequency of transcription

Histone Deacetylase (HDAC)

Enzyme that removes acetyl groups from histones; may be associated with repressors of transcription.

Bromodomain

Found in a variety of proteins that interact with chromatin; it is used to recognize acetylated sites on histones.

Heterochromatin Depends on Interactions with Histones

HP1 is the key protein in forming heterochromatin in many eukaryotes and acts by binding to histone H3 methylated at lysine 9. Rap1 initiates formation of heterochromatin in yeast by binding to specific target sequences in DNA. The targets of Rap1 include telomeric repeats and silencers at HML and HMR. Rap1 recruits Sir3/Sir4, which interact with the N-terminal tails of H3 and H4. Sir2 deacetylates the N-terminal tails of H3 and H4 and promotes spreading of Sir3/Sir4. RNAi pathways promote heterochromatin formation at centromeres.

Heterochromatin Propagates from a Nucleation Event

Heterochromatin is nucleated at a specific sequence or chromosome feature, and the inactive structure propagates along the chromatin fiber. Genes within regions of heterochromatin are inactivated. The extent of heterochromatin spreading can vary from cell to cell; as a result, a gene close to a heterochromatin region can be silenced in a subset of cell lineages, causing *position effect variegation (PEV).* Heterochromatin spreading continues until proteins required for heterochromatin are depleted or an obstacle (such as an insulator) is encountered. Similar spreading effects occur at telomeres *(telomeric silencing).*

Amyloid Fibers

Insoluble fibrous protein polymers with a cross -sheet structure generated by prions or other dysfunctional protein aggregations (such as in Alzheimer disease).

Mechanism of Action of Activators and Repressors

Many activators work by making protein-protein contacts with the basal factors. Activators often work via coactivators. Both activators and repressors are regulated in many different ways. Activators and repressors can both act by recruiting factors that alter chromatin structure. Repressors can also function by binding to and masking activators to prevent nuclear entry, DNA binding, or activation functions.

Methylation of Histones and Methylation of DNA Are Connected

Methylation of both DNA and specific sites on histones is a feature of inactive chromatin. The SET domain is part of the catalytic site of protein methyltransferases Chromodomains and other conserved domains can bind to specific methylation sites on histones. DNA and histone methylation are connected.

Histone Acetylation Is Associated with Transcription Activation

Newly synthesized histones are acetylated at specific sites and then deacetylated after incorporation into nucleosomes. Histone acetylation is associated with activation of gene expression. Transcription activators are associated with histone acetylase activities in large complexes. Histone acetyltransferases vary in their target specificity. Deacetylation is associated with repression of gene activity. Deacetylases are present in complexes with repressor activity.

Chromatin Remodeling Is an Active Process

Numerous ATP-dependent chromatin remodeling complexes use energy provided by hydrolysis of ATP. All remodeling complexes contain a related ATPase catalytic subunit and are grouped into subfamilies containing more closely related ATPase subunits. Remodeling complexes can alter, slide, or displace nucleosomes. Remodeling is required to establish NFRs at promoters. Some remodeling complexes can exchange one histone for another in a nucleosome.

X Chromosomes Undergo Global Changes

One of the two female X chromosomes is inactivated at random in each cell during embryogenesis of placental mammals. In exceptional cases where there are more than two X chromosomes, all but one are inactivated (the n - 1 rule). The Xic (X-inactivation center) is a cis-acting region on the X chromosome that is necessary and sufficient to ensure that only one X chromosome remains active. Xic contains the Xist gene, which encodes an RNA that is found only on inactive X chromosomes. Xist recruits Polycombcomplexes, which modify histones on the inactive X. Tsix, an lncRNA that is antisense to Xist, protects the future active X from Xist-dependent inactivation. Different dosage compensation mechanisms equalize X-linked gene expression in other species.

DNA Methylation Is Responsible for Imprinting

Paternal and maternal alleles may have different patterns of methylation at fertilization. Methylation is usually associated with inactivation of the gene. When genes are differentially *imprinted*, survival of the embryo may require that the functional allele be provided by the parent with the unmethylated allele. Survival of heterozygotes for imprinted genes is different, depending on the direction of the cross. Imprinted genes occur in clusters and often depend on a local control site that protects germline methylation patterns from reprogramming in the zygote. Imprinted genes are controlled by methylation of cis-acting sites.

Polycomb and Trithorax Are Antagonistic Repressors and Activators

Polycomb group proteins (PcGs) perpetuate a state of repression through cell divisions. TrxG proteins antagonize the actions of the PcG and promote accessible chromatin structures. There are a number of different PcG and TrxG complexes—most contain subunits that directly catalyze or remove specific histone modifications, recognize specific modifications, or bind RNA, DNA, or other chromatin components. Histone modifications resulting from PcG or TrxG complex activity can stabilize or destabilize recruitment of other PcG or TrxG complexes. The PRE is a PcG-recruiting DNA sequence that contains a number of transcription factor-binding sites. Mammalian PcG complexes associate with hypomethylated CGIs.

Gene Activation Involves Multiple Changes to Chromatin

Remodeling complexes can facilitate binding of acetyltransferase complexes, and vice versa. Histone methylation can also recruit chromatin-modifying complexes. Different modifications and complexes facilitate transcription elongation. Histone phosphorylation is linked to transcription, repair, chromosome condensation, and cell cycle progression.

How is a Gene Turned On?

Some transcription factors may compete with histones for DNA after passage of a replication fork. Some transcription factors can recognize their targets in closed chromatin to initiate activation. The genome is divided into domains by *boundary elements (insulators).* Insulators can block the spreading of chromatin modifications from one domain to another.

Yeast Prions Show Unusual Inheritance

The Sup35 protein in its wild-type soluble form [psi-] is a termination factor for translation. It can also exist in an alternative form of oligomeric aggregates [PSI+ ], in which it is not active in protein synthesis. The presence of the oligomeric form causes newly synthesized protein to acquire the inactive structure. Conversion between the two forms is influenced by chaperones. A number of other prion-forming proteins, such as Swi1, have been identified in yeast; all share Gln/Asn-rich domains.

Negative Control

The default state of genes that are under negative control is to be expressed. A specific intervention is required to turn them off.

Positive Control

The default state of genes that are under positive control in that they cannot be expressed unless a positive regulator is bound

Chromatin Remodeling

The energy-dependent displacement or reorganization of nucleosomes that occurs in conjunction with activation of genes for transcription.

Constitutive Heterochromatin

The inert state of permanently nonexpressed sequences, often satellite DNA

Helix-Turn-Helix

The motif that describes an arrangement of two a-helices that form a structure that binds to DNA, with one helix fitting into the major groove of DNA and other lying across it.

Helix-Loop-Helix (HLH)

The motif that is responsible for dimerization of a class of transcription factors called HLH proteins. A bHLH protein has a basic DNA-binding sequence close to the dimerization motif.

Prions Cause Diseases in Mammals

The protein responsible for scrapie exists in two forms: the wild-type noninfectious form PrPC, which is susceptible to proteases, and the disease-causing form PrPSc, which is resistant to proteases. The neurological disease can be transmitted to mice by injecting the purified PrPSc protein into them. The recipient mouse must have a copy of the PrP gene encoding the mouse protein. The PrPSc protein can perpetuate itself by causing the newly synthesized PrP protein to take up the PrPSc form instead of the PrPC form. Multiple strains of PrPSc may have different conformations of the protein

Activators Interact with the Basal Apparatus

The specificity of activators is determined by a DNA-binding domain that recognizes a specific sequence in the target promoter or enhancer. The DNA-binding domain is responsible for localizing a transcription-activating domain in the proximity of the *basal apparatus.* Some activators that contact the basal apparatus directly have a DNA-binding domain flexibly linked to an activating domain. An activator that does not have an activating domain may work by binding a *coactivator* that has an activating domain. Coactivators also act to modulate chromatin structure directly. Several factors in the basal apparatus are targets with which activators or coactivators interact. RNA polymerase may be associated with various alternative sets of transcription factors in the form of a holoenzyme complex.

Steroid Receptor

Transcription factors that are activated by binding of a steroid ligand

Eukaryotic Gene Expression

Usually controlled at the level of initiation of transcription by opening the chromatin.

Facultative Heterochromatin

he inert state of sequences that also exist in active copies, for example, one mammalian X chromosome in females or loci silenced in one cell type but active in another.