Description and Methods
Excerpted from the
Vista Enhancer Handbook and Methods page at the Lawrence Berkeley
National Laboratory (LBNL) website:
The VISTA Enhancer Browser
identifies distant-acting transcriptional enhancers in the human genome by
coupling the identification of evolutionary conserved non-coding sequences with
a moderate throughput mouse transgenesis enhancer assay.
The "Experimental Dataset" of conserved non-coding human sequences has been
tested for enhancer activity in transgenic mice.
As of October 2006, approximately 300 elements were found in this portion of
the database, and this number is expected to grow steadily. These sequences are
based on UCSC human assembly hg17 (May 2004).
Non-coding elements identified as conserved in human, mouse, and rat are lifted
with primers, and the PCR fragment is cloned into a reporter vector that has a
minimal promoter fused to LacZ. This is then injected into a fertilized mouse
egg and the 11.5 day embryo is assayed for activity with lacZ stain.
Whole-embryo in situ pictures are available on the LBNL website..
To be defined as a positive enhancer, an element has to show
reproducible
expression in the same structure in at least three independent transgenic
embryos. An element is defined as negative if at least five
transgenic embryos
have been obtained, but no reproducible expression was observed in any structure
in at least three different embryos.
Users should keep in mind that the assay captures only a single embryonic
timepoint. A negative result reported in the experimental dataset does not
necessarily imply that this conserved element is not a transcriptional
enhancer, because it might be active at earlier or later timepoints in
development.
Display Conventions and Configuration
Elements that tested positive are assigned a score of 900 and
display in black
in the annotation track. Those that tested negative are given the
score 200 and appear as light grey.
Credits
Thanks to Len Pennacchio at Lawrence Berkeley National Laboratory for providing the
enhancer track.
References
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt
A, Lewis KD et al.
In vivo enhancer analysis of human conserved non-coding sequences.
Nature. 2006 Nov 23;444(7118):499-502.
PMID: 17086198
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