cell differentiation and gene expression

Question 1

define cell lineage

Answer 1

the series of successive cell types leading from the zygote to a particular mature cell type.

Question 2

define determination

Answer 2

the stability of cell differentiation, even after cessation of any inducing signal.

Question 3

define household/housekeeping gene

Answer 3

a gene expressed in all or nearly all cell types, e.g. tubulin

Question 4

define luxury gene

Answer 4

a gene expressed in only one or a few cell types.

Question 5

define master gene regulator

Answer 5

a transcription factor that coordinately regulates many or all of the genes specifically expressed in a particular cell type.

Question 6

define modulation of gene expression

Answer 6

a simple, reversible change in gene expression with no change in cell type.

Question 7

what are pioneer factors

Answer 7

transcription factors that can bind condensed or uncondensed chromatin, remodel it and initiate cell-fate and differentiation. They are master regulators

Question 8

what is a precursor or progenitor cell?

Answer 8

any immature cell type able to differentiate into another cell type(s).

Question 9

define terminal differentiation

Answer 9

production of a mature functional cell type that cannot divide (e.g. neurons, skeletal muscle, granulocytes).

Question 10

define transit cell

Answer 10

A cell that is undergoing terminal differentiation towards a functional cell type but is still itself able to divide.

Question 11

why are hepatocytes and neurons morphologically different ?

Answer 11

They have the same DNA and the same number of chromosomes. What makes them different is the differential expression of the genes. This why they are specialised to carry out different functions and have different morphologies

Question 12

describe the process of cell differentiation

Answer 12

• Cell differentiation is the process through which a cell undergoes changes in gene
  expression and gene activity to specialise and take on specific roles in an organism.
  -the endpoint is a wide variety of specialised cell types.
  -this process is irreversible.

Question 13

give examples of cells that are adapted so specific functions

Answer 13

hepatocytes, cardiomyocytes or lymphocytes,

Question 14

give an example of a cell which has general functions and are present in a wide range of organs

Answer 14

fibroblasts

Question 15

describe the state of cells in adults

Answer 15

• In adults :
o Majority of the cells are terminally differentiated (they cannot divide).
o A small minority are capable of cell division:
 Some actively dividing during their entire life
 Some quiescent and dividing only occasionally. Only when needed they divide.

Question 16

define stem cell

Answer 16

: undifferentiated and unspecialised cells of the human body. It is a single cell that can replicate itself, or differentiate into many cell types. They can be found in embryos ( embryonic stem cells) and in adults ( adult stem cells ) .

Question 17

what are the 2 characteristics of stem cells

Answer 17

able to differentiate into many cells of an organism and have the ability to renew themselves by cell divison

Question 18

outline the different levels of stem cells

Answer 18

Totipotent: can differentiate into every type of cell in the body. Totipotency has the highest differentiation potential and it allows cells to form both embryo and extraembryonic structures. Zygote is the only totipotent cell. Its formed after sperm fertalises the egg. These cells can later develop into any of the three germ layers or the placenta. After approx 4 days, the inner cell mass of the blastocyte becomes pluripotent.

Pluripotent: can differentiate into most, but not all type of cells. Pluripotent stem cells form the cells of all the germ layers but not the extraembryonic structures such as the placenta. Eg embryonic stem cells that are derived from the inner cell mass of the preimplantation embryo ie cells within the blastocyst that form shortly after fertilization. Another example is induced pluripotent stem cells.

Multipotent: can differentiate into a limited number of cell types. E.g hematopoietic and mesenchymal stem calls.
Unipotent: can form one type of differentiated cell only. E.g spermatogonial stem cells and dermatocytes.

Question 19

what kind of stem cells are embryonic ? and what kind of stem cells are adult stem cells ?

Answer 19

• In general, embryonic cells are pluripotent. Adult stem cells are multipotent.

Question 20

describe the two ways stem cells can divide

Answer 20

1) Asymmetric division. a stem cell produces one differentiated cell and one stem cell. Different microenvironments where they receive different external chemical signals, cause one of the two remaining stem cells and the other to become a progenitor cell committed to differentiate. The fate regulator ( e.g polarity protein) distributes unequally in the daughter cells. It makes one stay as a stem cell and the other differentiate
2) Symmetric division. common and is the way to balance between stem cell renewal and differentiation. A stem cell produces two differentiated cells or two stem cells. Some cells may divide to give identical daughter stem cells while other stem cells divide to generate two progenitor cells committed to differentiation.

Question 21

describe embryonic stem cells

Answer 21

-pluripotent
-• Derived from a 4- or 5-day old human embryo in the blastocyst phase of development.
• Pluripotent cells of the embryo have been shown to be transiently existing cells, not stem cells. Ie short life before they differentiate into many types of cells.

Question 22

describe adult stem cells

Answer 22

• Multipotent
• Typically give rise to various types of differentiated cells within the tissue they reside in. they are tissue specific stem cells.
• Function: dead cells replacement (cell turnover). These stem cells will differentiate when the pool of differentiated cells needs to be renewed.
• Low number in tissues where there is a low rate of cell turnover (adult brain) and abundant in tissues such as intestine epithelium and blood cells.

Question 23

what are stem cell niches

Answer 23

• Tissue-specific stem cells are maintained in special supportive microenvironments called stem cell niches.

Question 24

why is the ECM and the neighbouring niche cells important in the microenviroments.

Answer 24

• All the chemical signals sent by the neighbouring cells and the extracellular matrix to the receptors of the stem cells are important to support the stem cell activity, and their renewal and to supress stem cell differentiation when needed.

Question 25

list the factors that are important to regulate stem-cell characteristics within the nice of the stem cell

Answer 25

cellular components, secreted factors, inflammation and scaring, extracellular matrix, physical factors, hypoxia and metabolism.

Question 26

where are blood cells formed ?

Answer 26

• Blood cells initially made in certain embryonic structures. From foetal week 20 onward they originate from the bone marrow

Question 27

describe the two types of cells in the bone marrow

Answer 27

• Hematopoietic stem cells (HSCs): multipotent stem cells anchored to fibroblast-like osteoblasts of the marrow of long bones. Produce all blood cells and some immune system cells. Regular self-renewal.
• Mesenchymal stem cells (MSCs): stromal cells found in bone marrow and other organs. Poorly defined and heterogeneous. They do not self-renew very regularly but they are multipotent, only difference is they don’t self renew as regularly as hematopoietic stem cells. Give rise to cartilage (chondrocytes), bone (osteoblasts) and muscle cells (myocytes) and adipocytes.

Question 28

which stem cell can be found in the hemopoietic lineage ?

Answer 28

progenitor cells . they are also called oligopotent progenitors because their potency to differentiate is lower than the potency of the hematopoietic multipotent stem cells.

Question 29

what is the difference between the hematopoietic stem cells and progenitor cells ?

Answer 29

multipotent hematopoietic stem cells can replicate indefinitely and can differentiate into both lineages, lymphoid and myeloid , whereas progenitor cells can divide only a limited number of times and can differentiate into only one type of lineage

Question 30

how do cells differentiate ?

Answer 30

differential gene expression

Question 31

what are 2 things that play a key role in differential gene expression

Answer 31

• The types and number of proteins a cell generates help to determine how a cell differentiates.
• Rna sequencing and microarrays assays allow to analyse the transcription profile of each cell.
• Some genes need to be switched off and others, switched on during differentiation.  transcription factors.

Question 32

describe the different binding sites of transcription factors

Answer 32

• Transcription factors bind to regulatory regions of a gene and affect its expression by switching it on/off
• Certain TFs are tissue specific and different TFs are associated with differentiation of stem cells into different tissues.
  1) transcriptional start site :
  where the RNA pol II will bind to initiate transcription of that gene. it is where TATA box in the promotor binds to basal/general transcription factors for all genes.

2) upstream in the promotor ( which is approx 200-500bp) , there are DNA elements or motifs ( short sequences eg GATA ) which is recognised and bound by specific transcription factors.
3) Enhancers , due to the chromatin loop can come closer to the promotor. it binds to specific transcription factors and promotors.

Question 33

describe basal/general transcription factors

Answer 33

Basal/general transcription factors are necessary for the RNA pol II to function at the site of transcription in eukaryotes. They are considered the most basic set of proteins needed to activate a gene transcription. They bind to the 5’ region on the DNA to activate transcription.

Question 34

describe specific transcription factors

Answer 34

Specific transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA or promotor regions called DNA elements or motifs. Specific transcription factors are critical to ensure the genes are expressed in the right cell at the right time and in the right amount, depending on the state and requirement of the organism at that moment.

Question 35

What does RNA pol II need to have access to for transcription to occur?

Answer 35

• For transcription to occur, RNA pol II needs to have access to the chromatin. Specific transcription factors are then able to regulate the chromatin status. They are called pioneer factors.

Question 36

give an example of luxury genes

Answer 36

haemoglobin gene needs to be transcribed and expressed only in red blood cells

Question 37

what are pioneer factors.

Answer 37

• They are Transcription factors that can bind to condensed/closed chromatin and remodel it (open it), or they can bind to uncondensed chromatin in order to close it/condense it. They can work in both directions, closing or opening the chromatin and depending on this, they will initiate cell-fate and differentiation. They are also called master regulators e.g OCT4, BMP4, SOX2, and NANOG. So basically, pioneer factors can open and close chromatin.
• Highly expressed in embryonic stem cells and needed to maintain their pluripotency.
• Summary : pioneer transcription factors have the unique ability to alter the chromatin environment. Either increasing opening or decreasing the accessibility of a network of regulatory sequences.

Question 38

how can pioneer factors activate or inhibit gene expression

Answer 38

they can open or close the chromatin
this is achieved by :
o Histone modification
o DNA methylation blockage.

Question 39

what is DNA methylation

Answer 39

• Epigenetic mechanism that occurs by the addition of a methyl (CH3) group to DNA. ( not HISTONES)
• Covalent addition of the methyl group at the 5’ carbon of the cytosine ring resulting in 5-methlycytosine (5-mC). so, the cytosine ring is converted
• In somatic cells, 5-mC occurs on CpG sites (CpG sites are regions located upstream the gene transcription start site. cytosine nucleotides are located next to a guanine nucleotide (CGCGCGCG) rich In cytosine and guanine nucleotides). Exception embryonic stem cells, where methylation can also be present in non-CpG regions.
• So in somatic cells methylation only occurs in CpG sites, whereas embryonic cells, methylation can occur at any part of the gene.

Question 40

outline the process of DNA methyltion

Answer 40

• As it’s an epigenetic change, its inherited. This means that the methylenation pattern is ‘remembered ‘ in daughter cells.
• During differentiation, unmethylated CpG pairs can become methylated by a de novo methyltransferase.
• Methyl transferase is a protein in charge of adding methyl groups.
• When one strand has been methylated, the opposite strand also on the CpG side, will also be methylated by a maintenance methyltransferase. So it is copied to the opposite strand ( also CpG) by a maintenance methyltransferase.
• Methylation of a gene ( especially its promotor or control sequence ) increase folding ( heterochromatin ) and silencing transcription. Ie closed chromatin
• Genes whose CpG islands are methylated wont be transcribed.
• When those genes need to be expressed, the CpG islands will be unmethylated. The methyl groups will be removed and the expression of that gene will be activated.

Question 41

in embryonic stem cells, the majority of CpG islands are ? and why

Answer 41

o In embryonic stem cells the majority of CpG sites are unmethylated. Because most of the genes need to be expressed.

Question 42

in globin genes, are the promotors methylated or unmethylated

Answer 42

o Globin genes are expressed and unmethylated in the red blood cell lineage, but not elsewhere. Their promoters are methylated in other cell types.

Question 43

in sperm cells, are the genes methylated or unmethylated

Answer 43

o In sperm, most genes are silenced by methylation. DNA very heterochromatic.

Question 44

give 2 applications of stem cells

Answer 44

Somatic cell nuclear transfer (scnt), and induced pluripotent stem cells (iPSC)

Question 45

Describe SCNT

Answer 45

• Artificial removal of the nucleus of a differentiated somatic cell and its placement in a denucleated egg cell. The egg and sperm cell are highly differentiated cells and when they fuse, they form a totipotent zygote. This is possible because the cytoplasm of the egg contains factors that naturally reprogramme the DNA in the zygote. These factors involve epigenetic marks, eg, the removal of repressive methylation signals and those genes that were not expressing start to be expressed.
• Introduced nucleus is reprogrammed by factors in the egg cytoplasm.
• The new egg cell with the somatic cell nucleus behaves like a zygote (totipotent) and can give rise to a novel organism. The cell resulting from this process is a clone.
• Challenging and time consuming.

Question 46

describe induced pluripotent stem cells

Answer 46

• More efficient and cheaper than SCNT, can be done in the lab without a need for an animal
• Pluripotent stem cells artificially produced from somatic cells.
• Differentiation is a non-reversible process however this is an exception.
• We can take somatic cells and reprogram those cells and convert them into induced pluripotent stem cells that will be able to potentially produce almost all cells of the organisms.
• Somatic Cells are exposed to 4 transcription factors : OCT4, SOX2, KLF4 and c-MYC, these cells can give rise to different types of cells.
• They are reprogrammed into pluripotent stem cells.

Question 47

what are some uses of iPSC

Answer 47

gene therapy, regenerative medicine/cell transplantation, model disease and drug screening.

Question 48

what is an iPsc

Answer 48

artificial stem cells which are grown in vitro in a lab

Question 49

what are the 2 types of regulators of the gene expression ?

Answer 49

transcription factors and dna methylation