In Situ Chromatin Interaction Mapping Across Tissue Sections
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Solution Overview
Problem
Existing methods fail to analyze chromatin interaction events in situ with spatial resolution across a tissue section, hindering the understanding of regulatory element interactions and their role in gene regulation.
Innovation Solution
A method involving the use of probes that hybridize to specific chromatin regions, forming bridged or circular probes to detect chromatin interaction events, followed by amplification and detection to analyze chromatin interactions in situ.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional chromatin interaction methods are used, then chromatin interactions can be detected, but spatial resolution across tissue sections cannot be achieved
Solution Approach 1:
The method segments the detection process into distinct stages: (1) in situ hybridization of probes to chromatin regions in fixed tissue sections, (2) ligation of probe ends to form circularized probes only when chromatin regions are in proximity, and (3) amplification and detection of circularized probes. This segmentation enables spatial resolution by maintaining tissue architecture while detecting chromatin interactions.
Solution Approach 2:
The invention transitions from analyzing chromatin interactions in one dimension (linear DNA sequence) to three dimensions (spatial proximity in tissue sections). By performing hybridization and ligation in situ within fixed tissue architecture, the method captures spatial relationships between chromatin regions that are separated by large linear distances but proximal in 3D space.
2Loss of information
If chromatin regions separated by large linear distances are analyzed, then regulatory element interactions can be detected, but the method cannot resolve spatial proximity in tissue context
Solution Approach 1:
The method performs preliminary fixation of tissue sections to preserve spatial architecture before any chromatin interaction analysis. This preliminary action maintains the spatial context of chromatin regions throughout the subsequent hybridization and ligation steps, ensuring that spatial relationships are preserved even when analyzing interactions between regions separated by large genomic distances.
Solution Approach 2:
The invention uses nucleic acid probes as intermediaries to bridge distant chromatin regions. These probes hybridize to specific chromatin regions and, when regions are in spatial proximity, their ends can be ligated together. The probes act as mediators that translate spatial proximity into detectable molecular connections without disrupting the underlying tissue architecture.
3Manufacturing precision
If in situ analysis with spatial resolution is implemented, then regulatory element interactions across cell populations can be revealed, but the procedural complexity increases significantly
Solution Approach 1:
The method employs universal reagents and procedures that can be applied to analyze multiple different chromatin interactions across cell populations in the same tissue section. The same in situ hybridization and ligation protocol can target different chromatin regions by simply changing the probe sequences, enabling multiplexed analysis without developing separate methods for each interaction.
Solution Approach 2:
The invention replaces complex mechanical dissection and manipulation of chromatin with biochemical reactions (hybridization and ligation) that occur in situ. This substitution of mechanical procedures with molecular recognition events simplifies the overall process while maintaining spatial resolution, as the biochemical reactions naturally occur at the precise locations where chromatin regions are positioned in the tissue architecture.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables the analysis of chromatin interactions across cell populations in a tissue sample with spatial resolution, revealing regulatory element interactions and their functional roles.
Implementation Method 1
the probe hybridizes to a nucleic acid sequence in the first chromatin region or in the second chromatin region
Data Source
AI summary
In some embodiments described herein are methods performed in situ for analyzing chromatin interaction events in a cell or in cells of a sample such as a non-homogenized tissue sample. The methods can comprise the spatial analysis of chromatin interaction events across cell populations in a biological sample. The methods can further comprise obtaining a biological sample, hybridizing probes to target nucleic acid sequences involved in chromatin interaction events and producing a nucleic acid sequence comprising all or part of the target nucleic acid sequences, amplifying the nucleic acid sequence so produced and detecting the amplified nucleic acid sequence in situ.