The Rockefeller University

Other

University of Vermont

The Rockfeller University

Envoy Therapeutics, Inc.

Nathaniel Heintz

Xiangdong W Yang

Weining Jiang

Andrew W Shyjan

Tito A Serafini

Michael K Skinner

Peter Model

John Gubbay

Paul Greengard

Anne Schaefer

Joseph Dougherty

Nicholas H Heintz

Joseph P Doyle

Julie M Miwa

Myriam Heiman

Lisa A Dailey

Mark S Caddle

Ines Ibanez-Tallon

Shiaoching Gong

Xiao Xu

Joseph D Dougherty

Joseph Pn Doyle

Methods and compositions are provided for translational profiling and molecular phenotyping of specific tissues, cells and cell subtypes of interest. The methods provided herein facilitate the analysis of gene expression in the selected subset present within a heterogeneous sample.

Methods and compositions for translational profiling and molecular phenotyping

The invention provides methods for isolating cell-type specific mRNAs by selectively isolating ribosomes or proteins that bind mRNA in a cell type specific manner, and, thereby, the mRNA hound to the ribosomes or proteins that bind mRNA. Ribosomes, which are riboprotein complexes, bind mRNA that is being actively translated in cells. According to the methods of the invention, cells are engineered to express a molecularly tagged ribosomal protein or protein that binds mRNA by introducing into the cell a nucleic acid comprising a nucleotide sequence encoding a ribosomal protein or protein that binds mRNA fused to a nucleotide sequence encoding a peptide tag. The tagged ribosome or mRNA binding protein can then be isolated, along with the mRNA bound to the tagged ribosome or mRNA binding protein, and the mRNA isolated and further used for gene expression analysis. The methods of the invention facilitate the analysis and quantification of gene expression in the selected cell type present within a heterogeneous cell mixture, without the need to isolate the cells of that cell type as a preliminary step.

Non human transgenic mammal comprising a transgene comprising a nucleotide sequence encoding a ribosomal protein fused to a peptide tag

The present invention provides a novel family of polypeptides which are ligand-gated channel receptor accessory molecules or ligands, denoted Lynx. This invention provides an isolated polypeptide comprising an amino acid sequence of a Lynx polypeptide in which the amino acid sequence is set forth in SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:15, including fragments, mutants, variants, analogs, homologs, or derivatives of the amino acid sequences set forth in SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:15. This invention further provides an isolated immunogenic polypeptide; an isolated nucleic acid; pharmaceutical compositions and diagnostic and therapeutic methods of use of the isolated polypeptides and nucleic acids of the present invention; assays for compounds which mimic, alter or inactivate the polypeptides of the present invention for use in therapy; and methods of isolating Lynx polypeptides and the nucleic acids encoding such polypeptides.

Lynx polypeptides

The invention provides methods and compositions for isolation and assessment of riboprotein complexes.

Method for isolating cell type-specific mRNAs

A simple method for modifying genes in a recombination deficient host cell is disclosed. Such modifications include generating insertions, deletions, substitutions, and/or point mutations at any chosen site in the independent origin based cloning vector. The modified gene is contained in an independent origin based cloning vector that is used to introduce a modified heterologous gene into a cell. Such a modified vector may be used in the production of a germline transmitted transgenic animal, or in gene targeting protocols in eukaryotic cells. In particular, high throughput methodology is provided for generating the modified the independent origin based cloning vectors of the present invention.

Methods of performing homologous recombination based modification of nucleic acids in recombination deficient cells and use of the modified nucleic acid products thereof

A method of efficiently sequencing multiple exons from complex genomic DNAs is disclosed. The methodology includes the use of bacterial and bacteriophage-derived artificial chromosomes (BBPACS) in novel gene trapping protocols. Targeted gene trapping by homologous recombination, and random gene trapping with the use of a transposon system are exemplified. Included in the invention are methods of preparing a gene map from BBPAC contigs, the resulting gene maps, methods of constructing a cDNA library from BBPAC contigs, and the resulting cDNA libraries.

Methods of performing gene trapping in bacterial and bacteriophage-derived artificial chromosomes and use thereof

A method of efficiently sequencing multiple exons from complex genomic DNAs is disclosed. The methodology includes the use of bacterial and bacteriophage-derived artificial chromosomes (BBPACs) in novel gene trapping protocols. Targeted gene trapping by homologous recombination, and random gene trapping with the use of a transposon system are exemplified. Included in the invention are methods of preparing a gene map from BBPAC contigs, the resulting gene maps, methods of constructing a cDNA library from BBPAC contigs, and the resulting cDNA libraries.

Methods of performing gene trapping in bacterial and

A simple method for modifying genes in a recombination deficient host cell is disclosed. Such modifications include generating insertion, deletions, substitutions, and/or point mutations at any chosen site in the independent origin based cloning vector. The modified gene can be contained in an independent origin based cloning vector that is used to introduce a modified heterologous gene into a cell. Such a modified vector may be used in the production of a germline transmitted transgenic animal, or in gene targeting protocols in eukaryotic cells.

Methods of performing homologous recombination based modification of

The present invention identifies cDNA collections enriched in genes regulated in prostate homeostasis, prostate regression, and in genes regulated in programmed cell death. These novel cDNA collections provide cDNAs that encode proteins that are either unique to general programmed cell death or unique to prostate regression. These transcripts can be used as markers to screen, monitor and/or to diagnose diseased conditions including prostate cancer. In addition, these cDNA collections can be used in methods of designing novel therapeutic agents useful for treating prostate cancer. Methods of making these collections through subtraction hybridization are described.

CDNA collections encoding proteins regulated during programmed cell

The present invention identifies cDNA collections enriched in genes regulated in prostate homeostasis, prostate regression, and in genes regulated in programmed cell death. These novel cDNA collections provide cDNAs that encode proteins that are either unique to general programmed cell death or unique to prostate regression. These transcripts can be used as markers to monitor and/or to diagnose diseased conditions. Methods of making these collections through subtraction hybridization are described.

A replication initiator protein complex for eukaryotic cells is disclosed which includes protein fractions of about 60 kD and 100 kD size. The protein complex comprises a protein in purified form that is capable of origin-specific DNA binding and ATP-dependent DNA helicase activity. The 60 kD fraction is named RIP60 and is primarily active in origin-specific DNA binding. The 100 kD fraction is named RIP100 and is primarily active as a DNA helicase. The protein complex and its fractions are active only during S phase and thereby commend their investigation and use toward the development of specific diagnostic and therapeutic modalities against pathogens to which cell division is critical. Diagnostic and therapeutic utilities are accordingly proposed, and testing procedures, materials in kit form, recombinant materials and procedures, and pharmaceutical compositions are likewise set forth.

Growing community of inventors

Pelham Manor, NY, United States of America

Nathaniel Heintz