Lecture 15- RNA processing and eukaryotic genes exp.

• rRNA makes up the structure of ribosomes (made up of
• 300 genes)

• tRNA carries free amino acids to mRNA during protein
• synthesis (made up of 500 genes)

mRNA is the code from DNA to make protein

• miRNA regulates gene expression (made up of 1000
• genes)

• snRNA is involved in mRNA splicing (made up of 80
• genes)

• snoRNA is involved in pre mRNA processing and RBA
• modification (made up of 85 genes)

• telomerase RNA is a template for addition of
• telomeres (made up of 1 gene)

pre-rRNA

RNA polymeras I transcibes into pre-rRNA of 28S____5.8S____18S. THis then is cleaved by RNases

• The precursors to rRNA are synthesized by RNA polymerase
• I (pol I). This pathway utilizes
• initiation factors involving histones H3 and H4, upstream activating factor
• UAF, TATA box protein (TBP), core factor (CF) and other protein units. The initiation complex attracts pol I and Rrn3p
• to the transcription site. Pol I and
• transcription is regulated by the core factor promoter and the upstream factor
• which is associated with H3 and H4). The core factor is associated with TBP, but
• there is no actual TATA sequence in this case.
• After the transcription initiation complex is formed, Pol I is loaded
• and elongation can begin.

tRNAs, 5S rRNA, snRNA

• RNA polymerase III uses an initiation complex
• involving TFIIIC, TFIIIB and TFIIIA.
• This complex recruits pol III forming the preinitiation complex for
• transcription of the 5S-rRNA gene

• The 5’ end capping is a processing reaction for pre
• mRNA. The cap helps stabilize pre tRNA
• and permits initiation of translation

• Intramolecular hydrogen bonding in the pre tRNA
• strand
• Uracil residues at 3’ end of pre tRNA are converted
• to CCA sequence in mature tRNA
• Some bases are modified in the maturation process

• mRNA
• miRNAs
• snRNAs

• TBP = tata binding protein
• TF = transcription factor
• Nescent RNA = new strand
• CTD = carboxyl terminal domain
• Transcription is initiated when TBP binds
• the TATA box and recruits transcription factor TFIIB. Pol II binds, and several
• other transcription factors (TFIIF, TFIIE, TFIIH) follow it to complete the Pol
• II preinitiation complex. Finally, in order for Pol II to become activated so
• that elongation can begin, it must be phosphorylated at its CTD which triggers the elongation step of
• transcription. TFIIH plays a critical role in phosphorylating this domain.

• CTF at CAAT box, SP1 at GC box, and TFIID at TATA box
• Enhancer can fold over on top and aid in polII recruitment

Cortisol, retinoic acid, thyroxine, other lipid-soluble homrones bind to receptor located in nucleus and cytoplasm. The receptor acts as a transcription factor

Hormone binds to recepor binding domain and releases inhibiotr. The receptor goes into teh nucleus where it dimerizes and uses its zinc fingers in DNA and acts as TF

• NfkB is a nuclear transcription factor. It is turned on my lots of factors such as a virus infection, bacteria, fungi, ionizing radiation, TNF-alpha receptor and IL
• receptors. NFkB plays a key role inregulating the immune response to infection

The factors cause poly ubiquitination of sequestered NfkB which then frees it and lets it go into nucleus

cAMP binds to regulatory subunits of protein kinase A. This allows the catalytic subunit to go into nucleus and phosporylte CRE binding protein (CREB). CREB binds to CRE on DNA and attracts CBP(CREB binding protein) and starts transcription

• pelitropic developmental abnormailites: Rubinstein Taybi syndrome
• - heart defects, die before age 2, stubby feet and hands

• -gene essential for osteoblast differentiation
• - heterozygotes have cleidocranial dysplasia
• -mice homo for null allel do not make bone

• Factor IX is blood clotting factor
• -Mutation at -20 causes hemophilia B leyden
• -reduces HNF4 binding
• -AR bind also and can produce so individuals normalize after puberty

-Mutation at -26 affects both receptors and last through life