Large-scale analysis of RNA-DNA interactions

Aleksandra Galitsyna, Anastasia Zharikova, Maria Logacheva, Sergey Razin, Andrey Mironov, Alexey Gavrilov

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We have performed large-scale analysis of RNADNA contacts in chromatin based on our own experimental data for K562 human cells and GRID-Seq. We have devised RNA-Seq controls and validated the resulting interactions with known chromatin-associated RNAs. We propose a pipeline for the analysis of RNA-DNA interactions, a noise correction procedure and clustering by the distance preference approach. We have compared the obtained interactomes with DNA-DNA contacts (Hi-C) for the same cell line and report the association of contacts with active compartment A and boundaries of topologically associating domains (TADs). We have detected a fraction of chromatin-enriched RNAs and report their chromatin properties. We also describe classes of RNAs by their contact preferences with DNA.

Original languageEnglish
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2474-2475
Number of pages2
ISBN (Electronic)9781538654880
DOIs
Publication statusPublished - 21 Jan 2019
Externally publishedYes
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: 3 Dec 20186 Dec 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Country/TerritorySpain
CityMadrid
Period3/12/186/12/18

Keywords

  • chromatin
  • epigenetics
  • high-throughput sequencing
  • large-scale data analysis
  • NGS
  • non-coding RNAs
  • proximity ligation
  • RNA-DNA
  • RNA-DNA contacts
  • RNA-DNA insteractome
  • RNA-DNA interactions

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