Author Correction: The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Reiff, Sarah B.; Schroeder, Andrew J.; Kırlı, Koray; Cosolo, Andrea; Bakker, Clara; Mercado, Luisa; Lee, Mi Kyung; Veit, Alexander D.; Balashov, Alexander; Vitzthum, Carl; Ronchetti, William; Pitman, Kent M.; Johnson, Jeremy A.; Ehmsen, Shannon; Kerpedjiev, Peter; Abdennur, Nezar; Imakaev, Maxim; Öztürk, Serkan; Çamoğlu, Uğur; Mirny, Leonid A.; Gehlenborg, Nils; Alver, B.; Park, Peter J.

doi:10.1038/s41467-022-34458-4

Cited by 4 publications

(2 citation statements)

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“…Initially the contact maps derived from Micro-C or MUSIC were logarithmically scaled; these were then normalized to their respective maximum values, resulting in all contacts being constrained within the range of [0, 1]. The Micro-C data used in this study were obtained from the 4DN portal 61 (4DNFI2TK7L2F) 34 . To extract raw contacts from the .hic file, the straw 62 tool was employed.…”

Section: Methodsmentioning

confidence: 99%

Single-cell multiplex chromatin and RNA interactions in ageing human brain

Wen,

Luo,

Zhao

et al. 2024

Nature

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Dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA1–3. Chromatin complex compositions change during cellular differentiation and ageing, and are expected to be highly heterogeneous among terminally differentiated single cells4–7. Here we introduce the multinucleic acid interaction mapping in single cells (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression and RNA–chromatin associations within individual nuclei. When applied to 14 human frontal cortex samples from older donors, MUSIC delineated diverse cortical cell types and states. We observed that nuclei exhibiting fewer short-range chromatin interactions were correlated with both an ‘older’ transcriptomic signature and Alzheimer’s disease pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci and a promoter tends to be that in which these cis expression quantitative trait loci specifically affect the expression of their target gene. In addition, female cortical cells exhibit highly heterogeneous interactions between XIST non-coding RNA and chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploration of chromatin architecture and transcription at cellular resolution in complex tissues.

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Section: Methodsmentioning

confidence: 99%

Single-cell multiplex chromatin and RNA interactions in ageing human brain

Wen,

Luo,

Zhao

et al. 2024

Nature

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show abstract

“…Subsequently, the scaled contact maps were normalized to their respective maximum values, resulting in all contacts being constrained within the range of [0, 1]. The Micro-C data used in this study was obtained from the 4DN portal 59 (4DNFI2TK7L2F) 34 . To extract the raw contacts from the .hic file, the straw 60 tool was employed.…”

Section: Methodsmentioning

confidence: 99%

Single-cell multiplex chromatin and RNA interactions in aging human brain

Luo

Wen

Zhao

et al. 2023

Preprint

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The dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA. Here, we introduce the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique to enable simultaneous profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within a single nucleus. We applied MUSIC to profile >9,000 single nuclei in the human frontal cortex. MUSIC-derived single-nucleus transcriptomes provide a comprehensive categorization of cortical cell types, subtypes and cellular states. The genomic sequences of highly-expressed genes frequently co-complex with their flanking genomic regions, forming what we refer to as Gene-Expression-Associated Stripes (GEAS), which exemplify the intricate coordination between transcription and chromatin architecture at the single-cell level. Additionally, we observed significant heterogeneity among female cortical cells in the association between the XIST long non-coding RNA (lncRNA) and the X chromosome (XIST-chrX association, quantified as XAL). Cells with high XAL demonstrated a greater difference in spatial organization between the XIST-associated (Xi) and non-associated (Xa) X chromosomes compared to XAL-low cells. Notably, excitatory neurons displayed enrichment in XAL-high cells and exhibited a more pronounced disparity in spatial organization between Xi and Xa compared to other cell types. The MUSIC technique offers a powerful tool for future investigations into chromatin architecture and transcription at a cellular resolution within complex tissues.

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