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Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures

https://doi.org/10.1093/nargab/lqae136

Sexton, Corinne E.; Victor Paul, Sylvia; Barth, Dylan; Han, Mira V. (October 2024, NAR Genomics and Bioinformatics)

Abstract We can now analyze 3D physical interactions of chromatin regions with chromatin conformation capture technologies, in addition to the 1D chromatin state annotations, but methods to integrate this information are lacking. We propose a method to integrate the chromatin state of interacting regions into a vector representation through the contact-weighted sum of chromatin states. Unsupervised clustering on integrated chromatin states and Micro-C contacts reveals common patterns of chromatin interaction signatures. This provides an integrated view of the complex dynamics of concurrent change occurring in chromatin state and in chromatin interaction, adding another layer of annotation beyond chromatin state or Hi-C contact separately.
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The essential but enigmatic regulatory role of HERVH in pluripotency

https://doi.org/10.1016/j.tig.2021.07.007

Sexton, Corinne E.; Tillett, Richard L.; Han, Mira V. (January 2022, Trends in Genetics)

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Paired-end mappability of transposable elements in the human genome

https://doi.org/10.1186/s13100-019-0172-5

Sexton, Corinne E.; Han, Mira V. (December 2019, Mobile DNA)

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Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

https://doi.org/10.1186/s13100-019-0180-5

Chung, Nicky; Jonaid, G. M.; Quinton, Sophia; Ross, Austin; Sexton, Corinne E.; Alberto, Adrian; Clymer, Cody; Churchill, Daphnie; Navarro Leija, Omar; Han, Mira V. (December 2019, Mobile DNA)

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Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution

https://doi.org/10.1007/s00239-016-9761-9

Navarro Leija, Omar; Varghese, Sanju; Han, Mira V. (October 2016, Journal of Molecular Evolution)

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