Methods of identifying combinations of transcription factors
AssigneePresident and Fellows of Harvard College
InventorsHon Man Alex Ng, George M. Church, Parastoo Khoshakhlagh
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Abstract
Provided herein, in some embodiments, are methods and compositions for identifying combinations of transcription factors, for example, those involved in cell type conversion processes, such as cell differentiation.
Claims36
A method of identifying at least one transcription factor, comprising:
- (a) contacting cells that comprise a transposase with a population of nucleic acids, wherein each nucleic acid comprises a cargo element flanked by terminal repeat sequences that are recognized by the transposase,
- wherein each cargo element comprises
- (i) a first promoter operably linked to a first nucleotide sequence encoding a transcription factor and a barcode, and
- (ii) a terminator having a 5′ end,
- wherein the barcode uniquely identifies the transcription factor and is located within 100 nucleotides of the 5′ end of the terminator;
- (b) detecting differences in gene expression in the cells compared to control cells and identifying differentiated cells, wherein the differentiated cells have decreased expression of one or more stem cell markers compared to control cells;
- and
- (d) detecting one or more barcodes in the differentiated cells and identifying a transcription factor or a combination of transcription factors in the differentiated cells.
A population of nucleic acids, wherein each nucleic acid comprises a cargo element flanked by terminal repeat sequences that are recognized by a transposase,
- wherein the cargo element of each nucleic acid comprises:
- (a) a first promoter operably linked to a first nucleotide sequence encoding at least one transcription factor and a barcode;
- and
- (b) a terminator, and
- wherein the barcode uniquely identifies the transcription factor and is located within 100 nucleotides of the 5′ end of the terminator.
A population of cells, wherein each cell comprises a transposase and a nucleic acid that comprises a cargo element flanked by terminal repeat sequences that are recognized by a transposase,
- wherein the cargo element of each nucleic acid comprises:
- (a) a first promoter operably linked to a first nucleotide sequence encoding at least one transcription factor and a barcode;
- and
- (b) a terminator, and
- wherein the barcode uniquely identifies the transcription factor and is located within 100 nucleotides of the 5′ end of the terminator.
Dependencies are inferred from the claim text.