Question

1.) Transcription

a.) Every non-general transcription factor (e.g. CREB1) needs at least two functional domains to initiate

transcription. Name and describe the function of these two domains. (15 words per domain)(10 points)

b.) How is chromatin around active promoters different from a transcriptionally inactive areas of the genome? (30 words) (10 points)

c.) TFIIH is a general transcription factor with Helicase and Kinase activity. Describe how these two activities

assist RNA Pol II with transcription initiation? (30 words) (10 points)

Answer 1

1.a. Every transcription factor usually contain two domains.

DNA-binding domain (DBD), which attaches to specific sequences of DNA (enhancer or promoter) adjacent to regulated genes. DNA sequences that bind transcription factors are often referred to as response elements.

Trans-activating domain (TAD), which contains binding sites for other proteins such as transcription coregulators. These binding sites are frequently referred to as activation functions (AFs).

b.Chromatin structure is an essential regulator of transcriptional accessibility and many of the effects of transcription factors on promoters and enhancers translate into changes in chromatin structure near transcriptionally active genes, via the interactions with histone deacetylases (HDAC), acetyltransferases (HAT) or methyltransferases, and other cofactors remodeling and displacing nucleosomes which makes some changes in the base sequence by modifying them.

c.TFIIH consists of ten subunits, 7 of which (ERCC2/XPD, ERCC3/XPB, GTF2H1/p62, GTF2H4/p52, GTF2H2/p44, GTF2H3/p34 and GTF2H5/TTDA) form the core complex. The cyclin activating kinase-subcomplex (CDK7, MAT1, and cyclin H) is linked to the core via the XPD protein. Two of the subunits, ERCC2/XPD and ERCC3/XPB, have helicase and ATPase activities and help create the transcription bubble. Two other TFIIH subunits, CDK7 and cyclin H, phosphorylate serine amino acids on the RNA polymerase II C-terminal domain and possibly other proteins involved in the cell cycle. Next to a vital function in transcription initiation,