SR-BI nucleic acids and uses therefor

Abstract

The present invention is based at least in part on the discovery of the genomic structure of the human SR-BI gene and on the identification of polymorphic regions within the gene. Accordingly, the invention provides nucleic acids having a nucleotide sequence of an allelic variant of an SR-BI gene and nucleic acids having an SR-BI intronic sequence. The invention also provides methods for identifying specific alleles of polymorphic regions of an SR-BI gene, methods for determining whether a subject has or is at risk of developing a disease which is associated with a specific allele of a polymorphic region of an SR-BI gene, and kits for performing such methods.

What is claimed is:  
     
         1 . An isolated nucleic acid comprising an intronic sequence of an SR-BI gene.  
     
     
         2 . An isolated nucleic acid of  claim 1 , wherein the SR-BI gene is a mammalian gene.  
     
     
         3 . An isolated nucleic acid of  claim 2 , wherein the SR-BI gene is a human gene.  
     
     
         4 . An isolated nucleic acid of  claim 1  comprising an intron/exon border.  
     
     
         5 . An isolated nucleic acid of  claim 1 , wherein the intronic sequence comprises a nucleotide sequence of intronic sequences of FIG. 2 or any of SEQ ID Nos. 1-121, or complements thereof or homologs thereof.  
     
     
         6 . An isolated nucleic acid of  claim 1 , which is capable of hybridizing under an appropriate stringency to an intron of an SR-BI gene comprising an intronic nucleotide sequence or FIG. 2 or any of SEQ ID Nos. 1-121 or complements thereof or homologs thereof.  
     
     
         7 . An isolated nucleic acid of  claim 1 , further comprising at least a portion of an exon.  
     
     
         8 . An isolated nucleic acid of  claim 1 , comprising from about 15 to about 30 nucleotides.  
     
     
         9 . An isolated nucleic acid of  claim 1 , comprising at least about 31 nucleotides.  
     
     
         10 . An isolated nucleic acid of  claim 8 , comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 41 to SEQ ID NO: 64, SEQ ID NO: 83 to SEQ ID NO: 84, and SEQ ID NO: 89-94.  
     
     
         11 . An isolated nucleic acid of  claim 1 , which is single stranded.  
     
     
         12 . An isolated nucleic acid of  claim 1 , which further comprises a label.  
     
     
         13 . An isolated nucleic acid, comprising an allelic variant of a polymorphic region of an SR-BI gene, which allelic variant differs from the allelic variant set forth in SEQ ID NO: 1 or 3.  
     
     
         14 . An isolated nucleic acid of  claim 13 , wherein the polymorphic region is located in an exon.  
     
     
         15 . An isolated nucleic acid of  claim 14 , wherein the exon is exon 8.  
     
     
         16 . An isolated nucleic acid of  claim 15 , wherein the allelic variant comprises a nucleotide sequence set forth in SEQ ID NO: 65.  
     
     
         17 . An isolated nucleic acid of  claim 13 , wherein the polymorphic region is located in an intron.  
     
     
         18 . An isolated nucleic acid of  claim 17 , wherein the intron is intron 5.  
     
     
         19 . An isolated nucleic acid of  claim 18 , wherein the allelic variant comprises a nucleotide sequence set forth in SEQ ID NO: 66.  
     
     
         20 . An isolated intronic nucleic acid sequence of a genomic DNA sequence comprising an SR-BI gene, wherein the intronic nucleic acid sequence comprises a nucleotide sequence of any of SEQ ID NO: 18-40, SEQ ID NO: 66, or SEQ ID NO: 97.  
     
     
         21 . A kit for amplifying, and/or for determining the molecular structure of, at least a portion of an SR-BI gene, comprising a probe or primer which is capable of hybridizing to an SR-BI gene and instructions for use.  
     
     
         22 . A kit of  claim 21 , wherein the SR-BI gene is a human SR-BI gene.  
     
     
         23 . A kit of  claim 21 , wherein the probe or primer is capable of hybridizing to an SR-BI intron.  
     
     
         24 . A kit of  claim 23 , wherein the SR-BI intron comprises a nucleotide sequence of intronic sequences of FIG. 2 or any of SEQ ID Nos. 1-121, or complements thereof or homologs thereof.  
     
     
         25 . A kit of  claim 21 , wherein the homolog is an allelic variant.  
     
     
         26 . A kit of  claim 21 , wherein the probe or primer is capable of hybridizing to a nucleic acid comprising an intron/exon border of an SR-BI gene.  
     
     
         27 . A kit of  claim 21 , wherein the probe or primer is capable of hybridizing to an allelic variant of a polymorphic region of an SR-BI gene, and wherein the allelic variant differs from the allelic variant set forth in SEQ ID NO: 1 or 3.  
     
     
         28 . A kit of  claim 27 , wherein the polymorphic region is located in an exon.  
     
     
         29 . A kit of  claim 28 , wherein the exon is exon 8.  
     
     
         30 . A kit of  claim 29 , wherein the allelic variant of a polymorphic region has a nucleotide sequence set forth in SEQ ID NO: 65.  
     
     
         31 . A kit of  claim 27 , wherein the polymorphic region is located in an intron.  
     
     
         32 . A kit of  claim 31 , wherein the intron is intron 5.  
     
     
         33 . A kit of  claim 32 , wherein the allelic variant of a polymorphic region has a nucleotide sequence set forth in SEQ ID NO: 66.  
     
     
         34 . A kit of  claim 21 , further comprising a second probe or primer.  
     
     
         35 . A kit of  claim 21 , wherein the probe or primer has a nucleotide sequence from about 15 to about 30 nucleotides.  
     
     
         36 . A kit of  claim 35 , wherein the probe or primer comprises a nucleotide sequence selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID Nos 41-64, SEQ ID Nos 67-82, SEQ ID Nos 83-84, SEQ ID Nos. 89-94, and SEQ ID Nos 98-121.  
     
     
         37 . A kit of  claim 36 , wherein the kit has two primers selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID Nos. 41-64, SEQ ID Nos. 83-84, and SEQ ID Nos. 89-94.  
     
     
         38 . A kit of  claim 21 , wherein the probe or primer is a single stranded nucleic acid.  
     
     
         39 . A kit of  claim 21 , wherein the probe or primer is labeled.  
     
     
         40 . A kit of  claim 21 , wherein determining the molecular structure of at least a portion of an SR-BI gene is determining the identity of the allelic variant of a polymorphic region.  
     
     
         41 . A kit of  claim 40  for determining whether a subject has, or is at risk of developing, a disease or condition associated with a specific allelic variant of the polymorphic region of an SR-BI gene.  
     
     
         42 . A kit of  claim 41 , wherein the disease or condition is characterized by an aberrant SR-BI activity.  
     
     
         43 . A kit of  claim 42 , therein the aberrant SR-BI activity is an aberrant SR-BI protein level.  
     
     
         44 . A kit of  claim 42 , wherein the aberrant SR-BI activity is an aberrant expression of an SR-BI gene.  
     
     
         45 . A kit of  claim 41 , wherein the disease or condition is abnormal lipid metabolism, inappropriate lipid levels, a cardiovascular disease, atherosclerosis, gallstone formation, or an abnormal body mass index.  
     
     
         46 . A kit of  claim 40 , which is for use in selecting the appropriate drug to administer to a subject to treat a disease or condition.  
     
     
         47 . A kit of  claim 46 , wherein the disease or condition is abnormal lipid metabolism, inappropriate lipid levels, a cardiovascular disease, atherosclerosis, gallstone formation, or an abnormal body mass index.  
     
     
         48 . A kit of  claim 21 , wherein determining the molecular structure comprises determining the identity of at least one nucleotide.  
     
     
         49 . A kit for determining whether a subject is at risk of developing a disease or condition characterized by an abnormal SR-BI activity, comprising a probe or primer which is capable of hybridizing to an SR-BI gene and instructions for use.  
     
     
         50 . A method for determining the identity of the allelic variant of a polymorphic region of an SR-BI gene in a nucleic acid obtained from a subject, comprising contacting a sample nucleic acid comprising an SR-BI gene sequence with a probe or primer having a sequence which is complementary to an SR-BI gene sequence, to thereby determine the identity of the allelic variant.  
     
     
         51 . A method of  claim 50 , wherein the probe or primer is capable of hybridizing to an SR-BI intron.  
     
     
         52 . A method of  claim 50 , wherein the probe or primer is capable of hybridizing to an allelic variant of a polymorphic region, and wherein the allelic variant differs from the allelic variant set forth in SEQ ID NO: 1 or 3.  
     
     
         53 . A method of  claim 50 , wherein determining the the identity of the allelic variant comprises determining the identity of at least one nucleotide of the polymorphic region.  
     
     
         54 . A method of  claim 50 , wherein determining the identity of the allelic variant consists of determining the nucleotide content of the polymorphic region.  
     
     
         55 . A method of  claim 54 , wherein determining the nucleotide content comprises sequencing the nucleotide sequence.  
     
     
         56 . A method of  claim 50 , wherein determining the identity of the allelic variant comprises performing a restriction enzyme site analysis.  
     
     
         57 . A method of  claim 50 , wherein determining the identity of the allelic variant is carried out by single-stranded conformation polymorphism.  
     
     
         58 . A method of  claim 50 , wherein determining the identity of the allelic variant is carried out by allele specific hybridization.  
     
     
         59 . A method of  claim 50 , wherein determining the identity of the allelic variant is carried out by primer specific extension.  
     
     
         60 . A method of  claim 50 , wherein determining the identity of the allelic variant is carried out by an oligonucleotide ligation assay.  
     
     
         61 . A method of claim,  50 , wherein the SR-BI gene is a human SR-BI gene.  
     
     
         62 . A method of  claim 50 , wherein the probe or primer has a nucleotide sequence from about 15 to about 30 nucleotides.  
     
     
         63 . A method of  claim 62 , wherein the probe or primer is selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID Nos. 1-121 or complement thereof.  
     
     
         64 . A method of  claim 63 , wherein the method comprises hybridizing the sample nucleic acid with two primers selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID Nos. 41-64, SEQ ID Nos. 83-84, or SEQ ID Nos. 89-94.  
     
     
         65 . A method of  claim 50 , wherein the probe or primer is a single stranded nucleic acid.  
     
     
         66 . A method of  claim 50 , wherein the probe or primer is labeled.  
     
     
         67 . A method of  claim 50 , wherein the probe or primer is capable of hybridizing to an intron/exon border of an SR-BI gene.  
     
     
         68 . A method of  claim 50  for determining whether a subject has, or is at risk of developing, a disease associated with a specific allelic variant of a polymorphic region in the human SR-BI gene.  
     
     
         69 . A method of  claim 68 , wherein the disease or condition is characterized by an aberrant SR-BI activity.  
     
     
         70 . A method of  claim 69 , wherein the aberrant SR-BI activity is an aberrant SR-BI protein level.  
     
     
         71 . A method of  claim 70 , wherein the aberrant SR-BI activity is an aberrant expression of an SR-BI gene.  
     
     
         72 . A method of  claim 68 , wherein the disease or condition is an abnormal lipid metabolism, inappropriate lipid levels, a cardiovascular disease, atherosclerosis, gallstone formation or an abnormal body mass index.  
     
     
         73 . A method of  claim 68 , wherein the polymorphism is located in an exon.  
     
     
         74 . A method of  claim 73 , wherein the polymorphism is located in exon 8.  
     
     
         75 . A method of  claim 68 , wherein the polymorphism is located in an intron.  
     
     
         76 . A method of  claim 75 , wherein the polymorphism is located in intron 5.  
     
     
         77 . A method of  claim 68 , for use in selecting the appropriate drug to administer to a subject to treat a disease.  
     
     
         78 . A method of  claim 77 , wherein the disease or condition is abnormal lipid metabolism, inappropriate lipid levels, a cardiovascular disease, atherosclerosis, gallstone formation, or an abnormal body mass index.  
     
     
         79 . A method for selecting the appropriate drug to administer to an individual having a disease or condition, comprising determining the molecular structure of at least a portion of the SR-BI gene of the individual.  
     
     
         80 . A method of  claim 79 , wherein determining the molecular structure is determining the identity of the allelic variant of at least one polymorphic region of the SR-BI gene of the individual.  
     
     
         81 . A method of  claim 80 , wherein the disease or condition is abnormal lipid metabolism, inappropriate lipid levels, a cardiovascular disease, atherosclerosis, gallstone formation, or an abnormal body mass index.  
     
     
         82 . A method for treating a subject having a disease or condition associated with a specific allelic variant of a polymorphic region of an SR-BI gene, comprising 
 (a) determining the identity of the allelic variant; and    (b) administering to the subject a compound that compensates the effect of the specific allelic variant.    
     
     
         83 . A method of  claim 82 , wherein the polymorphic region is located in an exon.  
     
     
         84 . A method of  claim 82 , wherein the polymorphic region is located in an intron.  
     
     
         85 . A method of  claim 82 , wherein the specific allelic variant is a mutant allele.  
     
     
         86 . A method of  claim 82  wherein the polymorphic region is located in a promoter region.  
     
     
         87 . A method of  claim 82 , wherein the specific allelic variant is associated with an aberrant SR-BI activity.  
     
     
         88 . A method of  claim 87 , wherein the aberrant SR-BI activity is an aberrant SR-BI protein level.  
     
     
         89 . A method of  claim 87 , wherein the aberrant SR-BI protein level results from an aberrant splicing of an SR-BI pre-mRNA.  
     
     
         90 . A method of  claim 87 , wherein the aberrant SR-BI activity is an aberrant expression of the SR-BI gene.  
     
     
         91 . A method of  claim 82  wherein the compound modulates SR-BI protein levels.  
     
     
         92 . A method of  claim 82 , wherein the compound is selected from the group consisting of a nucleic acid, a protein, or a small molecule.  
     
     
         93 . A method of  claim 92 , wherein the protein is an SR-BI protein.  
     
     
         94 . An isolated nucleic acid of  claim 14 , wherein the exon is exon 1.  
     
     
         95 . An isolated nucleic acid of  claim 94 , wherein the allelic variant comprises a nucleotide sequence set forth in SEQ ID NO: 95.  
     
     
         96 . An isolated nucleic acid of  claim 14 , wherein the exon is exon 3.  
     
     
         97 . An isolated nucleic acid of  claim 96 , wherein the allelic variant comprises a nucleotide sequence set forth in SEQ ID NO: 96.  
     
     
         98 . An isolated nucleic acid of  claim 17 , wherein the intron is intron 10.  
     
     
         99 . An isolated nucleic acid of  claim 98 , wherein the allelic variant comprises a nucleotide sequence set forth in SEQ ID NO: 97.  
     
     
         100 . A kit of  claim 28 , wherein the exon is exon 1.  
     
     
         101 . A kit of  claim 100 , wherein the allelic variant of a polymorphic region has a nucleotide sequence set forth in SEQ ID NO: 95.  
     
     
         102 . A kit of  claim 28 , wherein the exon is exon 3.  
     
     
         103 . A kit of  claim 102 , wherein the allelic variant of a polymorphic region has a nucleotide sequence set forth in SEQ ID NO: 96.  
     
     
         104 . A kit of  claim 31 , wherein the intron is intron 10.  
     
     
         105 . A kit of  claim 104 , wherein the allelic variant of a polymorphic region has a nucleotide sequence set forth in SEQ ID NO: 97.