HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization Article Swipe
Matej Lexa
,
Monika Čechová
,
Son Hoang Nguyen
,
Pavel Jedlička
,
Viktor Tokan
,
Zdeněk Kubát
,
Roman Hobza
,
Eduard Kejnovský
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.12.18.473300
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.12.18.473300
The role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA segments in nuclei. We combined Hi-C data, plant reference genome data and tools for the characterization of genomic repeats to build a Nextflow pipeline identifying and quantifying the contacts of specific repeats revealing the preferential homotypic interactions of ribosomal DNA, DNA transposons and some LTR retrotransposon families. We provide a novel way to analyze the organization of repetitive elements in the 3D nucleus.
Related Topics
Concepts
Retrotransposon
Genomic organization
Genome
Transposable element
Computational biology
Biology
Pipeline (software)
DNA sequencing
DNA
Chromosome conformation capture
Genetics
Computer science
Gene
Programming language
Enhancer
Gene expression
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.12.18.473300
- https://www.biorxiv.org/content/biorxiv/early/2021/12/21/2021.12.18.473300.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 31
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4200282751
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4200282751Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2021.12.18.473300Digital Object Identifier
- Title
-
HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organizationWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-12-21Full publication date if available
- Authors
-
Matej Lexa, Monika Čechová, Son Hoang Nguyen, Pavel Jedlička, Viktor Tokan, Zdeněk Kubát, Roman Hobza, Eduard KejnovskýList of authors in order
- Landing page
-
https://doi.org/10.1101/2021.12.18.473300Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2021/12/21/2021.12.18.473300.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2021/12/21/2021.12.18.473300.full.pdfDirect OA link when available
- Concepts
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Retrotransposon, Genomic organization, Genome, Transposable element, Computational biology, Biology, Pipeline (software), DNA sequencing, DNA, Chromosome conformation capture, Genetics, Computer science, Gene, Programming language, Enhancer, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
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2022: 1Per-year citation counts (last 5 years)
- References (count)
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31Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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