How did you design your qRT-PCR primers? If you design your own primers with the forward primer targeting one exon and the other reverse primer targeting the following exon, then you'll be able to discriminate cDNA (mRNA derived molecules) dissociation curves from gDNA exon-intron-exon dissociation curves. INot only this but may be useful to perform a DNAse I digestion on extracted RNAs prior to cDNA synthesis for a proper gDNA cleanup. 

If your own primers are designed in this manner and you're already performing DNAse I treatment, then you may have premature Ct values even on housekeeping genes maybe because you performed cDNA synthesis on a bigger amount of total RNAs or they are less diluted and the Ct value decrease in order to a higher titer of mRNA. 

In addition you could have increased or decreased Ct values for housekeeping genes in different cell types and different tissues (such as actin in developing tissues or GAPDH in highly metabolic-active tissues). 

If you are obtaining significant values from the no RT controls, this implies pre existing DNA and genomic DNA contaminating your cDNA could be the reason. When you look at yuour melt curves do you see more than one peak ? This could imply a specific product derived from RNA and a bigger product including introns derived from gDNA

There are 2 things that prove effective when targetting cDNA specifically

1. The first is to situate your primers across exon exon boundaries so that they will only bind to cDNA and not nascent genomic DNA: If you go into a program called primer BLAST (part of the NCBI suite of tools) it will let you design primers to a genbank sequence or sequence pasted into it (which it then recognises as ref RNA) that will allow you to specify exon junction (or intron spanning) primers

2. More effective digestion of gDNA using Turbo rDNASe from Ambion: Most DNAses are purified and often contain small amounts of RNAse which therefore degrades RNA. To offset this it is often necessary to limit the time you digest your RNA for, e.g. 15-20 min. In contrast, Turbo rDNAse is a recombinant enzyme where just the ORF of DNAse I is cloned and expressed. Consequently you can digest your cDNA to remove gDNA for 2 x 30 min intervals with addition of an extra 1ul of rDNAse between first and second thirty minute incubation. This leads to much more effective removal of gDNA and I have never seen any evidence of concomintant degradation of parent RNA unlike purified enzymes

I have provided you with a link to my drop box which provided a protocol for using the Turbo rDNAse with up to 10ug of RNA to digest

I hope this helps !!

https://www.dropbox.com/s/ixs4txr0uz8pm0d/Ambion%20DNAse%20treatment_Turbo%20DNAse_small%20quantities_0115.doc?dl=0

Here is some more general info on Turbo DNAse

I should add that I dont work for Ambion !!!

https://www.dropbox.com/s/2j0eoa8a1muwety/Trbo%20DNAse.pdf?dl=0

thank you all very much. i will try the Dnase treatment