Homework_6

[lortizb]

My goal of this exercise is to be more familiar with Differential gene expression with RNA-seq.

[lortizb]

1- Paste the URL to the script in the GitHub issue URL to the script in the GitHub issue: https://github.com/lortizb/GENE8940.git

2- Report the Git revision that you used for your final analysis Git revision: commit dd5050d34a9929f63ad039b27bcb805430dfe054

3- Check in pdf with sleuth results and provide link to PDF The PDF file can be found in:
SleuthResults.pdf

4- Answer following questions a) What are the gene names for the two most significantly differentially expressed genes? The most significantly differentially expressed genes are lcl|NC_000913.3_cds_NP_414965.1_430 (cyoB gene) and lcl|NC_000913.3_cds_NP_414964.1_429 (cyoC gene).

lcl|NC_000913.3_cds_NP_414965.1_430 /gene="cyoB" /locus_tag="b0431" /gene_synonym="ECK0425" /product="cytochrome bo3 ubiquinol oxidase subunit 1" /protein_id="NP_414965.1" /db_xref="GeneID:945615"

lcl|NC_000913.3_cds_NP_414964.1_429 /gene="cyoC" /locus_tag="b0430" /product="cytochrome bo3 ubiquinol oxidase subunit 3" /protein_id="NP_414964.1" /db_xref="GeneID:946897"

b) What biological processes are these genes involved in? Both cytochromes are involved in the bacterial electron transfer reactions. Their main function is oxidise ubiquinol into ubiquinone and reduce oxygen to water.

c) Are the two genes upregulated or downregulated in the FNR mutant relative to wild type E. coli? They are both upregulated in the FNR mutant relative to wild type E. coli.

d) Where are these genes located in the MG1655 E. coli genome? cyoB is located in 448650-450641 bp and cyoC in 448046-448660 bp

e) Provide a biological hypothesis that explains for why these two genes are most significantly differentially expressed genes when comparing an FNR mutant to wild type E. coli? Include the direction of expression change and genomic location of these genes in your explanation. FNR supresses the cytochrome oxidase function. In FNR mutants (lacking FNR) expression of cyoB and cyoC is not suppressed compared to wild type E. coli.

[Watson-40]

Pasted the URL to the script in the GitHub issue incorrectly, should be https://github.com/lortizb/GENE8940/blob/master/HMW06_script 1/2 Report the Git revision that you used for your final analysis 2/2 Check in pdf with sleuth results and provide link to PDF 1/1 a) Gene names for the two most significantly differentially expressed genes NP_414964 - cyoC NP_414965 - cyoB 1/1 b) one of your biological processes these genes are involved in is given and correct (aerobic electron transport chain), but missing aerobic respiration 0.5/1 c) correct regulation direction (upregulated or downregulated) in the FNR mutant relative to wild type E. coli Both genes upregulated in the FNR mutant relative to wild type E. coli under anaerobic conditions. 1/1 d) Where are these genes located in the MG1655 E. coli genome? cyoB: NC_000913.3:448650-450641 (negative strand) cyoC: NC_000913.3:448046-448660 (negative strand) 1/1 e)cyoB and cyoC are neighboring genes and likely part of the same operon. Under anaerobic conditions, FNR binds to the promoters of many operons to upregulate genes needed for growth under anaerobic conditions and downregulate genes needed for growth under aerobic conditions. In the wild type, FNR binds to the promoter of the operon containing cyoB and cyoC to switch this operon off under anaerobic conditions. In the FNR mutant, FNR is unable to repress the operon containing cyoB and cyoC and thus the expression of these two genes is upregulated relative to the wild type. your hypothesis is correct. 1/1 8.5/10, excellent!