T3E: TRANSPOSABLE ELEMENT ENRICHMENT ESTIMATOR

Michelle Almeida da Paz; Leila Taher

doi:10.3217/978-3-85125-826-4-25

T3E: TRANSPOSABLE ELEMENT ENRICHMENT ESTIMATOR

Michelle Almeida da Paz^*, Leila Taher

^*Corresponding author for this work

Institute of Biomedical Informatics (7200)

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

Abstract

Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.

Original language	English
Title of host publication	Proceedings Annual Meeting of the Austrian Society for Biomedical Engineering 2021
Subtitle of host publication	ÖGBMT 2021
Publisher	Verlag der Technischen Universität Graz
Pages	95-98
Number of pages	4
DOIs	https://doi.org/10.3217/978-3-85125-826-4-25
Publication status	Published - 2021
Event	Annual Meeting of the Austrian Society of the Biomedical Engineering 2021: ÖGBMT 2021 - Graz University of Technology, Graz, Austria Duration: 30 Sept 2021 → 1 Oct 2021 https://oegbmt2021.tugraz.at/

Conference

Conference	Annual Meeting of the Austrian Society of the Biomedical Engineering 2021
Abbreviated title	ÖGBMT 2021
Country/Territory	Austria
City	Graz
Period	30/09/21 → 1/10/21
Internet address	https://oegbmt2021.tugraz.at/

Keywords

Transposable element
enrichment
ChIP-seq
histone modifications

Access to Document

10.3217/978-3-85125-826-4-25Licence: CC BY 4.0

Cite this

Almeida da Paz, M & Taher, L 2021, T3E: TRANSPOSABLE ELEMENT ENRICHMENT ESTIMATOR. in Proceedings Annual Meeting of the Austrian Society for Biomedical Engineering 2021: ÖGBMT 2021. Verlag der Technischen Universität Graz, pp. 95-98, Annual Meeting of the Austrian Society of the Biomedical Engineering 2021, Graz, Austria, 30/09/21. https://doi.org/10.3217/978-3-85125-826-4-25

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N2 - Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.

AB - Because of their repetitive nature, short sequencing reads derived from transposable elements (TEs) cannot be unambiguously mapped to the reference genome. As a result, most genomic analyses neglect over 50% of the human genome. Here, we present T3E, an algorithm to characterize the histone modifications associated with TEs from Chromatin Immunoprecipitation Sequencing (ChIP-seq) data. T3E relies on the structure of the ChIP seq control experiment to assess enrichment. When applying T3E to five ChIP-seq libraries we found consistently fewer enrichments compared to a strategy that assumes a random distribution of the reads across the genome, suggesting that the latter has a high false positive rate. This provides a framework for the functional analysis of TEs.

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KW - ChIP-seq

KW - histone modifications

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