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The QCD factorization theorem for diffractive processes in DIS is used to derive formulae for the leading twist contribution to the nuclear shadowing of parton distributions in the low thickness limit. Based on the current analyzes of diffraction at HERA we find that the average strength of the interactions which govern diffraction in the gluon sector at $x \le 10^{-3}, Q_0=2 GeV$ is ~50 mb. This is 3 times larger than in the quark sector and suggests that applicability of DGLAP approximation requires significantly larger $Q_0$ in the gluon sector. We use this information to estimate quark and gluon shadowing for heavy nuclei and to calculate its$Q^2$ depen- dence. For A~200 the amount of the gluon shadowing: $G_A/AG_N\sim 0.25-0.4$ at $x<10^{-3},Q=2GeV$ is sensitive to the probability of the small size configurations within wave function of the gluon 'partonometer' at the $Q_0$ scale. At this scale for $A\sim 200$ the nonperturbative contribution to the gluon density is reduced by a factor of 4-5 at $x \le 10^{-3}$ unmasking PQCD physics in the gluon distribution of heavy nuclei. Such shadowing would strongly modify the first stage of the heavy ion collisions at LHC, and would lead to large color opacity effects in $eA$ collisions at x<0.001. The leading twist contribution to the cross section of the coherent $J/\psi$ production off $A\ge 12$ nuclei at $\sqrt s \ge 70$ GeV is strongly reduced as compared to the naive color transparency expectations. The Gribov black body limit for $F_{2A}(x,Q^2)$ is extended to the case of the gluon distributions in nuclei and shown to be relevant for the HERA kinematics of $eA$ collisions. Properties of the final states are also briefly discussed

Diffraction at HERA, Color Opacity and Nuclear Shadowing in DIS off nuclei