Question

Eukaryotic gene regulation: transcription initiation

Initiation & the transcription initiation complex (including enhancers).

Promoter; TATA box; Conserved & variable regions in promoters.

Eukaryotic enhancers. Why is it important that there are multiple control elements in a single enhancer? What binds to the control elements? How is it possible for a small number of activator and transcription factor proteins to regulate a large number of genes?

Transcription: Elongation & RNA polymerase. RNA polymerase vs. DNA polymerase. Termination.

MyoD: What makes it a master regulator of differentiation? What genes does MyoD regulate? How is muscle differentiation related to cell proliferation?

Homeobox genes. How do they regulate other genes? Why are they so important for animals?

Answer 1

• During transcription ,the sequence of DNA is copied into RNA.
• Before the transcription,unwinding of the double helix of DNA occursat a region to be transcribed and this opened region is called Transcription bubble.
• Transcribing strand is called as the template strand and the other strand is called non template strand or coding strand.In the newly synthesising stand the Thiamines are replaced by Uracil.
• For the initiation RNA polymerase plays an important role.Rna polymerases are enzymes that transcribe DNA to RNA in 5' ---->3' direction.ie it adds nucleotides at the 3'end.
• Transcription is intiated at the PROMOTOR REGION where RNA polymerase binds on the DNA.
• Promotors are the - 10(TATAAT) and - 35(TTGACG) elements in eukaryotes.
• TATA box is an eukaryotic promotor present upstream of the transcription site where RNA polymerase binds and carries out transcription.TATA box contains lots of A and Ts which make it easy to pull the strands of DNA apart.
• To initiate transcription, a transcription factor (TFIID) is the first to bind to the TATA box. Binding of TFIID recruits other transcription factors, including TFIIB, TFIIE, TFIIF, and TFIIH to the TATA box.
• 
• Once this transcription initiation complex is assembled, RNA polymerase can bind to its upstream sequence. When bound along with the transcription factors, RNA polymerase is phosphorylated.
• This releases part of the protein from the DNA to activate the transcription initiation complex and places RNA polymerase in the correct orientation to begin transcription; DNA-bending protein brings the enhancer, which can be quite a distance from the gene, in contact with transcription factors and mediator proteins.
• Enhancers are located just upstream of a gene in the coding region of the gene and they increase the rate of transcription.ENhancers can stimulate any promotor in the vicinity and may act on more than one promotor.
• When a DNA-bending protein binds to an enhancer, the shape of the DNA changes. This shape change allows the interaction between the activators bound to the enhancers and the transcription factors bound to the promoter region and the RNA polymerase to occur.
• A nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter.
• Elongation :During elongation the RNA polymerase transcribes the template stand by adding new RNA nucleotides to the 3 ' end .
• Transcription terminationoccurs when it gets a termination signal .it is of two types
• Rho dependent termination where RNA contains site for the Rho factor.Rho factor binds to this sequence and starts climbing towards the RNA polymerase.Rho pulls the RNA transcript and template strand apart releasing RNA and there by ending transcription.
• Rho independent transcription where the termination occurs when RNA polymerase reaches a GC rich region where there is a hairpin loop .
• The synthesized new RNA strand is subjected to splicing to remove any errors .