General Concepts

Question 1

What is bidirectional transcription?

Answer 1

bidirectional transcription

• Transcription that occurs on both the positive and negative strands of DNA simultaneously, where the direction of RNA polymerase progression along each strand is either is convergent or divergent.

Question 2

What is nascent RNA?

Answer 2

• In eukaryotes, the nascent RNA is called primary transcript-RNA
  
  • It needs to be processed and transported to the cytoplasm for translation to occur.
• In prokaryotes, no RNA processing is necessary: – the nascent RNA is usually the mRNA.

Question 3

What is pluripotency?

Answer 3

• Pluripotent cells can give rise to all of the cell types that make up the body; embryonic stem cells are considered pluripotent.

Question 4

What are multipotent cells?

Answer 4

• Multipotent cells can develop into more than one cell type, but are more limited than pluripotent cells; adult stem cells and cord blood stem cells are considered multipotent.

Question 5

What is Oct4?

Answer 5

• Octamer-binding transcription factor 4
• Oct-4 is a homeodomain transcription factor.
• It is critically involved in the self-renewal of undifferentiated embryonic stem cells.
  
  • As such, it is frequently used as a marker for undifferentiated cells.
• Oct-4 expression must be closely regulated; too much or too little will cause differentiation of the cells.
• Important for ectoderm formation.

Question 6

What is a homeobox?

Answer 6

• A homeobox is a DNA sequence, around 180 base pairs long, found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis) in animals, fungi and plants.
• These genes encode homeodomain protein products that are transcription factors sharing a characteristic protein fold structure that binds DNA

Question 7

What is Nanog?

Answer 7

• NANOG is a transcription factor critically involved with self-renewal of undifferentiated embryonic stem cells.

Question 8

What is SOX2?

Answer 8

• SOX2 is a transcription factor that is essential for maintaining self-renewal, or pluripotency, of undifferentiated embryonic stem cells. Sox2 has a critical role in the maintenance of embryonic and neural stem cells.

Question 9

What is Stat3?

Answer 9

• Signal transducer and activator of transcription 3 (STAT3) is a transcription factor which in humans is encoded by the STAT3 gene

Question 10

Label each red box

Answer 10

Question 11

• _____ is crucial for the first embryonic lineage specification, and _____ is crucial for the second.
• In the embryonic stem cell Oct4, Sox2, Stat3, and Nanog are essential for __________.

Answer 11

• Oct4 is crucial for the first embryonic lineage specification, and Nanog is crucial for the second.
• In the ES cell Oct4, Sox2, Stat3, and Nanog are essential for self-renewal.

Question 12

Factors required for pluripotency and self‐renewal

• List the Transcription Factors
• List the Chromatin proteins

Answer 12

Question 13

What would happen to Nanog mutant embryonic stem cells?

Answer 13

• Extra non-normal growth would happen
  
  • too much cell proliferation

Question 14

• ____ binds upstream of its own gene and ____ and ____ are bound in close proximity.

Answer 14

• Oct4 binds upstream of its own gene and Sox2 and Nanog are bound in close proximity.

Question 15

What is Foxd3?

Answer 15

• Forkhead box D3 also known as FOXD3 is a forkhead protein that in humans is encoded by the FOXD3 gene
• This gene belongs to the forkhead protein family of transcription factors which is characterized by a DNA-binding forkhead domain.
• FoxD3 functions as a transcriptional repressor and contains the C-terminal engrailed homology-1 motif (EH1), which provides an interactive surface with a transcriptional co-repressor Grg4 (Groucho-related gene-4).

Question 16

What are Polycomb group proteins?

Answer 16

• Polycomb-group proteins are a family of proteins first discovered in fruit flies that can remodel chromatin such that epigenetic silencing of genes takes place.
• Polycomb-group proteins are well known for silencing Hox genes through modulation of chromatin structure during embryonic development in fruit flies

Question 17

What are Hox genes?

Answer 17

• Hox genes, a subset of homeotic genes, are a group of related genes that control the body plan of an embryo along the head-tail axis.

Question 18

What are NuRD co‐ repressors?

Answer 18

• The Mi-2/NuRD (Nucleosome Remodeling Deacetylase) complex, is a group of associated proteins with both ATP-dependent chromatin remodeling and histone deacetylase activities.
• As of 2007, Mi-2/NuRD was the only known protein complex coupling chromatin remodeling ATPase and chromatin deacetylation enzymatic functions.
• NuRD/Mi-2/CHD remodeling complexes primarily mediate transcriptional repression in the nucleus and are required for the maintenance of pluripotency of embryonic stem cells.

Question 19

What are Swi/Snf remodelers?

Answer 19

• SWI/SNF (SWItch/Sucrose Non-Fermentable), is a nucleosome remodeling complex found in both eukaryotes and prokaryotes.
  
  • In simpler terms, it is a group of proteins that associate to remodel the way DNA is packaged.
• It is composed of several proteins – products of the SWI and SNF gene as well as other polypeptides.
• It possesses a DNA-stimulated ATPase activity and can destabilize histone-DNA interactions in reconstituted nucleosomes in an ATP-dependent manner, though the exact nature of this structural change is unknown.

Question 20

What are HAT/nucleosome remodelers?

Answer 20

• Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.
• Such remodeling is principally carried out by
  
  1. covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and
  2. ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes.

Question 21

What would happen to Polycomb group proteins (PcG) mutant ESCs?

Answer 21

• Polycomb Gene complexes or PcG silencing consist of at least three kinds of multiprotein complex Polycomb Repressive Complex 1 (PRC1), PRC2 and PhoRC.
• Murine (rodents) null mutants in PRC2 genes are embryonic lethals while most PRC1 mutants are live born homeotic mutants that die perinatally.

Question 22

What is Yin‐Yang 1 (YY1)?

Answer 22

• Multifunctional YY1 is a ubiquitous and multifunctional zinc‐finger transcription factor that is involved in a variety of biological processes, including development, cell proliferation and differentiation, DNA repair, and apoptosis, etc.
• Essential gene
• Activator AND repressor ‐ hence the name

Question 23

What assay is this?

Question 24

What does this picture show?

Question 25

Seen here is a four step diagram depicting the usage of an enhancer. Within this DNA sequence, protein(s) known as transcription factor(s) bind to the enhancer and increase the activity of the promoter.

1. DNA
2. Enhancer
3. Promoter
4. Gene
5. Transcription Activator Protein
6. Mediator Protein
7. RNA Polymerase

Question 26

What is Arid1a?

Answer 26

• ARID1A is a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes.
• It possesses at least two conserved domains that could be important for its function.
  
  • First, it has an ARID domain, which is a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus.
  • Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation.
• It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions.

Question 27

What is the exosome?

Answer 27

a large protein complex whose interior is rich in 3ʹ-to-5ʹ RNA exonucleases

Question 28

Describe CRISPR

Answer 28

Question 29

What is the difference between Gro-Seq,, and CLIP in terms of Watson and Crick?

Answer 29

Look at tanners notes