Mammalian nuclei are complex organelles containing many functionally d
istinct nucleoprotein and protein particles in the size range 20-30 nm
. This complexity hinders the study of structure-function relationship
s within the mammalian nucleus. Element-specific mapping using the ene
rgy-filtered transmission electron microscope can provide novel inform
ation on protein and nucleic acid density within structures, facilitat
ing the identification of biochemical heterogeneity within morphologic
ally similar structures. We demonstrate that imaging phosphorus, nitro
gen and carbon can be useful in the characterization of protein and nu
cleoprotein structures within the nucleus. Additionally, electron spec
troscopic imaging (ESI) may be used to map the distribution of stains
relative to unstained material when biochemical-specific staining prot
ocols, such as EDTA-regressive staining of RNA with uranyl acetate, ar
e used. Relative mass may also be determined from ESI images and can b
e combined with elemental information further to distinguish biologica
l constituents. Using this approach, heterochromatin was found to be v
ariable in nucleic acid content although the morphology appeared relat
ively homogeneous. ESI shows substantial promise for the investigation
of structure-function relationships in biological specimens.