Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph

Name: Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph
Author: Sefer, Emre

İsim	Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph
Yazar	Sefer, Emre
Basım Tarihi:	2021
Basım Yeri	- Springer
Konu	Algorithms, Bioinformatics, Epigenetics, Hi-C, Set cover
Tür	Belge
Dil	İngilizce
Dijital	Evet
Yazma	Hayır
Kütüphane:	Özyeğin Üniversitesi
Demirbaş Numarası	978-303065350-7
Kayıt Numarası	053d5739-acf3-454a-befb-a9bc652ccc6c
Lokasyon	Computer Science
Tarih	2021
Örnek Metin	Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. Even though Hi-C interactions are not biased towards any of the histone modifications, previous analysis has revealed denser interactions around many histone modifications. Nevertheless, simultaneous effects of these modifications in Hi-C interaction graph have not been fully characterized yet, limiting our understanding of genome shape. Here, we propose Coverage Hi-C to decompose Hi-C interaction graph in terms of known histone modifications. Coverage Hi-C is based on set multicover with pairs, where each Hi-C interaction is covered by histone modification pairs. We find 4 histone modifications H3K4me1, H3K4me3, H3K9me3, H3K27ac to be significantly predictive of most Hi-C interactions across species and cell types. Coverage Hi-C is quite effective in predicting Hi-C interactions and topologically-associated domains (TADs) in one species, given it is trained on another species or cell types.
DOI	10.1007/978-3-030-65351-4_33
Cilt	944

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Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph

Yazar Sefer, Emre

Basım Tarihi 2021

Basım Yeri - Springer

Konu Algorithms, Bioinformatics, Epigenetics, Hi-C, Set cover

Tür Belge

Dil İngilizce

Dijital Evet

Yazma Hayır

Kütüphane Özyeğin Üniversitesi

Demirbaş Numarası 978-303065350-7

Kayıt Numarası 053d5739-acf3-454a-befb-a9bc652ccc6c

Lokasyon Computer Science

Tarih 2021

Örnek Metin Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. Even though Hi-C interactions are not biased towards any of the histone modifications, previous analysis has revealed denser interactions around many histone modifications. Nevertheless, simultaneous effects of these modifications in Hi-C interaction graph have not been fully characterized yet, limiting our understanding of genome shape. Here, we propose Coverage Hi-C to decompose Hi-C interaction graph in terms of known histone modifications. Coverage Hi-C is based on set multicover with pairs, where each Hi-C interaction is covered by histone modification pairs. We find 4 histone modifications H3K4me1, H3K4me3, H3K9me3, H3K27ac to be significantly predictive of most Hi-C interactions across species and cell types. Coverage Hi-C is quite effective in predicting Hi-C interactions and topologically-associated domains (TADs) in one species, given it is trained on another species or cell types.

DOI 10.1007/978-3-030-65351-4_33

Cilt 944