SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

Lee, Lindsay; Yu, Hongyu; Jia, Bojing Blair; Jussila, Adam; Zhu, Chenxu; Chen, Jiawen; Xie, Liangqi; Hafner, Antonina; Mishra, Shreya; Wang, Duan Dennis; Strambio-De-Castillia, Caterina; Boettiger, Alistair; Ren, Bing; Li, Yun; Hu, Ming

doi:10.1038/s41467-023-40658-3

Cited by 5 publications

(3 citation statements)

References 39 publications

(63 reference statements)

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“…Enhancer-promoter loop is a critical structural feature in chromatin conformation data and plays a key role in transcription regulation 22 . In our recent work, we have developed a loop caller, SnapFISH 23 , for multiplexed DNA FISH data. We applied SnapFISH to the 25 kb imputed DNA seqFISH+ data and benchmarked the loop-calling performance with both the loop set from the raw data and the HiCCUPS 24 output.…”

Section: Resultsmentioning

confidence: 99%

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SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

Yu,

Wu,

Mishra

et al. 2024

Commun Biol

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Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE.

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Section: Resultsmentioning

confidence: 99%

“…We analyzed the bulk Hi-C data 30 used as the benchmark dataset in the original SnapFISH paper 23 . Specifically, we ran FitHiC2 25 on the mESC replicate with G0 and G1 phase cells at 10 kb resolution and kept interactions with a q value <0.01.…”

Section: Methodsmentioning

confidence: 99%

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

Yu,

Wu,

Mishra

et al. 2024

Commun Biol

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show abstract

“…Enhancer-promoter loop is a critical structural feature in chromatin conformation data and plays a key role in transcription regulation. 22 In our recent work, we have developed a loop-caller, SnapFISH 23 , for multiplexed DNA FISH data. We applied SnapFISH to the 25kb imputed DNA seqFISH+ data and benchmarked the loop-calling performance with both the loop set from the raw data and the HiCCUPS 24 output.…”

Section: Imputation Improves Downstream Analysismentioning

confidence: 99%

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

Yu,

Wu,

Shen

et al. 2024

Preprint

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Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE.

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ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data

Fan,

Dang,

Gao

et al. 2024

Advanced Science

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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.

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SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

Cited by 5 publications

References 39 publications

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single‐Cell Hi‐C and RNA FISH Data

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