1. A scientist performs profiling of small RNAs.
Out of many small RNAs he identfied,
he chooses to do knockdown study on 3 small RNA. He get following results when he
knockdown them
Small RNA A: it's knockdown causes upregulation of RNA level only one gene.
Small RNA B: it's knockdown causes upregulation of RNA level of multiple genes.
Small RNA C: there is no change in expression of any gene however mRNA length of
many genes change.
Guess the type of RNAs for A , B and C and what are their functions.
2. A scientist has made a great breed of rice plant which can grow in dry weather and
give high yeild. However after 2 generation of testing he found that due to viral
infection, the next generation plants have lost the potential of good yield. What could
be happening and is there a way to recover back the high yield potential of that breed.
How this could be done.
3. Give at least 4 differences between siRNA amd miRNA and atleast 4 differences
between siRNA and piRNA.
4. What is the role of following histone modification and where can be they found in
genome
i). H3K27me3
ii). H3K27ac
iii). H3K9me3
iv). H3K9ac
v). H3K36me3
vi). H3K4me3
vii). H4K16ac
viii). H2AX
ix). H3S10P
x). H2AK110Ub
5. On a actively transcribing genes, sometimes we find regions which have repressive
histone modifications like H3K9me3 and H4K20me3. What could be the reason for this.
What could be the role of those regions.
6. What are poised or bivalent regions in genome and how they help in cellular function.
7. Suppose a chemist develops a new drug that neutralizes the poistive charges on the
tails of histone proteins. What would be the effect of this new drug on chromatin structure ?
Would this drug have any effect on gene expression? Explain your answer
8. In a country that is isolated we genotype 1000 individuals. Then we genotype 2000
children of those 1000 individuals. We find that 90% of regions in the genome follow
hardy-weinburg equilibrium, however many regions do not follow hardy-weinberg
equilibrium. How could this be possible. Explain ?
9. Which of the following pairs of sequences might be found at the end of insertion
chromosomes.
10. An insertion sequence contains a large deletion in its transposase gene. Under what
circumstances would this insertion sequence be able to transpose.
11. Although highly repetitive DNA is common in eukaryotic chromosomes, it does not encode
proteins; in fact, it is probably never transcribed in to RNA. If highly repetitive DNA does not
encode RNA or proteins, why is it present in eukaryotic genomes ? Suggest some possible
reasons for the widespread presence of highly repetitive DNA.
12. Describe in word and picture how telomerease function. Does its activity match
with retrotransposition.
12. A test-tube splicing system contains all the components (snRNAs, proteins,
splicing factors) necessary for the splicing of nuclear genes. When a piece of RNA
containing an intron and two exons are added to the system, the intron is removed
as a lariat and the exons are spliced out together. If the RNA molecule added to the
system has the following mutations, what intermediate product of the splicing
reactio will accumulate ? Explain your answer
a) GU at the 5' splice site is deleted
b) A at the branch point is deleted
c) AG at the 3' splice site is deleted.
13. what are DNA triplexes and where they can be found to enriched in genome.
14. what is genomic imprinting. Give one instance where it could be affecting
human health.
15. List 10 different kind of RNA and write about their function.
16. A scientist checked the epgenetic state at promoters for 4 genes using 3 histone
modifications (H3K4me3 , H3K27me3, H3K27ac). He observed following
Gene A promoter: high H3K4me3, high H3K27me3, low H3K27ac
Gene B promoter: high H3K4me3, low H3K27me3, high H3K27ac
Gene C promoter: low H3K4me3, low H3K27me3, low H3K27ac
Gene D promoter: high H3Kme3, low H3K27me3, low H3K27ac
Which of the above gene-promoters will not be Dnase hypersensitive
Can you explain the activity of each gene giving proper reasons.
17. what is the role of polymerase IV.