Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Embryology: Summer Semester > Unit 3.L3-Transcription Factors & Epigenetic in Development and Stem Cells > Flashcards

Unit 3.L3-Transcription Factors & Epigenetic in Development and Stem Cells Flashcards

1
Q

What experiment helped discover that differenct cell types of a multicellular organism have the same DNA blueprint?

A

A skin cell nucleus of an adult frog transplanted into an enucleated egg gives rise to an entire tadpole!

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

DNA sequence (6 Billion bases) in all cells of a person is the same? So how do we achieve cell diversity and body plan?

A

Other factors determine cell differentiation to form organs and whole body: TRANSCRIPTION FACTORS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the two types of differential gene expression in development?

A
  • House Keeping Gene
  • Tissue Specific Gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is an example of a House-keeping gene? What makes it a house-keeping gene?

A
  • β-actin is a House-keeping gene used by all cells all the time.
  • RNA is collected from 7 human tissue cell lines (β-actin mRNA: Expression is same in 7 tissue)
  • So the expression is same in all cells all the time
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is an example of a Tissue specific gene? Where in the body is the specific gene for?

A
  • Tyrosine Aminotransferase
  • Highly expressed Liver tissue Specific Gene (Tyrosine aminotransferase is seen to be expressed in liver but not in the other cell types)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What dictates cell fates in Development?

A

Active & Inactive Gene Loci

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is an actively expressed gene in cell Type-A far more than compared to Type-B cell (in which it is not expressed)?

  • Type A- Hematopoietic lineage; SYK or Spleen Tyrosine Kinase gene
  • Type B- Fibroblasts
A

An actively expressed gene in cell type-A (hematopoietic lineage; SYK or Spleen Tyrosine Kinase gene) is far more DNase-I Hyper-Sensitive (DHS) than in cell type-B (fibroblasts) in which it is not expressed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Related cells in different organs (all fibroblasts) have similar what?

A

DHS (DNase-I Hyper-Sensitive)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Distantly related cell types to fibroblast (i.e. hematopoietic cells) have what compared to fibroblasts? But have what within themselves (hematopoietic cells)?

A
  • Distantly related cell types to fibroblasts (i.e., hematopoietic cells) have different DHS signature when compared to fibroblasts
  • Have similar DHS signature within themselves (hematopoietic cells)

DHS (DNase-I Hyper-Sensitive)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q
  • 30% of DHS in adult cells overlap with what?
  • 30% of what is found in each adult cell type (~200 types)?
A
  • 30% of the DHS in adult cells overlap with ES (embryonic stem) cells
  • 30% of a unique DHS is found in each adult cell type (~200 types).

DHS (DNase-I Hyper-Sensitive)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is shown in a Dendrogram?

A

Dendrogram from all DHS maps showing relationship of gene activation in each cell type across the entire genome

DHS (DNase-I Hyper-Sensitive)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the relationship between the 3 germ layers and DHS? What types of cells cluster together for each one?

A

Each Germ layer has a strong relationship

  1. Mesoderm
  • Fibroblast (Paraxial Mesoderm) Cluster together
  • Hemocytoblasts (Lymphoid + Hematopoietic Prog.) Cluster together
  1. Ectoderm
  • Skin Keratinocytes/mammary epithelia Cluster together
  1. Endoderm
  • Airway & Esophageal Epithelia Cluster together
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What determine cell types during development?

A

Transcription Factors (TFs)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Where does selective gene expression differentiate cell types? Where do they later differentiate and what role do they play?

A

Selective gene expression differentiate cell types in three germ layers & later in each tissue of an organ, giving structure and function to an organ & embryo.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is selective gene expression dictated by?

A

Tissue-specific transcription factors (TFs)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What do TFs target and what type of expression do they have?

A

Tissue-specific transcription factors (TFs) that select target genes that have cell-lineage and stage-specific expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Mechanism of Cell Specification by Transcription Factors

  1. How many cells types are defined by the Distinct set of TFs?
  2. What turns on/off during successive generations of cells in development?
  3. What does TFs activate when a cell matures and goes through different stages?
  4. In subsequently cell-divisions what terminally differentiate a cell type?
A
  1. Distinct set of TFs define each of the >200 cell types in humans.
  2. Spatial-temporal expression of TFs turn on/off during successive generations of cells in development.
  3. As cells mature and go through different stages, TFs activate a gene repertoire and change the cell type.
  4. In subsequent cell-divisions, it is the combination of different TFs that terminally differentiate a cell type.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

About how many TFs in the human body is tissue specification dependent on?
What are the major families of TFs? (4)

A
  • About 2500 TFs in a human body expressed in different cell types→combination→Cell & Tissue-Type
  • Major Families of TFs
    1. Forkhead Box (FOX) family of TFs
    2. HOX family of TFs
    3. PAX family of TFs
    4. bHHL-family TFs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Tissue specfic TFs bind what? And how does it affect transcription?

A

Tissue specific TFs bind DNA-elements & activate or repress transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What does TFs dictate concering gene expression? What are the four parts of TFs?

A

TFs dictate cell specific gene expression for tissue & organ specification

  1. Promoters
  2. Enhancers
  3. Silencers
  4. Insulators
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Where are promoters and enhancers present on TFs? What are silencers and insulators and what are their functions?

A
  1. Promoters: Present in the proximal regulatory regions
  2. Enhancers (Activators): Present in the distal regulatory regions
  3. Silencers: DNA elements that bind repressors and silence gene transcription (near proximal promoter)
  4. Insulators: DNA boundary element that blocks the interaction between enhancers & promoters (@ either side of gene loci)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How does DNA looping result in liver specific expression of Transthyretin Gene (TTR)?

A

DNA-looping brings Enhancers bound to liver-specific TFs (HNF1,3, 4) to the promoter & TATA-box, resulting in TTR expression only in the liver

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q
  • How many members are part of the Forkhead Box (FOX) family?
  • What is strucure of Forkhead (FKH) BOX?
  • What is the function of FOX factors?
  • How do FOX TFs act as?
  • What part binds DNA?
A
  • >40 members in FOX-family play diverse roles in development
  • FKH BOX: : ~100 amino acids (wings; W1, W2 & Helix H1, H2, Helix-H3). H3 binds DNA at specific target genes (conserved domain)
  • FOX factors: open chromatin & act as gateway factors to make gene loci accessible for transcription
  • FOX TFs: act as transcription activators or repressors
  • Helix-3 (H3) binds DNA: note W1 & W2 (Wings) that form wings
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

List the different mutations that can arise for the FOX-family?

A
  • FOXC1 mutations
  • FOXC2 mutations
  • FOXP2 mutations
  • FOXP3 mutations
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Mutation of FOX-family

What developmental disorders (2) are caused by FOXC1 mutations?

A

Iris hypoplasia & Rieger syndrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Mutation of FOX-family

What developmental disorder is caused by FOXC2 mutations?

A

Lymphedema (Lymphedema of the limbs) and/or Distichiasis syndrome (double rows of eyelashes)

Ex. Elizabeth Taylor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Mutation of FOX-family

What developmental disorder is caused by FOXP2 mutations?

A
  • Language acquisition defects
  • Speech defects
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Mutation of FOX-family

What developmental disorder is caused by FOXP3 mutations?

A
  • IPEX Syndrome: X-linked immuno-dysregulation, poly-endocrinopathy and enteropathy (intestinal inflammation).
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is FOXP3 a master regulator for?

A

FOXP3 is a master regulator of the regulatory T cell lineage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

How were the Homeobox (Hox) family genes discovered?

A

Hox-family of Homeotic genes expressing TFs were discovered in Drosophila melanogaster

31
Q

What does a mutation in HOM-C gene cause?

A

Antennapedia: sprout legs instead of antennae on the head

32
Q

What is Hox gene Conservation & Collinearity of expression?

A

Physical order & expression of HOX genes along the anteroposterior axis is conserved from flies to humans

33
Q
  • What is the structure of HOX (Homeobox) family TFs?
  • What does it contain?
  • Which structure is the Recognition Helix?
  • What binds DNA at the TAAT or ATTA sequence?
  • What binds in the DNA-Major Groove?
  • What binds in the DNA-Minor Groove?
A
  1. Is a 50 Amino Acid conserved region (180 basepairs)
  2. Contains 3 Helices: H1, H2, H3 & an N-terminal tail region
  3. Helix-3 (H3) is the “Recognition Helix”
  4. H3 & N-terminus binds DNA at TAAT or ATTA sequence
  5. H3 binds in the DNA-Major Groove
  6. N-terminus tail binds in the DNA-Minor groove
34
Q

What are the four Homeobox (HOX) mutations that can occur?

A
  1. HOXA1 Mutations
  2. HOXA13 & HOXD13 Mutations
  3. EMX2 Homeobox gene Mutations
  4. NKX-2.5 Mutations (~40 mutations)
35
Q

HOX family Mutations

What defects occur d/t HOXA1 mutation?

A

Impaired human neural development

36
Q

HOX family Mutations

What defects occur d/t HOXA13 & HOXD13 mutation? What mutation specifically happens w/ HOXD13?

A
  • Limb malformations
  • Mutations in N-terminal, non–DNA binding part of HoxD13 cause→Webbing, Syndactyly, & Polydactyly.
37
Q

HOX family Mutations

What defects occur d/t EMX2 Homeobox gene mutations?

A

Schizencephaly (type II): Unilateral Full-Thickness cortex in the ventricles→ Seizures, Spasticity, and Mental deficiency

38
Q

HOX family Mutations

What defects occur d/t NKX-2.5 Mutations?

A
  • ~40 mutations
  • Diverse Congential Cardiac Defects
    1. Congenital CVM (Cardiovascular Malformation)
    2. ASD: Atrial Septal Defect
    3. AVB: Atrioventricular Block (block in impulse from the atria→ ventricles)
    4. DORV: Double Outlet Right Ventricle (PA + Aorta open in RV)]
    5. TOF: Tetralogy of Fallot (VSD + Pul. Valve Stenosis + RA-hypertrophy + moved aorta)
    6. VSD: Ventricular Septal Defect
    7. TVA: Tricuspid Valve Atresia
39
Q
  • What is the structure of all Paired box (PAX) family proteins?
  • What does PAX1 & PAX9 lack?
  • What is the function of PAX TFs?
  • What is the role of Pax6 in humans? What is it called in Drosophila? What occurs if there is a mutation? What occurs when there is ectopic expression?
  • What is Pax6 a master controller?
A
  • All PAX proteins have a bipartite DNA-binding motif (Paired Box; PAX), & most of them have a homeodomain
  • PAX1 & PAX9 do not have a homeodomain
  • PAX TFs activate or repress transcription of target genes
  • Pax6 (human)→ Eye formation; Drosophila Ortholog eyeless gene mutation→ no eyes→ Ectopic expression of eyeless→ additional eyes (antenna thorax & 6 legs)
  • Pax6 is a Master controller for eye development
40
Q

What are mutations in PAX genes that can occur?

A
  1. PAX6 mutations
  2. PAX3 and PAX7 Translocation and Fusion to FOXO1A
  3. PAX3 Mutation
41
Q

PAX family mutations

What defects occur d/t PAX6 Mutations?

A
  • Ocular malformations: Aniridia (absence of the iris) & Peter anomaly (central corneal opacity)
  • PAX6 Haploinsufficiency: Have some ocular defects.
  • PAX6- null patients have Anophthalmia
42
Q

PAX family mutations

What defects occur d/t PAX3 and PAX7 translocation to FOXO1A? What chimeras are formed?

A
  • Childhood Cancer:
    Alveolar rhabdomyosarcoma     (in the muscle) due to chromosomal translocation
  • Forms PAX3:FOXO1A or PAX7:FOXO1A chimeras

Chimeras: an organism or tissue that contains at least two different sets of DNA

43
Q

PAX family mutations

What defects occur d/t PAX3 Mutations?

A
  • Waardenburg syndrome type I (autosomal dominant disease)
  • Hearing deficits, ocular defects, epicanthal fold
  • Pigmentation abnormalities (typified by White Forelock)
44
Q
  • What does the Basic Helix-Loop-Helix (bHLH) TFs determine?
  • bHLH proteins contain what two things?
  • bHLH TFs bind target gene promoters via what?
A
  • bHLH determine cell fate and differentiation in many developing tissues.
  • bHLH proteins contain
    1. Basic, positively charged DNA-binding region (N-terminus)
    2. Two Alpha-Helices separated by a loop (C-terminus)
  • bHLH TFs bind target gene promoters via E-box DNA-sequence (CANNTG)

bHLH straddles the DNA (C-terminus binds to DNA, N-terminus stays outside)

45
Q

What is the role of the bHLF TFs listed below:

  • bHLH-TFs (Myogenin & MYOD)
  • bHLH-TFs (Neurogenin + NEUROD)
  • bHLH-TFs (ASCL1 + NEUROD3)
A
  • bHLH-TFs (Myogenin & MYOD)→ Differentiation to muscles in embryo.
  • bHLH-TFs (Neurogenin + NEUROD) → Differentiation to neurons in embryo
  • bHLH-TFs (ASCL1 + NEUROD3) are proneural genes that convert neuroepithelium to neuroblasts
46
Q

What is the definition of Epigenetics?

A

The change in gene expression pattern (repression or activation) that alters the phenotype without altering the DNA sequence of a genome

47
Q

What are the major mechanisms that causes Epigenetic regulation? (4)

A
  1. Histone acetylation
  2. Histone methylation
  3. DNA methylation
  4. miRNAs
48
Q

What are the monomers that make up a histone?

A
  • H2A
  • H2B
  • H3
  • H4
49
Q

How does histone monomers become a dimer?

A

Handshake interactions (evolutionarily conserved)

50
Q

What is the structure of Histone Octamers?

A

Pair of H2A, H2B, H3 + H4 subunits

51
Q

What is the structure of a Nucleosome?

A

Histone Octamer (Pair of H2A, H2B, H3 + H4 subunits) + DNA (~147 bps)

52
Q

What is the structure of a Chromatin?
What are major modifications on Chromatin?

A
  • Nucleosome + Linker Histone H1= Chromatin
  • Major Modifications
    1. Acetylation
    2. Methylation
53
Q

What are the 3 steps of the Dynamic Histone Code and what enzymes play a role in each step?

A
  1. Writing
  • Acetylases
  • Methylases
  • Phosphorylases
  1. Erasing
  • Deacetylases
  • Demethylases
  • Phosphatases
  1. Reading
  • Bromodomain
  • Chromodomain
  • PHD finger
  • WD40 repeat
54
Q

What are the writer protein, eraser protein and reader protein that are involved in the Epigenetic Modifications listed below:

  1. Histone Acetylation
  2. Histone Methylation
  3. DNA Methylation
A
  1. Histone Acetylation
  • Writer protein: Histone acetyltransferases (HATs): E1A binding protein, 300-KD (EP300)
  • Eraser protein: Histone deacetylases (HDACs): HDAC1
  • Reader protein: Chromatin remodeling enzymes: SMARCA4 (formerly BRG1)
  1. Histone Methylation
  • Writer protein: Histone methylases (HMTs): EZH2
  • Eraser protein: Histone demethylases: JARID1C
  • Reader protein: Polycomb repressive complex: CBX2
  1. DNA Methylation (5th position on Glycine)
  • Writer protein: DNA methylases: DNMT1
  • Eraser protein: Tet oncogene family members: methylcytosine dioxygenases (TET1)
  • Reader protein: MECP2
55
Q

What are disorders of chromatin remodeling that can arise during development?

A
  1. Rett Syndrome
  2. Rubinstein-Taybi syndrome
  3. Alpha-thalassemia/X-linked mental retardation syndrome
  4. Many types of cancers
56
Q

What is the role of histone acetylation? Histone methylation?

A
  • Histone Acetylation- Gene Activation
  • Histone Methylation-Silencing Genes
57
Q

What are histone tails acetylated by? What is the function of Histone Acetyl Transferases (HATs) and Histone deacetylases (HDACs)?

A
  • Histone tails are acetylated by enzymes
  • Histone Acetyl Transferases (HATs): Add acetyl groups (Writers) on histone tails = Gene Activation
  • Histone deacetylases (HDACs), which remove acetyl groups (Erasers) from histone tails = Gene Silencing
58
Q

What are Histone Lysines on the tails modified by? What removes the modifications?

A
  • Histone Lysines on the tails are modified by methyl group added by ENZYME WRITERS histone methyltransferases (HMTs)
  • These modifications are removed by ENZYME ERASERS: histone demethylases (HDMs)
59
Q

Which histone proteins acetylated/demethylated Active Chromatins?

A

HATs (Histone Acetyl Transferases) + HDMs (histone demethylases)

60
Q

Which histone proteins deacetylated/methylated Silenced Chromatins?

A

HDACs (Histone deacetylases) + HMTs (histone methyltransferases)

61
Q
  • What is DNA methylation used for?
  • At Embryo Implantation, what is methylated? What methylates it and what is the outcome to the gene?
  • As Embryo develops, what is silenced by DNA methylation and why?
  • What happens to DNA methylation in Primordial Germ Cells (PGCs)?
A
  • DNA methylation is used for the long-term repression of genes
  • At Embryo Implantation: Cytosines at GC dinucleotides are methylated by DNA methyltransferases (DNMTs); most genes silenced
  • As Embryo develops: Pluripotency genes are silenced by DNA Methylation→ Cells differentiate into 3 germ layers
  • In Contrast: In Primordial Germ Cells (PGCs): DNA Methylation is erased to re-express pluripotency genes
62
Q

What is Methyl-Cytosine-Binding Protein 2 (MECP2)?

A

MECP2; a reader enzyme is a methylation-dependent transcriptional modulator (binds to DNA on the cytosine that are methylated)

63
Q

What does a mutation in MECP2 (Methyl-Cytosine-Binding Protein 2) result in?

A

Results in abnormal expression at gene locus→leads to a developmental disorder: Rett syndrome

64
Q

What is Rett Syndrome? What clinical effects does it cause? Who is most affected?

A
  • Neurological developmental disorder, which alters brain development
  • Causing a progressive inability to use muscles for eye and body movements & speech
  • Found almost exclusively in girls (show frequent seizures and intellectual disability)

Mutation in MECP2

65
Q

What are MicroRNAs (miRNAs)? When do they act? What do they contribute to?

A
  • MicroRNAs (miRNAs or miRs) are conserved 22-nucleotide small noncoding RNAs that act post-transcriptionally to silence functional RNAs in a cell
  • It contributes to cell differentiation and cell-fate without changing DNA sequence –thus is an epigenetic event
66
Q

What are the steps in the production of miRNA? What is the function?

A
  1. Transcription: Long primary-miRNA is formed from the genome
  2. DROSHA cuts & matures it to a 70 bp stem-loop (pre-miRNA) in the nucleus
  3. 70 bp stem-loop-miRNAs is exported out & binds RNase (DICER), which processes it to mature 22 bp miRNA duplexes
  4. RISC-Complex binds complementary miRNA strand
  • Function: RISC-miRNA:→ 1) Inhibits Translation or 2) Degrades mRNA→NO PROTEIN

3-protein interplay

67
Q

What are dieases that can be caused by altered miRNA expression?

A
  • Different developmental disorders
  • Oncomirs→miRNA associated with cancer
  • DICER1: (Germline mutations)→Familial Tumor Predisposition Syndrome:
  • Diseases: Pleuropulmonary blastema, Cystic nephroma, & Medulloepithelioma
68
Q
  • Totipotent (morula) stems are?
  • Pluripotent (inner blastula) are?
  • Stem cells self-renew by?
A
  • Totipotent (morula) stem cells are→all 3 primary germ layers + extra-embryonic tissues
  • Pluripotent (inner blastula)→cell of only 3 primary germ layers but NOT extra-embryonic tissues
  • Stem cells self-renew by: (1)Symmetric (vertical) or (2) Asymmetric (horizontal) cell divisions

Symmertric division→Replenishment
Asymmetric division→ Differentiated

69
Q

What are the different types of Stem Cells? (4)

A
  1. ESCs (Embryonic Stem cells)
  2. ASCs (Adult Stem Cells)
  3. iPSCs (induced Pleuripitent Stem Cells)
  4. CSCs (Cancer Stem Cells)
70
Q

What do ESC (Embryonic Stem Cells) express? and what is there function?

A

(ESCs) express TFs (SOX2 & OCT4) that repress differentiation & maintain STEMNESS
required for replenishment of stem cell pool

71
Q

How do Adult Stem cells (ASCs) or Embryonic Stem cells (ESCs) divide symmetrically?

A

2 equivalent daughter stem cells in a vertical cell division; the plane of mitosis is perpendicular to the neural ventricle surface

72
Q

How do Adult Stem cells (ASCs) or Embryonic Stem cells (ESCs) divide asymmetrically?

A

Daughter stem cell + Neuroblast cell; horizontal cell division; the plane of mitosis is parallel to the ventricular surface

  • The progenitor cell loses stem cell factors (geometric shapes)
  • The progenitor cell expresses new proteins→Alar and Basal Plate
73
Q

Embryonic Stem Cells (ESCs) & Induced pluripotent stem cells (iPSCs) have the capacity to do what? (4)

A
  1. Self-renew to Stem Cells
  2. Apoptosis/cell death
  3. Become progenitor Cells
  4. Differentiate into various types of Cells.
74
Q

What can Adult, differentiated somatic cells (skin fibroblast) be reprogrammed into? by expressing what?

A

Adult, differentiated somatic cells (skin fibroblasts), can be reprogrammed into iPSCs by expressing master transcription factors: (SOX2 + OCT3/4 + KLF4)

Induced pluripotent stem cells (iPSCs)

Embryology: Summer Semester (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions