HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data
The explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to ass...
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| Format: | Article |
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MDPI AG
2021-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/15/8123 |
| _version_ | 1797525534697062400 |
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| author | Anna Macioszek Bartek Wilczynski |
| author_facet | Anna Macioszek Bartek Wilczynski |
| author_sort | Anna Macioszek |
| collection | DOAJ |
| description | The explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to assess the proteins associated with different non-coding DNA regions genome-wide. While the analysis of such data related to transcription factor binding is relatively straightforward, many modified histone variants, such as H3K27me3, are very important for the process of gene regulation but are very difficult to interpret. We propose a novel method, called HERON (HiddEn MaRkov mOdel based peak calliNg), for genome-wide data analysis that is able to detect DNA regions enriched for a certain feature, even in difficult settings of weakly enriched long DNA domains. We demonstrate the performance of our method both on simulated and experimental data. |
| first_indexed | 2024-03-10T09:15:12Z |
| format | Article |
| id | doaj.art-aa047394f1a443c6962ed2c7e80e122c |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T09:15:12Z |
| publishDate | 2021-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-aa047394f1a443c6962ed2c7e80e122c2023-11-22T05:43:38ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-07-012215812310.3390/ijms22158123HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq DataAnna Macioszek0Bartek Wilczynski1Faculty of Mathematics, Informatics and Mechanics, Univeristy of Warsaw, 00-927 Warszawa, PolandFaculty of Mathematics, Informatics and Mechanics, Univeristy of Warsaw, 00-927 Warszawa, PolandThe explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to assess the proteins associated with different non-coding DNA regions genome-wide. While the analysis of such data related to transcription factor binding is relatively straightforward, many modified histone variants, such as H3K27me3, are very important for the process of gene regulation but are very difficult to interpret. We propose a novel method, called HERON (HiddEn MaRkov mOdel based peak calliNg), for genome-wide data analysis that is able to detect DNA regions enriched for a certain feature, even in difficult settings of weakly enriched long DNA domains. We demonstrate the performance of our method both on simulated and experimental data.https://www.mdpi.com/1422-0067/22/15/8123peak callingChIP-seqhistone methylation |
| spellingShingle | Anna Macioszek Bartek Wilczynski HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data International Journal of Molecular Sciences peak calling ChIP-seq histone methylation |
| title | HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data |
| title_full | HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data |
| title_fullStr | HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data |
| title_full_unstemmed | HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data |
| title_short | HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data |
| title_sort | heron a novel tool enables identification of long weakly enriched genomic domains in chip seq data |
| topic | peak calling ChIP-seq histone methylation |
| url | https://www.mdpi.com/1422-0067/22/15/8123 |
| work_keys_str_mv | AT annamacioszek heronanoveltoolenablesidentificationoflongweaklyenrichedgenomicdomainsinchipseqdata AT bartekwilczynski heronanoveltoolenablesidentificationoflongweaklyenrichedgenomicdomainsinchipseqdata |