Genomic analysis of a hypertension QTL on Rat chromosome 1

Clemitson J, Dixon RJ, Haines S, Hall L, and Samani, NJ Department of Cardiovascular Sciences, University of Leicester

MOUSE RAT HUMAN

Introduction Gene list (concensus SISA6000 list) Results Summary
Calc-b

By analysing crosses between the spontaneously Calc-a

The SISA 6000 QTL has been positioned on the Rat

NOVEL - NM_024514
NOVEL - ENSRNOG00000011367
Pde3b

hypertensive rat (SHR) and the Wistar-Kyoto (WKY) rat, we(1,2) NOVEL - RNOR01008459.2542.7655
NOVEL - RNOR01008461.14636.41822
NOVEL - LOC293167
NOVEL - ENSRNOG00000011405 genome sequence.
have previously shown that a region in the mid-portion of rat NOVEL - ENSRNOG00000011736

This genomic region lies within a conserved syntenic

Psma1
Copb1
NOVEL - LOC293168
chromosome 1, contains quantitative trait loci (QTLs) NOVEL - LOC293169
NOVEL - LOC293170
R-RAS2 segment between Rat, Mouse (chromosome 7) and Human
affecting blood pressure (BP). This region has been captured F-SPONDIN
NOVEL - RNOR01008488.143.251
NOVEL - LOC293171
NOVEL - LOC293172 (chromosome 11).
in reciprocal congenic strains derived from SHR and WKY. NOVEL - LOC293173
NOVEL - LOC293174
NOVEL - LOC293177
NOVEL - LOC308888 The Rat SISA 6000 genomic region is 3.9Mb in size.
Further work, has indicated that the major proportion of the NOVEL - ENSRNOG00000014315
NOVEL - ENSRNOESTG00000001427
Pth
NOVEL - LOC308889 Using a comparative genomics approach to identify the
BP effect of these loci is mediated through the kidney(3). NOVEL - LOC308890
Arntl
NOVEL - LOC308891
NOVEL - LOC308892
NOVEL - LOC308893
majority of the genes within this QTL minimal region - a
NOVEL - LOC308894
NOVEL - ENSRNOG00000014885
NOVEL - ENSRNOG00000015087 comparative gene map was created (Figure 2).
The region containing one of these BP QTLs, has now been NOVEL - LOC293178

The comparative gene map suggests 49 putative genes lie

TEAD-1
Parva
NOVEL - LOC293180
narrowed down further and isolated in a congenic sub-strain, NOVEL - ENSRNOG00000016244
NOVEL - LOC308895
Dkk-3
NOVEL - LOC308896
within this region.
named SISA 6000 (Figure 1). As this region is < 4 Mb in size, NOVEL - LOC308897
NOVEL - RNOR01008624.1581.2180
NOVEL - LOC293181 The orientation of this conserved segment (gene list) is the
it is now feasible to directly search for the BP susceptibility NOVEL - LOC308898
NOVEL - LOC293182

KEY KEY same in Rat but reversed in Mouse & Human.

genes within the region. Homologs found in Human & Mouse
Homologs found in Mouse only
Rat predicted gene with RAT EST support
Rat predicted gene with mammalian EST homology support
Rat EST Transcripts - transcript predictions made by Ensembl using EST evidence alone
Gene found in Human only - falls within Gap in Rat / Mouse
Homologs found in Human & Mouse
Homologs found in Mouse only
Rat predicted gene with RAT EST support
Rat predicted gene with mammalian EST homology support
Rat EST Transcripts - transcript predictions made by Ensembl using EST evidence alone
Gene found in Human only - falls within Gap in Rat / Mouse

FIGURE 1(a). Dissection of SISA1 congenic region on Rat

FIGURE 2. Comparative gene map of SISA 6000 region Work in progress
chromosome 1
SISA 1 Using available Rat cDNA sequence for all (but one) of the
congenic SISA 6000 SISA 9000 Methods putative genes within the SISA 6000 region, oligonucleotide
region Translation of Genetic Map to Physical Map. primers have been designed to enable screening of these
Genetic markers defining the region of interest, were genes for expression differences in the kidney of the rat
Chromosome 1

positioned on the physical Rat genome sequence, by strains of interest, using RT-PCR methodology. So far, 12 of
using BLAST and BLAT searches of the Rat genome the loci have been tested in the 25 week and 6 week
sequence within three genome browsers (Ensembl, WKY/SHR strains.
SHR genotype UCSC and NCBI), with genetic marker associated In tandem with this work full length rat cDNA sequencing
WKY genotype sequence data. is being undertaken to identify possible sequence variations
FIGURE 1(b). Blood pressure measurements in congenic between the rat strains. So far, 7 of the loci have been
substrains at 20 weeks Creation of Comparative Gene Map. investigated for cDNA sequence variations, with the Calc-a
Rat genome annotation from the three genome browsers sequence exhibiting a synonymous point mutation between
SHR
was examined and integrated for the SISA 6000 region. the strains.
The annotation of the complementary syntenic regions
SISA 1
in Mouse and Human was also investigated within the
SISA 6000 three genome browsers and integrated with Rat SISA
References
6000 annotation, to create a putative gene list with (1) Frantz, S., et al. Hypertension (1998), 32, p639-646
various degrees of confidence in accordance with (2) Frantz, S., et al. Hypertension (2001), 38, p216-221
SISA 9000
175 185 195 annotation evidence (Figure 2). (3) Clemitson, J.R., et al. Hypertension (2002), 40, p292-297
Blood Pressure (mmHg)