cps.php from eXtensible Genome Data Broker at Krugle

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<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>

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<DIV ID="mainWLS">

<H1>Locating the Cleavage / Polyadenylation Site (CPS)</H1>
<H3>( the 3' boundary of the mature mRNA )</H3>

<DIV ID='abstract'>
<P>Determining the exact nucleotide (or nucleotide region) at which transcription concludes for a gene
has been an active field of study for over three decades. However, with the increased availability of genomic sequence,
and thus an inherent need for gene annotation, tools and methods for accurate prediction of the downstream extent
of a gene are in demand now more than ever. Herein we discuss current knowledge of the biological properties
of the CPS as well as methods for locating an approximate region of termination given available EST and cDNA evidence.
</P>
</DIV>

<IMG ID='tfig' SRC='./figa.png'>
<DIV ID='methods'>
<H3>The Biology</H3>
<P CLASS='synopsis'>In eukaryotes, the common RNA-POL II transcribed gene undergoes the processes of maturation
(ie. capping, splicing, and polyadenylation) concurrent with transcription. While the exact mechanism which
terminates transcription is unproven, the common assumption is that a lack of processivity of the RNA-POL II 
caused by dissociation of stabilizing elongation factors in concert with cleavage/polyadenylation allow termination
to occur at the next thermodynamically favorable location (Zhao, 1999). Thus the exact point of pre-mRNA transcript termination
may or may not be conserved. However the site of cleavage/poyladenylation is generally static as shown by mutation
studies which produce transcriptional run-off when this site is altered. While the extent of transcriptional excess
may have regulatory consequences, identification of the cleavage/polyadenylation site is sufficient to determine the 
sequence extent of mature mRNA as related to the annotation of a given transcriptional unit.
</P>

<H3>Genomic Landmarks for Locating a CPS</H3>
<P CLASS='synopsis'>Cleavage / Polyadenylation sites are largely difficult to predict based
on sequence motifs due to their short and often degenerate nature. 3' Expressed Sequence Tags (ESTs) however, provide 
an empirical method for locating the CPS. By accurate spliced alignment of the 3' ESTs, cluster groups can be used to 
determine a localized region containing the CPS (Gautheret, 1998). For this analysis, 98,313 3' ESTs were clustered into 13,148 multi-member
clusters. Variation of the aligned 3' boundary within these Three-Prime EST Groups (TPEGs) is shown in figure 1. 
As previously observed (Graber, 1999), multiple CPS signals closely spaced (on the order of tens of nucleotides) 
result in variation of the 3' EST aligned ends (again on the order of tens of nucleotides). This analysis confirms
that over 95% of the current gene-model annotations containing TPEGs have 3' boundaries within 150 nucleotides of the TPEG defined
CPS (the vast majority have less than a 10 base difference). However exceptions do exists and have been flagged as 
possible alternative polyadenylation sites, false gene extensions, and false intronic gene mergers.
</P>
</DIV>

<DIV CLASS='figure'>
<H3>Figure 1: Three-Prime EST Group Variance</H3>
<IMG SRC='./fig1.png'>
<P CLASS='footnote'>This graph represents the difference in nucleotide position of each Three-Prime EST Group member 
(ie. each 3' EST) as compared to the median 3' boundary of the cluster. Values range from 0 to 93. The most prevalent 
positional difference is 0 representing alignment termination at a common nucleotide. 95% of the TPEG member ESTs have
variance of less than 16 nucleotides.
</P>
<span style='clear:right;' /><!-- hack to get IE to extend the DIV -->
</DIV>

<DIV CLASS='figure'>
<H3>Figure 2: TPEG CPS -vs- GeneModel Boundary</H3>
<IMG SRC='./fig2.png'>
<P CLASS='footnote'>This graph represents the difference in nucleotide position of each predicted TPEG defined CPS as compared 
to the annotated 3' boundary of the containing Gene Model. 95% of all TPEG defined CPSs lie within 150 nucleotides of the 
annotated 3' gene boundary. Variations much larger than this threshold are considered flagable events (alternative polyadenylation,
, false gene extensions, and false intronic gene mergers).
</P>
<span style='clear:right;' /> <!-- hack to get IE to extend the DIV -->
</DIV>


<DIV ID='discussion'>
<A HREF='./index.php'>Return to GAEVAL page</A>
</DIV>

</DIV>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>
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