Provided are a method for analyzing the methylation status of at least one target sequence in a sample including providing a sample comprising DNA, wherein the DNA comprises at least one target sequence; contacting the sample with at least one methyltransferase that methylates non-cytosine nucleotides; and assaying the sample for the methylation status of one or more cytosine nucleotides in the at least one target sequence, and other related methods.

Provided are a method for analyzing the methylation status of at least one target sequence in a sample including providing a sample comprising DNA, wherein the DNA comprises at least one target sequence; contacting the sample with at least one methyltransferase that methylates non-cytosine nucleotides; and assaying the sample for the methylation status of one or more cytosine nucleotides in the at least one target sequence, and other related methods.

The present invention relates to methods and kits for preserving genomic DNA sequence complexity within chemically and/or enzymatically converted DNA by an enzyme or series of enzymes that adds a methyl group to a cytosine outside of CpG dinucleotide sequences of genomic DNA. Further, the present invention relates to methylation analysis of the genomic DNA.

The present invention relates to methods and kits for preserving genomic DNA sequence complexity within chemically and/or enzymatically converted DNA by an enzyme or series of enzymes that adds a methyl group to a cytosine outside of CpG dinucleotide sequences of genomic DNA. Further, the present invention relates to methylation analysis of the genomic DNA.

The present invention relates to targeted conversion of alpha-hydroxyalkylated residues in biomolecules in the presence of a directing methyltransferase, namely to targeted removal of the alpha-hydroxyalkyl moieties to give unmodified residues, or targeted derivatization of the alpha-hydroxyalkyl groups by covalent coupling of non-cofactor compounds represented by formula HQ-LX, wherein X represents a functional group or a reporter group attached via a linker moiety L, and QH is selected from HS, HSe, HOH.sub.2N, HN.sub.3 or HCN in the presence of a directing methyltransferase. Further development of the method of targeted conversion comprises methods for targeted labeling a biomolecule and method for detecting hydroxymethylated target sites in a biomolecule according to the present invention.

The present invention relates to targeted conversion of alpha-hydroxyalkylated residues in biomolecules in the presence of a directing methyltransferase, namely to targeted removal of the alpha-hydroxyalkyl moieties to give unmodified residues, or targeted derivatization of the alpha-hydroxyalkyl groups by covalent coupling of non-cofactor compounds represented by formula HQ-LX, wherein X represents a functional group or a reporter group attached via a linker moiety L, and QH is selected from HS, HSe, HOH.sub.2N, HN.sub.3 or HCN in the presence of a directing methyltransferase. Further development of the method of targeted conversion comprises methods for targeted labeling a biomolecule and method for detecting hydroxymethylated target sites in a biomolecule according to the present invention.

Provided herein are methods of analyzing DNA molecules in a sample (e.g., including identifying methylated and hydroxymethylated cytosine positions), the DNA molecules comprising first and second strands and asymmetric adapters, the method comprising: synthesizing first complementary strands which are complementary to the first strands and second complementary strands which are complementary to the second strands; optionally glucosylating a 5-hydroxymethylated cytosine in at least one first or second strand before or after synthesizing the first and second complementary strands; methylating a cytosine in at least one first complementary strand or second complementary strand, wherein the methylation converts a hemimethylated CpG to a fully methylated CpG; deaminating an unmodified cytosine in at least one first or second strand, thereby producing treated DNA molecules; and sequencing at least a portion of the treated DNA molecules; optionally wherein the asymmetric adapters are Y-shaped adapters or bubble adapters.

Provided herein are methods of analyzing DNA molecules in a sample (e.g., including identifying methylated and hydroxymethylated cytosine positions), the DNA molecules comprising first and second strands and asymmetric adapters, the method comprising: synthesizing first complementary strands which are complementary to the first strands and second complementary strands which are complementary to the second strands; optionally glucosylating a 5-hydroxymethylated cytosine in at least one first or second strand before or after synthesizing the first and second complementary strands; methylating a cytosine in at least one first complementary strand or second complementary strand, wherein the methylation converts a hemimethylated CpG to a fully methylated CpG; deaminating an unmodified cytosine in at least one first or second strand, thereby producing treated DNA molecules; and sequencing at least a portion of the treated DNA molecules; optionally wherein the asymmetric adapters are Y-shaped adapters or bubble adapters.

Methods, compositions and kits are provided to amplify an amount of genomic methylated DNA that can be subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

Methods, compositions and kits are provided to amplify an amount of genomic methylated DNA that can be subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.