Fine Mapping of Lrp11 Trans-eQTL on Mouse Chromosome 5 Using SNP Markers .


43 views
Uploaded on:
Description
110 MF1 mice. Genotypes (1813 SNPs). Gene Expression (24078 traits). Physiological Traits (21 traits). Genome Wide Association. Fig. 2: Study design to correlate genotype with expression and physiological data from MF1 mice. Image courtesy of Dr. Anatole Ghazalpour, UCLA.
Transcripts
Slide 1

110 MF1 mice Genotypes (1813 SNPs) Gene Expression (24078 qualities) Physiological Traits (21 attributes) Genome Wide Association Fig. 2: Study outline to correspond genotype with expression and physiological information from MF1 mice. Picture civility of Dr. Anatole Ghazalpour, UCLA. Table 1: PCR preliminary combine outline utilizing MGI successions and Primer3. Groundwork successions are saved over every one of the eight ingrained mouse strains and checked for uniqueness utilizing NCBI-BLAST (information not appeared). Enhanced district incorporates LI-COR sequencing groundwork arrangement. "any", self-complimentarity score. "3\'", 3\' self-complementarity score. Table 2: LI-COR marked groundwork outline utilizing MGI successions and Primer3. Groundworks for nine SNPs polymorphic over each of the eight innate mouse strains are being utilized to grouping SNP areas for the eight ingrained strains and the MF1 outbred stock. Groundwork arrangements are monitored over the eight innate mouse strains and checked for uniqueness utilizing NCBI-BLAST. Fig. 3: QTL mapping of SNPs in Lrp11-related area of chromosome 5. Picture graciousness of Dr. Anatole Ghazalpour, UCLA. A. B. Fig. 4: 1% agarose gel affirmation of PCR result of 1:1, 1:10, and 1:100 weakenings of format mouse genomic DNA utilizing unlabeled groundwork match for rs31562818 (Table 1). An) A/J, 1 kbp step (Promega), C3H, BALB/C, C57BL/J6. B) DBA/2J, I/LnJ, RIIIS, 1 kbp step (Promega), AKR. All responses take after weakening example of 1:1, 1:10, 1:100. MF1 Fig. 1: The proposed eight hereditary innate mouse strains for outbred MF1 stock. Picture civility of Dr. Aldons J. Lusis, UCLA. Fig. 5: LI-COR sequencing gel of SNP rs31562818 for strains AKR, RIIIS, A/J, C3H, BALB/C, and C57BL/J6 utilizing LI-COR ® IRDye700 marked custom preliminary (Table 2). Path arrange: ACTG. Aliyah Khan 1 , Karolina Khlebnikova 2 , Gracejeet Sroya 2 , Anjali D. Tapadia 3 1 Dept. of Physiological Sciences, 2 Dept. of Chemistry and Biochemistry, 3 Dept. of Molecular, Cell, and Developmental Biology, UCLA, Los Angeles, CA ABSTRACT MATERIALS AND METHODS Here we report the preparatory aftereffects of the push to fine-delineate already recognized 3.5 Mbp quantitative quality locus (QTL) connected with variety in Lrp11 expression levels utilizing 110 MF1 outbred mice. The Undergraduate Genomics Research Initiative (UGRI) at UCLA is utilizing genotype information to recognize the causal variety for Lrp11. In view of the C57BL/J6 standard innate mouse strain, we composed preliminary matches and color named custom LI-COR preliminaries for nine equidistant SNP locales chose to be polymorphic crosswise over eight ingrained strains (C57BL/J6, BALB/c, AKR, DBA/2, A/J, C3H, RIIIS, I/LnJ) in the recognized QTL district. We have sequenced PCR-intensified SNP areas for the eight standard ingrained strains. We particularly sequenced areas encompassing SNPs rs29732770 and rs31562818, of which rs31562818 effectively distinguished the polymorphism in the eight strains. We plan to test our composed introductions on the staying seven SNP locales for every single innate strain to affirm polymorphisms over each of the eight strains. This will empower us to genotype the 110 MF1 mice utilizing the composed preliminaries to fine guide and distinguish the competitor gene(s) for the Lrp11 trans-eQTL on Chr5 locus. These outcomes ought to demonstrate useful for comprehension associations among the human LRP11 transgene, LRP11, and LDL levels. DNA ISOLATION AND QTL MAPPING DNA detached from 10 mg mouse spleen utilizing standard Qiagen DNeasy ® unit convention Focusing on beforehand recognized Lrp11 trans-eQTL applicant locale on mouse chromosome 5, somewhere around 78 and 81.5 Mbp, for fine mapping (Fig. 3) FINE MAPPING STRATEGY USING SNP MARKERS Isolating polymorphic SNPs in QTL area Confirm polymorphism crosswise over 8 innate strains, A/J, AKR, C57BL/J6, BALB/c, C3H/He, DBA/2J, RIIIS, I/LnJ utilizing the accompanying open assets: Mouse Genome Informatics MGI Database 5 Obtained base combine characters at SNP destinations SNPs in light of NCBI fabricate 37 get together Mouse Phenome Database 6 Obtained flanking successions BLAT (BLAST-like Alignment Tool) 7 Ensured grouping irregularity in genome Used entire genome BLAT Primer Design Primer3 8 Derived preliminaries, acquired softening temperatures and lengths (Tables 1,2) BLAT inquiry of groundworks 7 Ensured uniqueness of preliminary arrangements in genome Ensured that groundwork groupings were rationed crosswise over beginning 6 strains SEQUENCING SNP REGION FROM GENOMIC AND AMPLIFIED DNA Sequenced tests specifically from genomic DNA, and additionally PCR intensified SNP district DNA (Table 2) Sequenced PCR increased SNP areas utilizing LI - COR ® 4200 and 4300 DNA Analyzers (Fig. 5) PCR response performed utilizing Bio-Rad MyCycler™ thermocycler: 92.0 °C for 2 minutes; 30X: 92.0 °Cfor 0:30, 54.0°C for 0:30, 70.0°C for 1:00; 70°C for 1:00; 4.0°C hold Sequencing response utilized named custom IRDye700 groundworks 5.5% acrylamide gel utilizing KB Plus Gel Matrix, keep running for 8 hours Sequence sent out by means of e-Seq V3.0 in FASTA design and affirmed utilizing NCBI-BLAST Analyzed to find SNP destinations Fine Mapping of Lrp11 Trans - eQTL on Mouse Chromosome 5 Using SNP Markers INTRODUCTION Elevated levels of low-thickness lipoprotein (LDL) in people have been involved in atherosclerosis and coronary illness 1 . Low-thickness lipoprotein-related receptor protein 11 (Lrp11) on chromosome 10 controls LDL levels in mice through clathrin-intervened endocytosis 2,3 . A late study has recognized a trans-eQTL locus for Lrp11 expression on mouse Chr5. The hopeful locale distinguished ranges a 3.5 Mbp area (from 78Mbp to 81.5 Mbp on Chromosome 5). Moreover, Lrp11 displays homology to human and chimpanzee LRP11 on chromosome 6 3 . We are keen on fine mapping the area of the trans-eQTL by genotypping denser SNP markers inside the Chromosome 5 locus. To accomplish high-determination mapping, 110 mice of an industrially accessible outbred stock, MF1 (Harlan, Indianapolis, Indiana, USA), were utilized since they can be dealt with as a ultrafine mosaic of standard innate strains as portrayed in Yalcin et al 4 . The genome of MF1 mice looks like the hetergenous stock mice which were set up from 8 standard innate strains (C57BL/6, BALB/c, RIIIS, AKR, DBA/2, I/LnJ, A/J and C3H) in the 1970s (Fig. 1). All inclusive affiliation investigations of 1813 SNP markers, led by UCLA community analyst Dr. Anatole Ghazalpour, recognized a 3.5 Mbp quantitative quality locus (QTL) impacting Lrp11 expression levels (Fig. 2). The long haul point of this venture is to fine guide the Chr5 locus to locate the causal quality in this district. To this end, we have outlined groundworks for nine equidistant SNP locales (Fig. 3) utilizing eight innate strains and are PCR enhancing and sequencing the items. The LI-COR ® sequencer assumes a momentous part in our examination extend as far as checking the nearness of distributed SNPs in the diverse mouse strains (Fig. 4). So far, groundworks for nine markers have been intended for the eight ingrained strains. Taking after fruitful preparatory sequencing of SNP locales in ingrained mice, we will genotype SNP destinations of the 110 MF1 mice of the first QTL think about. It is assessed that roughly 62 keeps running on the LI-COR ® sequencer would be required to finish our exploration extend. Synopsis RESULTS Only PCR enhanced DNA utilizing unlabeled groundwork sets (Table 1) yielded sequencing signal. PCR preliminaries for rs31562818 indicated dependable flags after SNP area intensification (Fig. 4). DBA/2J demonstrated flawed enhancement. Staying seven strains demonstrated satisfactory enhancement. Polymorphisms for rs31562818 were effectively recognized utilizing LI-COR ® sequencing (Fig. 5). rs31562818 marker found in successions from AKR, RIII, A/J, C3H, BALB/c, and C57BL/J6. rs29732770 marker PCR intensification neglected to give an item for any of the 8 ingrained strains. Encourage upgrades of groundwork plan ought to empower fruitful PCR intensification and sequencing. Affirmations Special on account of Dr. Gaston Matthias-Udo Pfluegl and Karen Flummerfelt for their important mentorship, direction, direction, and specialized help, Drs. Anatole Ghazalpour and Aldons J. Lusis for all mouse DNA and QTL area information, and Kristin Toliver and Priya Thaker for their commitments to preliminary plan and sequencing. CONCLUSIONS REFERENCES DISCUSSION Based on the outcomes yielded hitherto, we will keep on testing the rest of the SNP areas for the eight ingrained strains. From that point, we will enhance, arrangement, and genotype SNP markers for the 110 MF1 mice. We plan to utilize genotype information to distinguish the causal variety for Lrp11. Affiliation investigation utilizing marker relapse will be utilized to decide SNPs most profoundly corresponded with the Lrp11 trans-eQTL. APPLICATIONS AND FUTURE RESEARCH Confirmation ponders utilizing Lrp11 transgenic or knockout innovation to approve the easygoing quality Study the atomic association between the causal quality on Chr 5 and Lrp11 To contemplate if the Chr5 in mouse influences LDL levels 1. Mill operator, M, Ginsberg, HN, and Schaefer, EJ. 2008. Relative atherogenicity and prescient estimation of non-high-thickness lipoprotein cholesterol for coronary illness. Am J Cardiol 101:1003-8. 2. Chung, NS and Wasan, KM. 2004. Potential part of the low-thickness lipoprotein receptor family as go betweens of cell medication take-up. Propelled Drug Delivery Reviews 56:1315-1334. 3. Recovered from "MGI_4.01: Gene Detail", April 2008 <http://www.informatics.jax.org/javawi2/servlet/WIFetch?page= markerDetail&key=84155>. 4. Yalcin et al. 2004. Hereditary Dissection of a behavioral quantitative quality locus demonstrates that Rgs2 tweaks nervousness in mice. Nature Genetics 36:1197-1202. 5. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, et al. 2007. The Mouse Genome Database (MGD): new components encouraging a model framework. Nucleic Acids Res 35(Database issue):D630-D637.6. 6. Bogue, MA, Grubb, SC, Maddatu, TP, Bult, CJ. 2007. Mouse Phenome Database (MPD). Nucleic Acids Res 35(Database issue):D643-9. 7. Kent, WJ. 2002. BLAT- - the BLAST-like alignmen

Recommended
View more...