A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome

By Anthony D. Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine Tan, Yun Li, Shin Lin, Yiing Lin, C. Barr and 1 more. Cell Reports, 2016

832 citations recorded by the source corpus.

Summary The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we found topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate function of non-coding sequence variants.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4b905dad76227666d05e1218586cc966a0d29d91

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Ming Hu
2. Feng Yue
3. William Stafford Noble
4. Ross C. Hardison
5. Doron Lancet
6. Yanli Wang
7. Yun Li
8. Qunhua Li

In Plant Science

1. William Stafford Noble
2. Ming Hu

Citations in the corpus

• Functional mapping and annotation of genetic associations with FUMA (2017, methodology): “FUMA currently contains Hi-C data of 14 tissue types and seven cell lines from the study of Schmitt et al. 11 , yet new chromatin interaction data will be added when it becomes available and FUMA also allows users to upload Click row to display a regional plot of GWAS summary statistics.”
• HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient (2017, positive): “We further expanded this analysis using the recently published Hi-C data in 14 human primary tissues and two cell lines (Supplemental Table S4; Schmitt et al. 2016).”
• The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions (2017, background): “Identifying cell/tissue-specific chromatin interactions is important, as it has been shown that chromatin structure plays an important role in determining cellular identity [22, 23].”
• Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III (2020, background): “Mounting evidence has shown a strong correlation between transcription and 3D genome structures [12, 63, 64], while their relationship is still controversial before our study.”
• GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, background): “Future improvements in GeneHancer will include the integration of new data sources, for both enhancer annotations (38, 39) and enhancer–gene associations, e.g. novel chromatin contact maps (83) and topologically associated domains (84).”