METHOD FOR DETECTING CELLS
First Claim
1. A method for detecting the chromatin state of a cell comprisinga) contacting a sample containing cells with a first antibody capable of specifically binding to a histone protein,b) contacting the antibody:
- histone complex formed in step a) with a secondary antibody having at least one photoswitchable fluorophore adapted to be optically excited at a certain wavelength λ
2 and to emit light at a wavelength λ
2 different from λ
2,c) recording a super resolution image of nucleosome organization by means of a sensor being sensitive at least to the wavelength of emission of the photoswitchable fluorophore by exciting the sample with an optical radiation having a wavelength λ
2,d) correlating the image obtained in step c) with size of nucleosomal clutches, nucleosomal density and/or number of nucleosomes per nucleosomal clutches, ande) comparing data obtained in step d) with a corresponding reference value to obtain a score based on size of nucleosomal clutches, nucleosomal density and/or number of nucleosomes per nucleosomal clutch,wherein if the cell comprises smaller clutches, less densely compacted nucleosomes or less nucleosomes per clutches compared to the corresponding reference value then it is indicative that said cell is in an open chromatin state and wherein if the cell comprises bigger clutches, more densely compacted nucleosomes or more nucleosomes per clutches compared to the corresponding reference value then it is indicative that said cell is in a closed chromatin state.
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Abstract
The present invention relates to methods for detecting the chromatin state of a cell based on recording a super resolution image of nucleosome organization and correlating said imaged with size of nucleosomal clutches, nucleosomal density and/or number of nucleosomes per nucleosomal clutches. Additionally, the invention relates to a kit comprising a first antibody capable of specifically binding to a histone protein and a photo switchable fluorophore linked-secondary antibody and the use of the kit of the invention for detecting the chromatin state of a cell and isolating a cell in an open chromatin state or in a close chromatin state. The invention also relates to a device adapted to detect the chromatin state of a cell.
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Citations
19 Claims
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1. A method for detecting the chromatin state of a cell comprising
a) contacting a sample containing cells with a first antibody capable of specifically binding to a histone protein, b) contacting the antibody: - histone complex formed in step a) with a secondary antibody having at least one photoswitchable fluorophore adapted to be optically excited at a certain wavelength λ
2 and to emit light at a wavelength λ
2 different from λ
2,c) recording a super resolution image of nucleosome organization by means of a sensor being sensitive at least to the wavelength of emission of the photoswitchable fluorophore by exciting the sample with an optical radiation having a wavelength λ
2,d) correlating the image obtained in step c) with size of nucleosomal clutches, nucleosomal density and/or number of nucleosomes per nucleosomal clutches, and e) comparing data obtained in step d) with a corresponding reference value to obtain a score based on size of nucleosomal clutches, nucleosomal density and/or number of nucleosomes per nucleosomal clutch, wherein if the cell comprises smaller clutches, less densely compacted nucleosomes or less nucleosomes per clutches compared to the corresponding reference value then it is indicative that said cell is in an open chromatin state and wherein if the cell comprises bigger clutches, more densely compacted nucleosomes or more nucleosomes per clutches compared to the corresponding reference value then it is indicative that said cell is in a closed chromatin state. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19)
identifying connected regions of pixels representing values higher than the predefined threshold, for each connected region, providing a list of clutch positions by grouping the localization coordinates within said connected region according to a distance-based criterion being the position of the clutch the centroid position of the localization coordinates associated with said clutch.
- histone complex formed in step a) with a secondary antibody having at least one photoswitchable fluorophore adapted to be optically excited at a certain wavelength λ
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9. The method according to claim 8, wherein the size of each clutch is calculated as a measure of the spreading of the positions of all the localization coordinates associated with said clutch and/or the number of nucleosomes within said clutch.
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10. The method according to claim 8, wherein the density of nucleosomes within a clutch calculated as the number of nucleosomes within that clutch divided by the area occupied by said clutch.
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11. The method according to claim 1, wherein the histone protein is H2B.
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12. A method for isolating a cell in an open chromatin state comprising
a) detecting the chromatin state of a cell by a method according to claim 1, and b) isolating a cell having smaller clutches, less densely compacted nucleosomes or less nucleosomes per clutches. -
13. The method for isolating a cell in an open chromatin state according to claim 12 wherein the cell in an open chromatin state is selected from the group consisting of transcriptionally active cell, pluripotent cell, cancer cell and drug-perturbed cell.
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14. The method for isolating a cell in a close chromatin state
a) detecting the chromatin state of the cell by a method according to claim 1, and b) isolating a cell having bigger clutches, more densely compacted nucleosomes or more nucleosomes per clutches. -
18. A device adapted to detect the chromatin state of a cell comprising
a source of optical radiation adapted to emit light at a wavelength, over an interrogation area adapted to receive a biological sample, an optical sensor sensible to a second wavelength adapted to measure the optical radiation at λ -
2,
a control unit connected to the optical sensor and to the source of optical radiation wherein said control unit is adapted to carry out the method according to claim 1.
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2,
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19. A device adapted to detect the chromatin state of a cell comprising
a first source of optical radiation adapted to emit light at a wavelength λ -
2 over an interrogation area adapted to receive a biological sample,
a further second source of optical radiation adapted to emit light at a wavelength λ
2 over an interrogation area adapted to receive a biological sample,an optical sensor sensible to a second wavelength λ
2 adapted to measure the optical radiation at λ
2,a control unit connected to the optical sensor and to the first and to the second source of optical radiation wherein said control unit is adapted to carry out the method according to claim 3.
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2 over an interrogation area adapted to receive a biological sample,
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2. The method according to claim wherein the cell in an open chromatin state is selected from the group consisting of a transcriptionally active cell, a pluripotent stem cell, a cancer cell and a drug perturbed cell.
- 15. A kit comprising a first antibody capable of specifically binding to a histone protein and a photoswitchable fluorophore linked-secondary antibody.
Specification