PREDICTED
BEAF BINDING SEQUENCES IN D.MELANOGASTER:
Authors: Eldon Emberly and
Olivier Cuvier
USAGE:
The following links provide lists which will give links to launching
GBROWSE, the genome browser. When the browser is first launched, scroll
down to the '
Upload standard
annotations' and click both boxes. Then click '
Update URLs'. This will then show
all the known and predicted BEAF elements in the browser.
BEAF
ELEMENTS DEFINED:
A BEAF element is a 200 bp sequence that contains at least 3 BEAF
binding sites. There are 7045 BEAF elements in the D.melanogaster
genome. 1981 of these element have at lest 1 DREF
binding
site. In the browser, BEAF elements that contain a DREF site are
flagged via a '_D' in the element label.
DUAL-CORE ELEMENTS DEFINED:
A DCORE = dual-core is composed of two BEAF element predictions
separated by less than 800 bp. There are 494 predicted dual-core
elements in the genome.
DUAL-CORE LIKE ELEMENTS DEFINED:
We define a dual-core-like element to be one of the lone BEAF
elements which have a neighbouring cluster of 2 CGATA's (in a 100 bp
window) within 800 bp. There are 1226 such elements. The total set of
dual-cores and dual-core-like elements gives 1720 elements.
PREDICTIONS
& ANALYSIS:
DUAL-CORE BEAF ELEMENTS:
A
statistically significant fraction of BEAF elements are found to be
arranged
in pairs. From BE76, BE28 and scs', the spacer
sequence was found to be AT rich. Interestingly, these 'dual-core'
elements are often found connected with a promoter of a gene with one
BEAF element sitting over the promoter with the other sitting
up-stream. Following from this finding is the tendency for these
dual-core elements to sit between divergently spaced genes. Of the 7045
BEAF elements, 494 meet the criterion of being a dual-core element. The
following links give access to these elements (the distances to the
nearest neighbour (NN) and next-nearest neighbour genes (NNN) are
given):
Distribution
of distances between dual-core and nearest promoter
- this graph highlights that most dual-cores reside nearby
a promoter
LINK TO EXPERIMENTALLY KNOWN
BEAF ELEMENTS:
List of known BEAF elements identified from the literature and
unpublished
experiments:
Known
BEAF elements
LINKS TO PREDICTONS:
dual-core
elements in cdk7 locus
dual-core
elements in mei-S332 locus
dual-core elements sorted by
distance to nearest gene
dual-core elements sorted by
combined NN and NNN distance
PROMOTER ANALYSIS:
Each promoter was analyzed to see if a
prediction falls within a +/- 500 bp (1000 bp for dual-cores) of
it.
For each set of predictions there is a link to the list of genes which
have predictions in their promoters, and the GO analysis of these
genes. For the GO analysis, the table is sorted by p-value. (Note:
'total' = # of genes with the given GO,
'hits' = # of genes with predictions in promoter, 'expect' = # of hits
expected by chance). Clicking on a GO term will then take you to the
list of named genes which fall into that class (genes which are just
CG..., are not included in the gene list).
all BEAF promoters
DCORE
promoters
DCORE-like promoters
all BEAF promoters GO
DCORE promoters GO
DCORE-like promoters GO
BEAF only
promoters GO
DREF promoters
GO
SYNOPSIS: Gene Expression and GO Analysis
highlight BEAF in cell-cycle and chromatin dynamics
*NOTES:
a) all BEAF = 7045 predictions that contain 3 BEAF sites. It includes
1981 predictions that also bind DREF
b) BEAF only = 5064 predictions that contain 3 BEAF sites but
NO DREF
c) DREF = 680 lone DREF elements (only one DREF site, no 3rd BEAF) and
the 1981 BEAF elements that contain 1 DREF site
d) DCORE = 494 dual-core elements made from the 7045 BEAF predictions
e) DCORE-like = 1720 dual-core and dual-core-like elements
SUMMARY OF GO CORRELATIONS:
i) for BEAF/DCORE genes,
their GO is related to
ribosome, mRNA, chromatin, apoptosis, endocytosis, cell-cycle stuff and
are underepresented for more complex biological processes like
transport, nervous system stuff.
ii) there is some
separation of biological process for the BEAF only promoters compared
to DREF promoters. BEAF promoters are involved in cell organization,
chromosome stuff, and metabolism. DREF promoters are more directly
involved in RNA processing. There are some shared common processes.
iii)
During
embryogenesis, there is no drastic changes in the relative expression
of dref relative to that of beaf (Hart et al., 1999). On the contrary,
only BEAF possesses the ability to bind dual-cores during mitosis, yet
DREF is removed from chromatin at this stage. In the next G1 phase of
the cell-cycle, the ability of DREF to competes for BEAF may thus be
critical for expression of genes whose promoter overlap with
dual-cores. In fact, BEAF elements containing DREF are highly enriched
in GOs cell-cycle that are positively regulated. In
contrast, DREF lone elements are not enriched in genes positively
regulated through development that regulate cell-cycle, as most
correspond to a BEAF dual-core. BEAF elements without DREF are also
enriched in the GO cell-cycle for genes positively regulated.
Therefore, dual-cores appear to be essential in the regulation of
cell-cycle genes. However, while DREF may be required for their
activation at the G1/S transition, the chromatin organization at
dual-cores appear to be important to potentiate their
activation.
DIVERGENT
GENES/BIDIRECTIONAL
PROMOTERS & BEAF-ELEMENTS:
There are 2652 divergent gene pairs with a
spacer < 5 kb in between. 912 of these pairs have a BEAF element
within the bidirectional promoter region. Of these there are 136
pairs that have dual-core elements -- only 36 are expected by chance.
Divergent gene pairs with BEAF
elements
GENE EXPRESSION DATA:
This is analysis of gene expression and the connection to BEAF/DREF
elements.
1) Link to all gene expression data plots for all genes in the
drosophila genome:
Plots of
embryonic gene expression profiles
2) Correlation to
BEAF
expression:
List of genes
with BEAF dual-core in their promoter correlated and anti-correlated
with BEAF expression.
3) Correlation to
DREF
expression:
List of genes
with DREF element in their promoter correlated and anti-correlated with
DREF expression.
SUMMARY OF POSITIONAL CORRELATIONS:
Z score measures for various correlations between factors and genomic
organization.
Factor-Function correlations:
|
BEAF
|
DCORE
|
Promoters
|
Z
= 63.3
|
Z=22.83
|
Long
Genes
|
Z=0.86
|
Z=
-0.20
|
Voids
|
Z=
-3.47
|
Z=
-4.31
|
Gene
Clusters
|
Z=10.30
|
Z=2.44
|
Factor-chromosome correlations:
|
BEAF
|
DCORE
|
X
+ Xh
|
Z
= 14.4
|
Z
= 10.7
|
2L+2R+2h
|
Z
= -0.84
|
Z
= -2.02
|
3L+3R+3h
|
Z
= -4.59
|
Z
= -2.97
|
4
|
Z
= 4.80
|
Z
= 0.19
|