New England Biolabs, Inc.

Sriharsa Pradhan

George R Feehery

Pierre O Esteve

Hang-Gyeong Chin

Jurate Bitinaite

Chaithanya Ponnaluri

Fiona Stewart

James McFarland

Yu Brian Zheng

Shuang-Yong Xu

Geoffrey G Wilson

Richard J Roberts

Ming-Qun Xu

Romualdas Vaisvila

Ivan R Correa, Jr

Donald G Comb

Christopher J Noren

Elisabeth A Raleigh

Nan Dai

Luo Sun

Henry P Paulus

Lixin Chen

Thomas C Evans

Devora Cohen-Karni

Guoqiang Zhang

Inca Ghosh

Hang Gyeong Chin

Vishnu Udayakumaran Nair Sunitha Kumary

Julie Beaulieu

Pierre Olivier Esteve

Provided herein, among other things, are various compositions and methods for analyzing chromatin. In some embodiments, the composition may comprise a mixture of a nicking enzyme, four dNTPs, at least one labeled dNTP and, optionally, a polymerase. In some embodiments, this method may comprise: obtaining a sample comprising chromatin, reacting the sample with the composition to selectively label the open chromatin in the sample, and analyzing the labeled sample.

Analysis of chromatin using a nicking enzyme

Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided that may be used for binding to a target directly or via an antibody that binds to the target. The target may be a protein or structural feature of the DNA and its presence and location may correspond to a phenotype and/or pathology in a biopsy or other cell sample for diagnostic purposes. The background is reduced by the addition of a glycoaminoglycan (GAG) that reversibly inhibits binding of the NEFP to DNA. Nick translation in the presence of a strand displacing polymerase enables the incorporation of tagged nucleotides that (i) blocks re-nicking; (ii) facilitates immobilization of DNA fragments around the target for sequencing; and/or (iii) enables dye labelling of the chromosomal DNA within the cell nuclei for analysis by microscopy.

Compositions and methods for detecting molecular targets on chromosomal DNA

RNA molecules inhibiting a DNMT and methods and compositions incorporating or generating the RNA molecules are described.

DNMT inhibitors

Nucleic acids comprising &#x3b2;-glucosaminyloxy-5-methylcytosine; compositions, kits and methods of producing the nucleic acids using a glycosyltransferase; and methods of using the nucleic acids are described.

Compositions and methods for the transfer of a hexosamine to a modified nucleotide in a nucleic acid

Compositions and methods are provided for enriching mitochondrial DNA and optionally chloroplast DNA from eukaryotic cells in a simple rapid method that provides greater than 100 fold enrichment. Affinity protein-coated substrate in a buffer is used to efficiently bind chromosomal DNA and thereby remove it from the buffer. Mitochondrial sequencing reads reveal that non-biased sequence selection providing representation of a substantial proportion of mitochondrial DNA in the eukaryotic cells analyzed.

Methods and compositions for enriching either target polynucleotides or non-target polynucleotides from a mixture of target and non-target polynucleotides

Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modifying enzymes together with site-specific endonucleases to detect the hmNs.

Detection and quantification of hydroxymethylated nucleotides in a polynucleotide preparation

Compositions and methods are provided for enriching non-target polynucleotides from a mixture of non-target and target polynucleotides where differences between the target polynucleotides and the non-target polynucleotides include the extent of modified bases that are present in a greater density in the target polynucleotides than in the non-target polynucleotides. This permits the target polynucleotides to be selectively and rapidly bound to an affinity matrix such as affinity protein-coated magnetic beads providing enrichment of the non-target polynucleotides in the supernatant. One use of this enrichment is to remove human genomic DNA from a mixture of DNAs obtained from human tissue samples to enrich for polynucleotides in a microbiome so as to characterize the microbiome by DNA sequencing.

Compositions and methods are provided for facilitating the enrichment of single-stranded DNA containing methylated CpG in a mixture containing methylated and unmethylated DNA. The compositions relate to methylation-binding protein domains that selectively bind to methylated single strand DNA. In embodiments of the invention, the methylated DNA is eluted in 0.4M-0.6M NaCl while the unmethylated single strand DNA is eluted in less than 0.4M salt. The ability to readily enrich for methylated DNA permits high throughput sequencing of the methylated DNA and identification of abnormal methylation patterns associated with disease.

Method for enriching methylated CpG sequences

A new type of transgene system is disclosed which allows efficient protein expression in a target host such as a plant, but avoids the undesirable result of the migration of the transgene into related host system and/or to the environment via the pollen. The methods described herein may also be applied to the expression of virtually any protein of interest (e.g. a toxic protein) in eukaryotic (yeast, insect, mammalian cells, etc.) and prokaryotic (, etc.) organisms.

Method for generating split, non-transferable genes that are able to express an active protein product

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Wenham, MA, United States of America

Sriharsa Pradhan