chapter 15 eukaryotic gene regulation

accurate, developmental, differences, types

• eukaryotic gene regulation

  • multicellularity and a complex cell structure require a much greater level of gene regulation

  • regulation is necessary to ensure:

    • 1) expression of genes in an … pattern during the various …. stages of the life cycle

    • 2) … among distinct cell ….

proteins, polymerase, transcribe, pol, core promoter, elongation, basal transcription, new, rate, target, pol, begin, particular, 2, 3

• transcription factors

  • transcription factors are … that influence the ability of rna …. to … a given gene

  • there are 2 main types

    • 1) general transcription factors

      • required for the binding of the rna …. to the … … and its progression to the …. stage

        • required for … ….

    • 2) regulatory transcription factors (… material)

      • serve to regulate the … of transcription of …. genes

      • they influence the ability of rna … to … transcription of a … gene

    • … - … % of human genes encode transcription factors

cis, elements, near, promoter, control, regulatory, sequences, regulatory, control, associated, activator, enhancer, repressor, silencer

• regulatory transcription factors

  • regulatory transcription factors recognize … regulatory …. located … the core …

    • these sequences are known as … elements, … elements, or regulatory …

  • the binding of …. transcription factors to … elements affects the transcription of an … gene

    • a regulatory protein that increases the rate of transcription is termed an ….

      • the sequence it binds is called an ….

    • a regulatory protein that decreases the rate of transcription is termed a …

      • the sequence it binds is called a ….

combinatorial, activator, repressor, small effector, protein, protein, covalent, nucleosomes, promoter, methylation, activator, recruiting, chromatin, single

• most eukaryotic genes are regulated by many factors

  • this is known as … control

• common factors contributing to this control are:

  • 1 or more .. proteins may stimulate transcription

  • 1 or more … proteins may inhibit transcription

  • activators and repressors may be modulated by:

    • binding of … … molecules

    • … - … interactions

    • …. modifications

  • regulatory proteins may alter … near the ….

  • dna …. may inhibit transcription

    • prevent binding of an …. protein

    • … proteins that compact the …

• various combinations of these factors can contribute to the regulation of a … gene

domains, dna, effector, similar, proteins, loop, turn, zinc finger, leucine zipper, dna

• structural features of regulatory transcription factors

  • transcription factor proteins (like other proteins) contain regions, called …., that have specific functions

    • one domain could be for … binding

    • another could provide a binding site for … molecules

  • a motif is a domain, or a portion of a domain that has a very … structure in many different ….

    • helix-…-helix

    • helix-…-helix

    • … …

    • … ..

    • these domains help proteins bind to … and to each other

2 alpha, turn, dna, short alpha, long alpha, loop, long, dna, recognition helix, base, major groove, dna, alpha, nucleotide, transcription, dna

• different domain structures found in TFs

  • helix-turn-helix motif

    • … … helices are connected by a .., which bind to the …

  • helix-loop-helix motif

    • a … .. helix is connected to a .. .. helix by a …

      • the … helix binds to the …

  • the … … recognizes and makes contact with a … sequence along the … … of dna

    • hydrogen bonding between an … helix and .. bases is one way a … factor can bind to …

1 alpha, 2 beta, zinc, dna, major groove

• different domain structures found in TFs

  • zinc finger motif

    • composed of .. .. helix and .. .. sheets held together by a … metal ion

    • zinc fingers can recognize … sequences within the … …

alternating, zip up, protein dimerization, 2 alpha, intertwined, identical, different

• different domain structures found in TFs

  • leucine zipper motif

    • … leucine residues in both proteins interact (… ..) resulting in … …

    • … .. helices … due to leucine motifs

    • homodimers are formed by 2 … proteins (transcription factors)

    • heterodimers are formed by 2 … proteins (transcription factors)

increases, up regulation, decreases, down, orientation independent, bidirectional, forward, reverse, reponse, upstream, promoter

• enhancers and silencers

  • the binding of a TF to an enhancer …. the rate of transcription

    • this .. … can be 10 to 1,000 fold

  • the binding of a TF to. asilencer … the rate of transcription (called … regulation)

  • many response elements are .. … or ..

    • they can function in the … or … direction

  • most response elements are located within a few hundred nucleotides … of the …

    • however, some of found downstream etc

promote, inhibit, 2, transcribing, bind

• regulatory TFs act to … or … rna pol … from … a gene

• but most regulatory TFs dont actually … to the rna pol

tfiid, mediator, initaiton, elongation, promoter, nucleosome, activator, coactivator, tfiid, promoter, activates, enhanced, repressor, tfiid, promoter, inhibits, silenced, tata, rol

• regulatory TFs, TFIID, and Mediator

  • 2 common interactions that communicate the effects of regulatory transcription factors are:

    • 1) transcriptional activation/repression via binding ….

    • 2) stimulate the … to cause the switch from … to …

    • 3) recruiting proteins to the … that affect … composition

  • a) the …/… complex recruits … to the core … and … its function

    • transcription will be …

  • b) the .. protein inhibits the binding of ….. to the core … or … its function

    • transcription is …

  • TFIID is needed to bind the … box and recruit rna ….

activator, phosphorylation, carboxyl, terminal, polymerase, general, elongation, stimulates, pol, preinitiation, elongation

• transcriptional activation via mediator

  • the … protein interacts with mediator

  • this results in the … of the ..-… domain of rna ….

  • some .. transcriptonal factors are released, and rna polymerase proceeds to the .. phase of transcription

• transcriptional activator … the function of mediator

• this enables rna … to form a … complex

• it then proceeds to the … phase of transcription

repressor, prevents, phosphorylation, polymerase, cannot, elongation, inhibits, repressed

• transcriptional repression via mediator

  • the … protein interacts with mediator in a way that … the …. of rna …

  • therefore, it … proceed to the … phase of transcription

• transcriptional repressor … the function of mediator

• transcription is ….

small effector, protein, protein, covalent

• modulation of regulatory transcription factor functions

  • there are 3 common ways that the function of regulatory transcription factors can be modulated

    • 1) binding of a .. .. molecule

    • 2) ..-… interactions

    • 3) … modifications

regulatory, steroid, steroid receptors, transcription, transcription, endocrine glands, bloodstream, respond

• steroid hormones and regulatory TFs

  • … transcription factors that respond to … hormones are termed … …

    • the hormone actually binds to the … factor

  • the ultimate action of a steroid hormone is to affect gene ….

    • steroid hormones are produced by .. …

      • secreted into the …

      • then taken up by cells that … to the hormone

diffuses, plasma membrane, receptor, cytosol, nucleus, expression

• lipid soluble hormones

  • hormone … through … … into cell

  • binds to … in the … directly

  • receptor enters ..

    • alters gene …..

glucocorticoids, nutrient, immune, glucose utilization, fat mobilization, protein breakdown, immune, feedback, reduces, functioon, inflammation, gonadorcorticoids, estrogen, testosterone, growth, function, gonads

• steroid hormones and regulatory TFs

  • cells respond to steroid hormones in different ways

    • 1) ….

      • these influence … metabolism and … response

        • they promote .. …, … …, and .. …

        • involved in … system .. which … certain aspects of immune ….

          • such as reduction of …

    • 2) …

      • these include … and …

      • they influence the …. and … of the ….

dependent, structure, closed, tightly, difficult, impossible, open, transcription, place, few, expression, multiprotein machines, reposition, restructure

• chromatin remodeling and histones

  • atp-….. chromatin remodeling refers to dynamic changes in chromatin …

    • … conformation

      • chromatin is very … packed

      • transcription may be … or …

    • …. conformation

      • chromatin is accessible to …. factors

      • transcription can take ….

  • these changes range from a … nucleosomes to large scale changes that affect gene …

  • carried out by diverse … … that … and …. nucleosomes

position, particular, inactive, beta, promoter, activation, chromatin, dependent, hydrolysis, location, composition, more, less

• nucleosomes have been shown to change … in cells that normally express a .. gene compared with cells in which the gene is …

• for ..-globin, nucleosome positioning changes in the … region as part of gene ….

• a key role of some transcriptional activators is to orchestrate changes in … structure

• one way is through atp-… chromatin remodeling

  • energy of atp … is used to drive change in … and or … of nucleosomes

  • makes the dna .. or .. amenable to transcription

structure, accessible

• atp-dependent chromatin remodeling

  • the energy of atp is used to alter the .. of nucleosomes, and thus make the dna more ….

h1, h2a, h2b, h3, h4, duplication, standard, mutations, amino acid, variants, nucleosomes, specialized chromatin

• histone variants

  • the 5 histone genes are moderately repetitive

    • …..

    • …

    • ..

    • ..

    • ..

  • human genome contains over 70 histone genes (due to gene …. events during evolution)

    • most encode … histones

    • a few of these genes have accumulated … that alters the .. .. sequence

      • these gene produce histone …

  • some histone variants are incorporated into a subset of … to create … ….

50, amino terminal tails, histones, between, code, proteins, binding, structure, code, transcription, phosphate, ser, acetyl, lys, methyl, arg, lys

• histone code

  • over … enzymes have been identified in mammals that selectively modify the … … … of …

  • these modifications affect the level of transcription by influencing interactions …. nucleosomes

  • modifications occur in patterns (which is called the histone ….)

  • modification patterns are recognized by … and provide … sites for proteins that specify alterations to be made to chromatin …

    • these proteins bind based on the … and affect ..

  • p = … group (…)

  • ac = … group (…)

  • m = … group (…, …)

information, dna, chemical, histone, tails, methylation, epigenetic

• histone code

  • the histone code is a hypothesis that the transcription of genetic … encoded in … is in part regulated by … modifications to …. proteins, primarily on their ….

  • together with similar modifications, such as dna … it is part of the ….. code

amino acids, tails, repression, activation, histone, epigenetic, evicted, destabilized, pol, elongation, enzymes, pol, removal ahead, chaperones, reassembly, octamers, deacetylases, remove acetyl, histones, nucleosomes, reform

• summary:

  • specific patterns of covalent modifications to the .. … of the histone … lead to transcriptional .. or .. (many enzymes involved)

  • the pattern of modifications is called the … code, which is part of the … code

  • histones must be …. or … for the rna to transcribe

  • during transcription …., histone modifying … travel with the rna …., which facilitates histone … …. of the pol

  • evicted histones are transferred to histone … which will aid in the … of the .. after rna pol has passed

  • histone … will then .. .. groups on the histones, which promotes … to ….

activator, enhancer, close, start, far, activator, recruits, remodeling, swi, snf, enzyme, acetyltransferase, nucleosomes, histones, variants, modification, acetylation

• transcriptional activation

  • binding of activator:

    • … protein binds to … sequence

    • the enhancer may be … to the transcriptional .. site or … away

  • chromatin remodeling and histone modification

    • an … protein recruits a chromatin remodeling complex such as …/… and a histone modifying … such as histone …..

    • … may be moved, and histones may be evicted or replaced with …

    • some histones are subjected to covalent …. such as ….

general, 2, promoter, preinitiation, ahead, open, acetylation, behind, deacetylated, tightly, dna

• transcriptional activation

  • formation of the preinitiation complex

    • …. transcription factors and rna polymerase …. are able to bind to the core … and form a … complex

  • elongation

    • during elongation, histones … of the … complex are covalently modified by …. and evicted

    • … the open complex, histones are … and become .. bound to the …

methyl, structure, silenced, methyltransferase, common, yeast, drosophila, little, vertebrates, plants, abundant, 2, 7

• dna methylation

  • covalently attaching …. groups to dna usually changes the chromatin …. so that gene expression is ….

    • dna methylation is carried out by the enzyme dna ….

  • … in some euk species but not all

    • … and .. have … dna methylation

    • …. and … have abundant dna methylation

      • in mammals, ~… to … % of the dna is methylated

inhibits, eukaryotic, vicinity, promoter, cpg islands near, 1,000, 2,000, housekeeping, unmethylated, expressed, tissue, silenced, methylation, methyl, cpg, proteins, compaction, chromatin

• dna methylation usually .. the transcription of … genes, especially when it occurs in the … of the …

• in vertebrates and plants, many genes contain .. .. .. their promoters

  • these cpg islands are .. to … nucleotides long

  • in … genes, the cpg islands are … and …

  • in … specific genes - may be … by the … of the cpg islands

    • …-…-binding .. may recruit factors that lead to … of the …

methyl, cpg, protein, cpg island, recruits, deacetylase, closed, repression

• transcriptional silencing via methylation

  • a ..-…-binding … binds to the methylated .. ..

  • the methyl-cpg-binding protein … other proteins such as histone … that convert the chromatin to a .. conformation

  • leads to transcriptional …

long, one, neighboring, segments, dna, regulatory, other, barriers, remodeling, enhancers, chromosome looping

• insulators

  • since eukaryotic gene regulation can occur over … distances, it is important to limit regulation to … particular gene - dont want regulation to effect … genes

  • insulators are … of … that insulate a gene from the … effects of other genes

    • some act as … to chromatin …

    • others block the effects of …

      • may do this by … …

minutes, days, months, shortened, lengthened, mrna concentration, expression, length, polya tail, destabilizing

• stability of mrna (another way to regulate euk gene expression)

  • the stability of mrna varies between several … to several … or even …

  • half life is … or …

    • influences the mrna …. and gene …

  • factors that can affect mrna stability include

    • 1) … of the …. …

    • 2) .. elements

200, polya, protein, binds, stabilizes, shortened, cellular nucleases, less, 10, 30 adenosines, exo, endonucleases

• polyA tail

  • commonly about … nucleotides long

  • recognized by ..-binding … - … and ….

  • polyA tail is … by the action of .. ..

  • the polyA binding protein can no longer bind if the polyA tail is .. than … to … …. long

    • rapidly degraded by … and …..

short half lives, anywhere, 3, stop, polya tail, au rich element, destabilization

• destabilizing elements

  • found especially in mrnas that have … .. ….

  • these elements can be found … on the mrna

  • most common at the ..’ end between the … codon and the …. tail

  • ARE: … … … = …. element

micro, short, interfering, eukaroyitc, small rna, not, exogenous, viruses, lab, perfect

• rna interference

  • …. rnas (miRNAs) and ..-… rnas (sirnas) cause rna interference

    • miRNAs are encoded by genes in … organisms

      • encode .. .. molecules, typically 21 to 23 nucleotides

      • … usually a perfect match to mrnas

      • in humans, over 1000 genes encoding mirnas have been identified

    • siRNAs come from … sources (ex. …, produced in …)

      • usually a .. match or close to specific mrnas

degradation, double, c. elegans, antisense, oocytes silenced, double, inhibiting, corresponding, long

• discovery of double stranded rna and gene silencing

  • evidence for mrna … via … stranded rna came from studies in … …

    • injection of … rna (rna complementary to a specific mrna) into … … gene expression

      • injection of .. stranded rna was 10 times more potent at … the expression of the … mrna

      • also the effects of antisense rna persisted for a very … time

viral, experimental, dicer, double, rna, rna, induced silencing, one, degraded, cellular, complementary, p, body, stored, reused, degraded, partial, degraded, high

mechanism of rna interferece:

• pre-miRNA

• pre-siRNA may come from a … infection or from … treatment

• either pre-miRNA or pre-siRNA is recognized by a … and cut into … stranded … about 20 to 25 bp long

• the double stranded rna is recognized by a protein that associates with other proteins to form an ..-… … complex (RISC)

• … of the rna strands is …

• the RISC recognizes specific … mRNAs due to .. sequences

• miRNA

  • the mrna is sent to a ..-.. where it may be .. and later .. or it may be eventually .. (… complementarity)

• siRNA

  • the mrna is …. (… complementarity)

degrade, high, inhibit translational, low, cellular, storage, degradation

outcomes of RNAi

• RISC may …. mrna if miRNA/siRNA has … complementarity to mrna

• RISC may .. .. machinery if .. complementarity between miRNA/siRNA and mrna

• RISC/mRNA complex may be sent to a … processing body for … and later use or …..

level, defense, viruses, double, produce, reproductive, silencing, transposable, random insertion, cellular promoter, silencing

• benefits of rna interference

  • adds another … gene expression

  • may offer a … mechanism against certain …

    • rna viruses that have a … stranded rna genome

    • rna viruses that … a double stranded rnas during their … cycle

  • may play a role in …. certain … elements

    • … …. may place an element near a .. .. which will produce a …. rna