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Monitoring Stem Cell Research 
somatic donor cell, must be reactivated (Hochedlinger and Jaenisch, 
2002b; Rideout et cil., 2001). It is the failure to activate key 
“embryonic" genes that are required for early development that 
leads to the demise of most clones just after implantation. Recently, a 
set of about 70 key embryonic genes termed "Oct-4 like" genes have 
been identified that are active in early embryos but not in somatic 
donor cells. Importantly, the failure to faithfully activate this set of 
genes can be correlated with the frequent death of cloned animals 
during the immediate post-implantation period (Bortvin et al., 2003). 
These results define “faulty reprogramming" as the cause of early 
demise of cloned embryos as the failure to reactivate key embryonic 
genes that are silent in the donor cell. 
fii) Newborn clones misexpress hundreds of genes . 
Clones that survive to birth suffer from serious problems, many of 
which appear to be due to an abnormal placenta. The most common 
phenotypes observed in animals cloned from either somatic or ES cell 
nuclei are fetal grovsrth abnormalities such as increased placental 
and birth weight. This has suggested that surviving clones had 
accurately reprogrammed the "Oct-4 like” genes that are essential 
for the earhest stages of development, i.e. those immediately 
following implantation of the embryo into the uterus. The abnormal 
phenotype of those clones that do survive through these early stages 
and develop to birth indicates that other genes that are important for 
later stages of development but are not essential for early survival 
are not correctly reprogrammed. To assess the extent of abnormal 
expression of various genes in the cells of clones, global gene 
expression has been assessed by microarray analysis of RNA 
prepared from the placentas and livers of neonatal cloned mice, i.e., 
clones that survived development and were viable at birth; these 
clones had been derived by nuclear transfer (NT) of nuclei prepared 
either from cultured ES cells or from freshly isolated cumulus cells 
(somatic cells that surround the egg) (Humpherys et al., 2002). Direct 
comparison of gene expression profiles of over 10,000 genes (of the 
30,000 or so in the mammalian genome) showed that for both classes 
of cloned neonatal mice, approximately 4% of the expressed genes in 
their placentas differed dramatically in expression levels from those 
in controls, and that the majority of abnormally expressed genes 
were common to both types of clones. When imprinted genes, a 
class of genes that express only one allele (either from maternal or 
paternal origin), were analyzed, between 30 and 50% were not 
correctly activated. These data represent strong molecular evidence 
that cloned animals, even those that survive to birth, suffer from 
serious gene expression abnormalities. 
PRE -PUBLICATION VERSION 
