Question

In a ChIP-seq experiment, why do we get reads complementary to both the Watson and Crick strands?

a. Proteins bind only to the Watson strand
b. Proteins bind only to the Crick strand
c. Proteins bind to both DNA strands
d. ChIP-seq only reads one DNA strand

According to Pearson's correlation coefficient, where are ChIP-seq reads expected to map in relation to the binding site?

a. Both 3' and 5' ends on both strands
b. Only 5' ends on both strands
c. Only 3' ends on both strands
d. Exclusively on the Watson strand

Answer 1

In a ChIP-seq experiment, proteins bind to both DNA strands, resulting in reads that are complementary to both the Watson and Crick strands. ChIP-seq reads are expected to map to both 3' and 5' ends on both strands in relation to the binding site, according to Pearson's correlation coefficient.

Step-by-step explanation:

In a ChIP-seq experiment, we get reads complementary to both the Watson and Crick strands because proteins bind to both DNA strands. Proteins bind to specific regions of DNA, known as binding sites, and these binding sites can be present on either the Watson or Crick strand. Therefore, the ChIP-seq reads will be complementary to both strands.

According to Pearson's correlation coefficient, ChIP-seq reads are expected to map to both 3' and 5' ends on both strands in relation to the binding site. This means that the reads can be found at both ends of the DNA strands, regardless of whether they are on the Watson or Crick strand.