Whole genome expression profiling vs. Location profiling

Question

[redapple.209]

Hi everyone, the paragraph below compares and contrast whole genome expression profiling vs. location profiling. Please rephrase or paraphrase this information because it's very long and a bit complicated.

"Whole genome expression profiling and location profiling are two methods that can be used in order to determine information related to the expression of a transcription factor. Whole genome expression reveals which genes are differentially expressed in the absence of the transcription factor. This can be particularly of interest for determining what proportion of a genome is affected by the transcription factor. Location profiling shows where on the genome factors are binding. This is accomplished by crosslinking the transcription factor with an antibody, immunoprecipitating this with reads of DNA via pulldown assay, purifying and reverse crosslinking this mixture, and finally sequencing the reads which bound to the transcription factor and mapping these to the genome. These two techniques can be used in conjunction in order to give a more accurate sense of which genes are affected in the absence of the transcription factor, how significant these effect is, and what proportion of the whole genome is differentially expressed."

Any input is appreciated. Thanks a lot!

Answer 1

[WouterDeCoster]

It essentially discusses two techniques to study a transcription factor. I wouldn't chose the names which were used in the paragraph, but fine, doesn't matter. Whole genome expression profiling means that you'll create a knock out/knock down of the transcription factor, and by sequencing the RNA (so RNA-seq) you will investigate which genes are affected by the loss of that transcription factor. In location profiling you'll perform Chip-seq. The transcription factor is covalently linked (crosslinking) to anything it is in contact with, so also the DNA on which is functions. By pulling down the transcription factor and sequencing all DNA which is bound to it you can get an idea to which locations your transcription factor binds, to discover it's locations of function.

[redapple.209]

hi WouterDeCoster, thank you very much for your answer.

[redapple.209]

is there another way to say this? to make it more compact? thanks.