From caption: I) ChIP assays were performed on the IRE of Tnni2 in neonatal rat

Question

From caption: I) ChIP assays were performed on the IRE of Tnni2 in neonatal rat ventricular myocytes. Chromatin was immunoprecipitated with antibodies against HA, HDAC1, HDAC2, and NRSF. Precipitated DNA was analyzed by PCR using primers flanking the IRE. HDAC1 and HDAC2, but not NRSF, mediate repression of Tnni2 at basal levels. PCR was performed prior to immunoprecipitation as an input control .

From the paper : Although there is an NRSF- binding site within the IRE of the Tnni2 gene, NRSF was not detected on this element in neonatal rat cardiomyo- cytes (Fig. 6I), suggesting that HDAC1 and HDAC2 repress Tnni2 through an NRSF-independent mechanism

Why does the bottom band form in every lane and why is it particularly bright in the a-NRSF band? If NRSF didnt bind any sequences, shouldn't the PCR of precipitated sequences lead no band formed?

Explanation / Answer

The bottom band that is shown in the PCR gel is the non-specific band which are due to the formation of primer dimer. The reason behind the bright band in case of NRSF is due to more addition of primers during the reaction setting

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