ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data
Abstract Although multiplexed DNA fluorescence in situ hybridization (FISH) enables tracking the spatial localization of thousands of genomic loci using probes within individual cells, the high rates of undetected probes impede the depiction of 3D chromosome structures. Current data imputation metho...
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| Format: | Article |
| Language: | English |
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Wiley
2024-11-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202406364 |
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| author | Shichen Fan Dachang Dang Lin Gao Shihua Zhang |
| author_facet | Shichen Fan Dachang Dang Lin Gao Shihua Zhang |
| author_sort | Shichen Fan |
| collection | DOAJ |
| description | Abstract Although multiplexed DNA fluorescence in situ hybridization (FISH) enables tracking the spatial localization of thousands of genomic loci using probes within individual cells, the high rates of undetected probes impede the depiction of 3D chromosome structures. Current data imputation methods neither utilize single‐cell Hi‐C data, which elucidate 3D genome architectures using sequencing nor leverage multimodal RNA FISH data that reflect cell‐type information, limiting the effectiveness of these methods in complex tissues such as the mouse brain. To this end, a novel multiplexed DNA FISH imputation method named ImputeHiFI is proposed, which fully utilizes the complementary structural information from single‐cell Hi‐C data and the cell type signature from RNA FISH data to obtain a high‐fidelity and complete spatial location of chromatin loci. ImputeHiFI enhances cell clustering, compartment identification, and cell subtype detection at the single‐cell level in the mouse brain. ImputeHiFI improves the recognition of cell‐type‐specific loops in three high‐resolution datasets. In short, ImputeHiFI is a powerful tool capable of imputing multiplexed DNA FISH data from various resolutions and imaging protocols, facilitating studies of 3D genome structures and functions. |
| format | Article |
| id | doaj-art-c114ecf377fc4fe8a68d944c08a43825 |
| institution | OA Journals |
| issn | 2198-3844 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-c114ecf377fc4fe8a68d944c08a438252025-08-20T01:51:14ZengWileyAdvanced Science2198-38442024-11-011142n/an/a10.1002/advs.202406364ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH DataShichen Fan0Dachang Dang1Lin Gao2Shihua Zhang3School of Computer Science and Technology Xidian University Xi'an 710071 ChinaSchool of Automation Northwestern Polytechnical University Xi'an 710072 ChinaSchool of Computer Science and Technology Xidian University Xi'an 710071 ChinaNCMIS, CEMS, RCSDS Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 ChinaAbstract Although multiplexed DNA fluorescence in situ hybridization (FISH) enables tracking the spatial localization of thousands of genomic loci using probes within individual cells, the high rates of undetected probes impede the depiction of 3D chromosome structures. Current data imputation methods neither utilize single‐cell Hi‐C data, which elucidate 3D genome architectures using sequencing nor leverage multimodal RNA FISH data that reflect cell‐type information, limiting the effectiveness of these methods in complex tissues such as the mouse brain. To this end, a novel multiplexed DNA FISH imputation method named ImputeHiFI is proposed, which fully utilizes the complementary structural information from single‐cell Hi‐C data and the cell type signature from RNA FISH data to obtain a high‐fidelity and complete spatial location of chromatin loci. ImputeHiFI enhances cell clustering, compartment identification, and cell subtype detection at the single‐cell level in the mouse brain. ImputeHiFI improves the recognition of cell‐type‐specific loops in three high‐resolution datasets. In short, ImputeHiFI is a powerful tool capable of imputing multiplexed DNA FISH data from various resolutions and imaging protocols, facilitating studies of 3D genome structures and functions.https://doi.org/10.1002/advs.2024063643D genomessingle‐cell Hi‐C dataDNA FISH datamultimodal imagingimputation |
| spellingShingle | Shichen Fan Dachang Dang Lin Gao Shihua Zhang ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data Advanced Science 3D genomes single‐cell Hi‐C data DNA FISH data multimodal imaging imputation |
| title | ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data |
| title_full | ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data |
| title_fullStr | ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data |
| title_full_unstemmed | ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data |
| title_short | ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data |
| title_sort | imputehifi an imputation method for multiplexed dna fish data by utilizing single cell hi c and rna fish data |
| topic | 3D genomes single‐cell Hi‐C data DNA FISH data multimodal imaging imputation |
| url | https://doi.org/10.1002/advs.202406364 |
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