Methods of determining subcellular localization of nucleic acids, including RNA and DNA are described. In particular, the invention relates to a method combining proximity-specific labeling with crosslinking of nucleic acids to proteins and sequencing to identify nucleic acids within or near a particular subcellular compartment in vivo.

Methods of determining subcellular localization of nucleic acids, including RNA and DNA are described. In particular, the invention relates to a method combining proximity-specific labeling with crosslinking of nucleic acids to proteins and sequencing to identify nucleic acids within or near a particular subcellular compartment in vivo.

Provided herein is a method and system for analyzing a sample. In some embodiments the method makes use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, wherein each of the labeled nucleic acid probes specifically hybridizes with only one of the oligonucleotides. The sample is labeled with the capture agents en masse, and sub-sets of the capture agents are detected using iterative cycles using corresponding subsets of the labeled nucleic acid probes.

Provided herein is a method and system for analyzing a sample. In some embodiments the method makes use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, wherein each of the labeled nucleic acid probes specifically hybridizes with only one of the oligonucleotides. The sample is labeled with the capture agents en masse, and sub-sets of the capture agents are detected using iterative cycles using corresponding subsets of the labeled nucleic acid probes.

Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

Disclosed are methods for identifying a nucleic acid (e.g., RNA, DNA, etc.) motif which interacts with a ligand. The method includes providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support; contacting the plurality of immobilized ligands with a nucleic acid motif library under conditions effective for one or more members of the nucleic acid motif library to bind with the immobilized ligands; and identifying members of the nucleic acid motif library that are bound to a particular immobilized ligand. Also disclosed are methods for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, as well as methods for identifying a nucleic acid which interacts with a ligand.

The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample; the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample; the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxymethylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample. Compositions, kits, and related methods are also provided, including an embodiment in which truncated sequencing adapters are used in conjunction with barcoded PCR primers.

The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample; the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample; the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxymethylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample. Compositions, kits, and related methods are also provided, including an embodiment in which truncated sequencing adapters are used in conjunction with barcoded PCR primers.

The present invention provides a novel modified protein which is to be used, as a novel detection tool relating to gene expression, for detecting a chromatin open structure more easily at a higher sensitivity than by the conventional technique. The present invention relates to: a nucleic acid binding fluorescent protein, said protein containing a DNA binding domain in which 3 or more TAL-repeats are repeatedly connected, characterized by binding independently from base sequences; and a method for fluorescent labeling of an open chromatin in a vital cell, said method comprising a step for transferring a gene encoding a nucleic acid binding protein into the vital cell, characterized in that the nucleic acid binding protein is a protein comprising a DNA binding domain, in which 3 or more TAL-repeats are repeatedly connected, and a fluorescent protein directly or indirectly bound thereto and the DNA binding domain binds to a nucleic acid independently from base sequences.

The present invention provides a novel modified protein which is to be used, as a novel detection tool relating to gene expression, for detecting a chromatin open structure more easily at a higher sensitivity than by the conventional technique. The present invention relates to: a nucleic acid binding fluorescent protein, said protein containing a DNA binding domain in which 3 or more TAL-repeats are repeatedly connected, characterized by binding independently from base sequences; and a method for fluorescent labeling of an open chromatin in a vital cell, said method comprising a step for transferring a gene encoding a nucleic acid binding protein into the vital cell, characterized in that the nucleic acid binding protein is a protein comprising a DNA binding domain, in which 3 or more TAL-repeats are repeatedly connected, and a fluorescent protein directly or indirectly bound thereto and the DNA binding domain binds to a nucleic acid independently from base sequences.