The following studies describe the autophagy markers in relation to estrogenic stimulation

1. Guido et al. (Cell Cycle 11:  2911-21, 2012) -

PI3III, Beclin 1, AMBRA and UVRAG

2. Zeilniok et al., (BioMed Research International, 2014-  http://dx.doi.org/10.1155/2014/382653) -

 BECN1, ATG5, ATG3, and LC3B

3. Yang et al., (Apoptosis 18: 1363- 73, 2013) -

LC3, beclin1 and ULK1

So monitoring Beclin 1 and LC3 expression could be  best bet in your studies.