The QCD factorization theorem for diffractive processes in DIS is used to d
erive formulae for the leading twist contribution to the nuclear shadowing
of parton distributions in the low thickness limit (due to the coherent pro
jectile (photon) interactions with tare nucleons). Based on the current ana
lyzes of diffraction at HERA we find that the average strength of the inter
actions which govern diffraction in the gluon sector at x less than or equa
l to 10(-3), Q(0) = 2GeV is similar to 50mb. This is three times larger tha
n in the quark sector and suggests that applicability of DGLAP approximatio
n requires significantly larger Q(0) in the gluon sector. We use this infor
mation on diffraction to estimate the higher order shadowing terms due to t
he photon interactions with N greater than or equal to 3 nucleons which are
important for the scattering of heavy nuclei and to calculate nuclear shad
owing and Q(2) dependence of gluon densities. For the heavy nuclei the amou
nt of the gluon shadowing: G(A)(x, Q(0)(2))/AG(N) (x, Q(0)(2))\(x less than
or equal to 10-3) similar to 0.25 - 0.4 is sensitive to the probability of
the small size configurations within wave function of the gluon "partonome
ter" at the Q(0) scale. At this scale for A similar to 200 the nonperturbat
ive contribution to the gluon density is reduced by a factor of 4 - 5 at x
less than or equal to 10(-3) unmasking PQCD physics in the gluon distributi
on of heavy nuclei. We point out that the shadowing of this magnitude would
strongly modify the first stage of the heavy ion collisions at the LHC ene
rgies, and also would lead to large color opacity effects in eA collisions
at HERA. energies. In particular, the leading twist contribution to the cro
ss section of the coherent J/psi, production off A 2 greater than or equal
to 12 nuclei at root s greater than or equal to 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 distribut
ions in nuclei and shown to be relevant for the HERA kinematics of eA colli
sions. Properties of the final states are also briefly discussed.