lecture 20

Question 1

the number of different proteins greatly exceeds

Answer 1

the number of identified genes

Question 2

production of alternative mature mRNAs

Answer 2

increase protein variability
- trans splicing (rare)
- alternative promoter selection
- alternative (cis) splicing
- RNA editing

Question 3

trans splicing in nematodes

Answer 3

exons from different RNA molecules are fused together

• not known to occur in humans and other eukaryotes
• predominant mechanism of mRNA maturation in nematode worms
• in trans splicing, there is no lariat, but a Y shaped structure

Question 4

trans splicing is catalyzed by

Answer 4

spliceosomes, including U2, U4, U5, and U6 snRNPs, but not U1

Question 5

alternative promoter selection

Answer 5

approx 18% of all human genes

important mechanism for transcriptome diversity and the regylation of gene expression.

Question 6

alternative tail site selection

Answer 6

70% of human genes show alternative poly (A) site and 50% have three or more polyadenylation sites

distinct mRNA isoforms with different 3’ untranslated regions (3’ UTRs)

Question 7

alternative cis splicing

Answer 7

generates multiple products from a gene

• many mammalian genes have two or more alternatively spliced mRNAs derived from the same gene
• great increase of the complexity of the genome and provides opportunities for regulation at the level of pre-mRNA processing.
• 90% of human genes undergo alternative splicing

in some cases, genes could produce thousands alternative products (DSCAM from drosphilia - encodes an Ig superfamioly ptn) over 38,000 possibilities/isoforms of DSCAM protein

Question 8

major forms of alternative cis splicing

Answer 8

nucleotide sequences within the intron and at the borders between introns and exons play an important role in determining whether an exon is included in the mature mRNA

Question 9

complex transcripts

Answer 9

more than one site for cleavage and polyadenylation, or for alternative splicing patterns or both.

Question 10

spliceosome and splice site selection

Answer 10

• in animal premRNAs: exons - approx 150 nt and introns over 3000 (50-20,000 nt)
• correct sites are chosen because of
  1. co transcriptional loading of splicing machinery
  2. binding of SR (serine/arginine rich) proteins to exonic splicing enhancers (ESEs)

Question 11

alternaitve splicing is regulated by

Answer 11

activators
- trans acting bind to expnic or intronic splicing enhancers (cis acting ESE or ISE)

Question 12

Majority of known activators:

Answer 12

SR proteins composed of 2 functional domains
- RNA binding domain
- RS domain (recruitment of splicing apparatus)

Question 13

alternative splicing regulated by repressors

Answer 13

repressors bind to exonic or intronic splicing silencers (ESS or ISS)

Question 14

most of ESSs and ISSs

Answer 14

(splicing silencers), are recognized by member of heterogeneous nuclear ribonucleoprotein (hnRNP) family

Question 15

alternative splicing is finely regulated by

Answer 15

trans acting hnRNPs and SRs protein families

Question 16

RNA editing

Answer 16

by base deamination - common in mammals and their viruses

Question 17

ADAR

Answer 17

Adenosine Deaminase Acting on RNA - converts A to I

Question 18

ADAR, mechanism

Answer 18

Arg residue at this position results in a protein that is much more efficient for Ca2+ transport

Human glutamate receptor Ca2+ channel

glutamine –> arginine

Question 19

RNA editing - by base deamination

Cytidine Deaminase

Answer 19

Cytidine Deaminase acting on RNA - Converts C to U

Question 20

Guide RNA directied insertions and/or deletions

Answer 20

RNA EDITING

mechanism used in mitochondria of trypanosomes

guide RNA (gRNA) as template to add or remove bases from the mRNA

The premRNAs are edited after sunthesis by an enzyme that inserts some U residues and deletes others.

Question 21

Editosome:

Answer 21

20 S protein complex

Endonucleases: cut at the mismatch point between the gRNA and the unedited transcript

TUTase (terminal uridyltransferase): adds U resides from UTP to the 3’ end of the mRNA

U specific exoribonuclease: removed any unpaired u residues

RNA ligase