ARSs and replication origins

Vujcic, Marija Marija.Vujcic at RoswellPark.org
Wed Jul 12 16:14:44 EST 2000


Hello,

here are some answers and opinions from the lab that holds this topic dear
to our hearts :-))

For the long time there has been some mix up in using the terms ARS or
origin of replication, and part of the mix up was due to the lack of
scientific data. Today, there is enough data that very strongly suggest the
following:

- ARS (Autonomously Replicating Sequence) is just what the name says -
sequence that confers autonomous replication, i.e. plasmid replication
origin in yeast. That is how ARS elements were (and still can be) isolated
in the first place, so by definition, ARSs are sequences derived from the
chromosome that function as origins of replication on a plasmid. 

- so far, experiments in yeast DNA replication confirm that every
chromosomal origin in yeast is also an ARS element (i.e. can function as an
origin on a plasmid), but not every ARS element functions as chromosomal
origin in its native chromosomal location. That suggests that those kind of
ARS elements could either be inactive as chromosomal replicators,
incompetent for initiation of replication IN CHROMOSOMAL CONTEXT, or they
could be silent, repressed origins in their native chromosomal location, due
to different possible factors, such as chromatine structure, lack of certain
cis-elements or presence of some inhibitory elements, or since nowdays the
data about different replication timing of different origins during S phase
are avaliable, those origins could be just regulated to fire very, very late
in S phase and simply get overreplicated by forks coming from  nearby, early
firing origins before they have a chance to fire.
- for the particular ARS elements from the left arm of chromosome III, ARS
300-304, plus ARS 320, they all have been shown to be active plasmid
replicators (ARSs) but all inactive as chromosomal replicators IN THEIR
NATIVE CHROMOSOMAL LOCATION, regardless of mating type of yeast,
transcriptional status of nearby silent HML locus or induction of nearby
CHA-1 gene. However, at least some of them, 303 and 320, are competent to
fire on the chromosome if they are removed from their native chromosomal
context and transplaced to another location on the chromosome. They also
become active chromosomal replicators at their native location if closest,
active origin(s), ORI 305 and/or ORI 306 are deleted from the
chromosome.(Vujcic, Miller, Kowalski, MCB '99). The discrepancy with C.
Newlon data (that D. Dubey mentioned), is cleared since they used different
assay at that time which couldn't detect relatively weak initiation from
this location even when they deleted all active origins.
 So, for at least these particular ARSs, we can say that they are silent
chromosomal origins, but they are competent for firing once the replication
forks coming from the right are delayed (by deletion of early-firing ORI305
and ORI306). It has been shown that silent origins on the left end of chr
III when they fire, fire late in S phase (Diffley ref., for 301) so the
whole concept of regulation of replication timing mentioned above could be
an explanation for the silencing of these origins. 
Now, why is that so in the cell, and why is it important in the  nature
(since origins don't get deleted in yeast just like that so that silent ones
can get a chance to fire), is a whole another topic for discussion. Lately,
some data suggest that it has to do with cell's reaction to DNA damage, i.e.
survival after the damage.

- to clarify the nomenclature and confusion, lately in papers dealing with
this topic terminology is that the same sequence if refered to as a plasmid
replicator is called ARS and if refered to as a chromosomal replicator, is
called ORI - for example, ARS305 is called ORI305 on the chromosome, ARS1 is
ORI1 and so on. 

- and to (finally!) give opinion for the very first question in this thread
(hi Chuck!), ARSs should be given a clear distinction as PLASMID replication
origins as oposed to chromosomal replicators from which they were derived.
Genetic locus corresponding to a chromosomal replicator should be (and are,
lately in some papers) called ORIs. It is important to point that  ARSs and
their corresponding chromosomal replicators share a number of common
essential and important cis-acting sequences but reasons for some ARSs to be
silent in the chromosome are only begining to be clear and can probably be
different for different ARSs.

Well, I said that topic is dear to my heart,  sorry for the long message!

Marija Vujcic
Dept. of Cancer Genetics
Roswell Park Cancer Institute
Buffalo, NY


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