Genetics & Mol Bio Gu Fmbg

Front 1

What is the point of imprinting? What is one hypothesis that explains when it would be useful?
What is an example of an imprinted gene?

Back 1

GENE CONFLICT HYPOTHESIS- helps keep balance between two conflict of mom & dad.

Insulin- Like Growth Factor 2 (Ilgf2) is an example of an imprinted gene. (both receptor and hormone genes)

Front 2

What are "transient modifications of DNA that can be passed, influencing genetic inheritance?"

Back 2

EPIGENETICS- imformation passed from one generation to next (either cell--> daughter cells or parents--> offspring) but IS NOT ENCODED IN DNA SEQUENCES.

Front 3

What types of modifications can be imposed on the genome (DNA) and ensure stable transmission WITHOUT CHANGES TO THE DNA SEQUENCE? What do we call this

Back 3

The EPIGENOME--> DNA methylation/ imprinting, genomic silenceing, undermethlylation, overmethlyation, subtle expression patterns of methylation
*TRANS EPIGENTIC moditifaction--> (+) feedback cycle
*CIS EPIGENTIC modification--> modification of histones, DNA methylation, protien aggregation state.

Front 4

In vertibrates, where on the DNA does the methylation physically occur? Which nucleotide (G,C,T,A, or U)? at which locations?

Back 4

In vertebrates, this event is confined to selected CYTOSINE (C) nucleotides located in the sequence CG in a DNA DOUBLE-HELIX

Front 5

What are the distinct mechanisims that can produce and EPIGENETIC form of inheritance in an organisim? (4)

Back 5

1) Positive Feedback – Trans
2) DNA Modification - Cis
3) Histone Modification - Cis
4) Prions. When a protein is mis-folded after cell division and gene expression, you’ve technically inherited a new protein conformation state.

Front 6

Decribe the difference between trans and cis epigentics

Back 6

Trans epigenetic signals (yellow circles) are transmitted by partitioning of the cytosol during cell division and maintained by feedback loops. As an example, a simple regulatory loop in which the epigenetic signal induces its own expression is shown here. (B) Cis signals (yellow flags) are molecular signatures physically associated with the DNA and inherited via chromosome segregation during cell division.

Front 7

Usually in females, we have two X X chromosomes... If they are both active, we my see unusually high expresison of X chromosome. What ca we do to COMPENSATE for this double DOSE of (i.e. dosage compensation) for the X chromosom expression in females?

Back 7

We methlyate/ inactivate/ silence gene expression of one of the X chromosomes. Formerly known as barr bodies.
(Begins with synthesis from X-Inactivation SEQUENCE (XIST) from the X inactivation center) ...
RANDOMLY choosing/ silencing EITHER maternal OR paternal X chromosome.

Front 8

How do other animals (involved in sexual reproduction) achieve DOSAGE COMPENSATION? What do they all have in common?

Back 8

DOSAGE COMPENSATION--ALL INVOLVED STURCTURAL ALTERCATIONS OVER ENTIRE X CHROMOSOME

Humans: X-Inactivation in females

Drosophila: genes on single X present in males are expressed at 2-fold higher levels

Nematodes: genes on the two X chromosomes found on hermaphrodites are expressed at half the levels of the male single X chromosome

Front 9

How are DNA methylation sequences faithfully inherited?

Back 9

This methylation of DNA help mark parental strand for methylation--> bind more tightly to hemimethylated DNA--> "maitinace methylation" enzymes ensure accurate method of gaining genetic inheritance of DNA sequences.

In vertebrate DNAs, a large fraction of the cytosine nucleotides in the sequence CG are methylated. Because of the existence of a methyl-directed methylating enzyme (the MAINTENANCE METHLYTRANSFERASE), once a pattern of DNA methylation is established, that pattern of methylation is inherited in the progeny DNA, as shown.

Front 10

What is the difference between the methylation of a gene and the methylation of a paternal/ maternal strand?

Back 10

The paternal genome is demethylated prior to the first cell division of the zygote; maternally derived DNA is demethylated after several cleavage divisions (exceptions to this simplified model exist, including imprinted genes and repetitive elements). De novo methylation occurs in the inner cell mass (ICM) cells, which later differentiate into the embryo. Maintenance DNA methylation retains methylation patterns as differentiated cells undergo mitosis.

Front 11

Describe how DNA methylation:
1.) contributes to mechanisims of stable GENE REPRESSION
2.) may help TURN OFF genes

What is the purpose behind this?

Back 11

Expression is considered to be leaky & METHYLATION ENSURES DNA WILL NOT BE EXPRESSED.

Unneeded eukaryotic genes can be repressed very effectively, minimizing leaky expression. Expression rates can differ by 106-fold between tissues.

Multiple mechanisms contribute to stable gene repression. In this schematic example, histone reader and writer proteins, under the direction of gene regulatory proteins, establish a repressive form of chromatin. A de novo DNA methylase is attracted by the histone reader and methylates nearby cytosines in DNA, which are, in turn, bound by DNA methyl-binding proteins. During DNA replication, some of the modified (blue dot) histones will be inherited by one daughter chromosome, some by the other, and in each daughter they can induce reconstruction of the same pattern of chromatin modifications. At the same time, the mechanism will cause both daughter chromosomes to inherit the same methylation pattern. The two inheritance mechanisms will be mutually reinforcing, if DNA methylation stimulates the activity of the histone writer. This scheme can account for the inheritance by daughter cells of both the histone and the DNA modifications. It can also explain the tendency of some chromatin modifications to spread along a chromosome.
How DNA methylation may help turn off genes. The binding of gene regulatory proteins and the general transcription machinery near an active promoter may prevent DNA methylation by excluding de novo methylases. If most of these proteins dissociate from the DNA, however, as generally occurs when a cell no longer produces the required activator proteins, the DNA becomes methylated, which enables other proteins to bind, and these shut down the gene completely by further altering chromatin structure

Front 12

Describe how chronic High Fat Diet (HFD) in fathers program Beta-cell dysfunction in female rat offspring. What is this an example of?

What about female UNDERnutrition during pregnancy?

Back 12

developmental plasticity could contribute an adaptive model that includes the effects of environmental factors during early development.

Molecular network of differentiallly expressed ISLET genes of HFD female offspring. (IL-13ra2--> JAK-STAT pathway) In HFD, IL-13ra2 lower methylation--> lower transcription... change in (lowered) gene expression

basically the paternal HFD altered the EXPRESSION of many genes of the daughter cells.

The metabolic phenotype of prenatally UNDERnourished rats also caused changes in promoter methylation and gene expression.

Differrences: pregnant females considered multigenerational, males= just genetic material in sperm

. Environmental Cues during Development, Developmental Plasticity, and Determination of the Adult Phenotype. Prenatal cues predicting a nutritionally sparse environment will cause a shift in the trajectory of structural and functional development toward a phenotype matched to that environment. Such a phenotype will have a reduced capacity to cope with a nutritionally rich environment later in life, increasing the risk of metabolic disease. Postnatal cues, such as childhood overnutrition leading to compensatory growth, could further shift the positioning of the adult phenotype, exacerbating the mismatch (dashed lines) between phenotype and environment. Although there is a continuous range of possible developmental trajectories and multiple sequential cues that act during development, for simplicity only two developmental cues (before and after birth) and three trajectories are shown.

Front 13

What is GENOMIC IMPRINTING based on?

In general, which side of the genes (paternal or maternal) are most heavily methylated?

Back 13

Genomic Imprinting is Based on DNA METHYLATION

The top portion of the figure shows a pair of homologous chromosomes in the somatic cells of two adult mice, one male and one female. In this example, both mice have inherited the top homolog from their father and the bottom homolog from their mother, and the PATERNAL COPY of a gene SUBJECT to IMPRINTING (indicated in orange) is methylated, preventing its expression. The maternally derived copy of the same gene (yellow) is expressed. The remainder of the figure shows the outcome of a cross between these two mice. During germ cell formation, but before meiosis, the imprints are erased and then, much later in germ cell development, they are reimposed in a sex-specific pattern (middle portion of figure). In eggs produced from the female, neither allele of the A gene is methylated. In sperm from the male, both alleles of gene A are methylated. Shown at the bottom of the figure are two of the possible imprinting patterns inherited by the progeny mice; the mouse on the left has the same imprinting pattern as each of the parents, whereas the mouse on the right has the opposite pattern. IF THE TWO ALLELES OF A ARE DISTINCT, THESE DIFFERENT IMPRINTING PATTERNS CAN CAUSE PHENOTYPIC DIFFERENCES IN THE PROGENY MICE, EVEN THOUGH THEY CARRY THE EXACT SAME DNA SEQUENCES OF THE TWO A GENE ALLELES.

**Imprinting provides an important exception to classical genetic behavior, and several hundred mouse genes are thought to be affected in this way. The rules of Mendelian inheritance apply to most of the mouse genome, BUT...

Front 14

In general, what are the different ways we can convert a proto-oncogene to an oncogene?

Back 14

Gain of fxn mutation or loss of fxn mutation

Front 15

In general, what types of proteins are candidates for possible conversion to an oncogene.

Back 15

Most oncogenes code for proteins within growth and cell cycle pathways:

Growth factors

Growth factor receptors

Intracellular signal transducers

Nuclear transcription factors

Front 16

How can we explain the early onset at multiple sites in the body of an inherited form of cancer called hereditary retinoblastoma?

Back 16

Inheriting one germline copy of a damaged gene present in every cell in the body was not sufficient to enable this cancer to develop. A second hit (or loss) to the good copy in the gene pair could occur somatically, though, producing cancer. This hypothesis predicted that the chances for a germline mutation carrier to get a second somatic mutation at any of multiple sites in his/her body cells was much greater than the chances for a noncarrier to get two hits in the same cell.

Tumor suppressors act recessive at the phenotypic level (both alleles must be mutated/lost for cancer to develop), but the "first hit" germline mutation at the genotypic level is actually inherited in an autosomal dominant fashion.

Front 17

What is a Micro RNA (miRNA) and what do they do exactly?
How significant are they?

Back 17

Micro RNA (miRNA)
A high number: about 1% of the genes

miRNAs are well conserved in eukaryotic organisms and are thought to be a vital and evolutionarily ancient component of genetic regulation.

Basically, the regulate gene expression on the TRANSLATIONAL LEVEL

miRNAs are post-transcriptional regulators that bind to complementary sequences on target messenger RNA transcripts (mRNAs), usually resulting in translational repression or target degradation and gene silencing

Front 18

How is miRNA made and how is it different in plants versus animals?

Back 18

If the RNA:RNA match is extensive, as is commonly seen in plants, Argonaute cleaves the target mRNA, causing its rapid degradation.

In animals, the miRNA-mRNA match often does not extend beyond a short 7-nucleotide “seed” region near the 5¢ end of the miRNA. This less extensive base pairing leads to inhibition of translation, mRNA destabilization, and transfer of the mRNA to P-bodies, where it is eventually degraded.

Front 19

Define the subtle differences between miRNA, siRNA, and RNAi.

Back 19

RNA INTERFERENCE (RNAi) is a process within living cells that moderates the activity of their genes. Historically, it was known by other names, including co-suppression, post transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon. In 2006, Andrew Fire and Craig C. Mello shared the Nobel Prize in Physiology or Medicine for their work on RNA interference in the nematode worm C. elegans, which they published in 1998.
Two types of small ribonucleic acid (RNA) molecules – microRNA (miRNA) and small interfering RNA (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to other specific messenger RNA (mRNA) molecules and either increase or decrease their activity, for example by preventing an mRNA from producing a protein. RNA interference has an important role in defending cells against parasitic nucleotide sequences – viruses and transposons – but also in directing development as well as gene expression in general.

Front 20

How are MicroRNAs (miRNA) act differently in plants than in animals?

Which group is more picky in matching sequences? (Needs to be PERFECTLY matched, or gene is silenced?

Which group has more flexibility in their miRNA target sites because they are just for 3' untranslated regions (UTR)?

Back 20

miRNAs show very different characteristics between plants and animals:

In plants, repressions on the transcriptional level usually require a PERFECT or near-perfect target match, while a mismatched target can lead to gene silencing at the translational level.

In animals, on the other hand, miRNA complementarity typically encompasses the 5' bases 2-7 of the microRNA, the microRNA seed region, and one miRNA can target many different sites on the same mRNA or on many different mRNAs.

Another difference is the location of target sites on mRNAs:

In animals, the miRNA target sites are in the three prime untranslated regions (3'UTR) of the mRNA. This is how microRNA may target several mRNAs.

In plants, targets can be located in the 3' UTR but are more often in the coding region itself.

Front 21

What are the key protiens that aid in miRNA processing?

How do we get the miRNA made in the nucleus out in to the cytosol? Can't it just diffuse out?

Back 21

Pre-microRNA (pre-miRNA) is to bulky to diffused, and needs the RNA-GTP, Exportin 5 protien in order to fit through the door of the Nulear pore and go out into the cytosol to be processed properly.

Drosha, Pasha (pri-miRNA → pre-miRNA)
Spliceosome (pre-mRNA → intron lariat)
Debranching enzyme (intron lariat → RNA that can fold into pre-miRNA)
RAN-GTP, Exportin-5 (export from nucleus)
Dicer (pre-miRNA → miRNA)

1. MicroRNA (miRNA) genes are transcribed by RNA polymerase II (Pol II) into long (60–100-nucleotide (nt))--> primary miRNA (pri-miRNA) sequences that fold into stem–loop structures.
2. Pri-miRNAs--> cleaved by the Drosha–DGCR8 COMPLEX (DiGeorge syndrome critical region gene-8) to form ~70-nt pre-miRNA structures that contain 2-nt overhangs at their 3′ ends29.
3. Pre-miRNAs--> bind to exportin-5–RanGTP & transported to the cytoplasm
4. In the cytoplasm, pre-miRNA--> processed by Dicer (an Rnase III) into small (~22- nt) miRNAs
5. miRNAs --> assemble to RNA-induced silencing complex (RISC) for gene silencing.

Front 22

In the grand scheme of things, what does the MicroRNA (miRNA) need to combine with in the cytocol in order to carry out it's final step and function in the cell as a gene modifier?

Back 22

miRNAs--> assemble to RNA-induced silencing complex (RISC) for gene silencing.

RISC (RNA-Induced Silencing Complex) contains:
*ARGONAUTE protiens (AGO1, AGO2
*Dicer (RNase III)
*TRBP (HIV-1 transactivation responsive element (TAR) RNA-binding protein)
*RCK (also known as p54))
*unidentified proteins...

Front 23

What are some of the traits/ properties of MICRORNA (miRNA) that they have in common with TRANSCRIPTION FACTORS? (5 properties)

Back 23

pleiotrophy, combo & co-op, accesibility, regulation, and network motifs

Front 24

Define miRNA, siRNA, and RNAi.

Back 24

miRNA= Micro RNA
siRNA= small interfering RNA
RNAi= interference

Front 25

How do miRNA, siRNA, and RNAi all relate to human retroviruses like lentivirinae (HIV) and Oncovirinae? What roles do they play?

Back 25

Front 26

Define the subtle differences between miRNA, siRNA, and RNAi.

Back 26

MicroRNAs (miRNAs) are GENOMICALLY ENCODED non-coding RNAs that help regulate gene expression, particularly during development.

The siRNAs derived from long dsRNA precursors differ from miRNAs in that miRNAs, especially those in animals, typically have incomplete base pairing to a target and inhibit the translation of many different mRNAs with similar sequences. In contrast, siRNAs typically BASE-PAIR PERFECTLY and induce mRNA cleavage only in a SINGLE, SPECIFIC TARGET.

The phenomenon of RNA interference (RNAi) , broadly defined, includes both the ENDOGENOUS gene silencing effects of miRNAs *and* silencing triggered by FORGEIN dsRNA. RNAi is an RNA-dependent gene silencing process that is controlled by the RNA-induced silencing complex (RISC) and is initiated by short double-stranded RNA molecules in a cell's cytoplasm, where they interact with the catalytic RISC component ARGONAUTE (AGO)..

Front 27

Most transducing RETROVIRUSES like ONCOVIRIDAE (literally cancer causing virus) that integrate an oncogene into the host membrane, are DEFECTIVE viruses because they don't have all the elements they need to function by themselves. Why? How do they still work?

Back 27

Need HELPER VIRUS from the environment (i.e. a second viral infection) In order to make sure we have all the elements [gag] [pol] [env] and [oncogene] to produce oncogeme. Transducing retroviruses are typically defective,requiring a helper virus to provide gag, pol, & env.

Front 28

What are the different methods that we can INHIBIT protein expression at the TRANSLATIONAL LEVEL? (2 different RNA induced complexes can be formed)

What are the different protein complexes called?

Back 28

*RNA Induced Silencing Complex (RISC)= translations block (animals) or mRNA degredation (plants)
*RNA Induced Transcriptional Silencing (RIST) = siRNA mediated heterochromatin formation)-

Overview of RNA interference. The dicer enzymes produce siRNA from double-stranded RNA and mature miRNA from precursor miRNA. miRNA or siRNA is bound to an argonaute enzyme and an effector complex is formed, either a RISC (RNA-induced silencing complex) or RITS (RNA-induced transcriptional silencing) complex. RITS affects the rate of transcription by histone and DNA methylation, whereas RISC degrades mRNA to prevent it from being translated.

Front 29

Endogenous mircoRNAs (miRNAs) are a method cells can use to inhibit (silence/ repress) a protein being made at the TRANSLATIONAL step of gene expression. How could these endogenous miRNAs be linked to CANCER formation?

*hint* How could miRNA cause tumorgenesis? How could we use it instead to target tumors that have inappropriate expression (overexpression) of certain proteins?


**Hint**Think of what situations where certain miRNAs would be a good thing (possibly theraputic) and a bad thing (cause cancer formation either directly/indirectly)

Back 29

MicroRNAs (miRNA) can function as both ONCOGENES or TUMOR SUPRESSORS depending on their target. miRNAs can be involved in cancers by directly regulating cell growth or indirectly controlling apoptosis through targeting transcription factors or signaling pathways

Good: Artificial miRNAs could be synthesized to down-regulate oncogenes and prevent the formation of cancer.
Bad: when they promote tumor development by negatively inhibiting tumor suppressor genes and/or genes that control cell differentiation or apoptosis.


miRNA expression can result in the inhibition of apoptosis, and causes cancer pathogenesis in several organs, including lung cancer and lymphomas


Some miRNAs may be directly involved in cancer development by controlling cell differentiation and apoptosis, while others may be involved in cancers by targeting cancer oncogenes and/or tumor suppressors.

Because miRNAs function as oncogenes or tumor suppressors, it might be possible to regulate miRNA expression and/or inject miRNAs to regulate cancer formation

(i.e. miRNA targeting of Ribonucleotide Reductase in tumor cells --> decrease in necessary enzyme for DNA synthesis.

Front 30

What kinds of functional outcomes might we expect to see as a result of this miRNA mechanism of RNA inhibition in cells?

Back 30

If you derepress oncogene, oncogene is now expressed.

Front 31

You can get miRNAs taken up through diet, survive digestion, and occur at significanlty high levels in your blood. They can inhibit synthesis of receptors (control gene expression) in our own bodies. How do we know this is happening? Why is diet so important?

Back 31

can actually inhibit protein expression in our own bodies, and have physiological outcomes.
(i.e. decrease in expression of LDL receptors--> can affect cholesterol)

You are what you eat.