UMMS Affiliation
Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2019-09-01
Document Type
Article
Disciplines
Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Genetic Phenomena | Genomics | Integrative Biology | Nucleic Acids, Nucleotides, and Nucleosides
Abstract
Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because Alu elements are highly repetitive, it has been difficult to identify the Pol III-transcribed elements and quantify their expression levels. In this study, we generated high-resolution, long-genomic-span RAMPAGE data in 155 biosamples all with matching RNA-seq data and built an atlas of 17,249 Pol III-transcribed Alu elements. We further performed an integrative analysis on the ChIP-seq data of 10 histone marks and hundreds of transcription factors, whole-genome bisulfite sequencing data, ChIA-PET data, and functional data in several biosamples, and our results revealed that although the human-specific Alu elements are transcriptionally repressed, the older, expressed Alu elements may be exapted by the human host to function as cell-type-specific enhancers for their nearby protein-coding genes.
Keywords
transposons, Alu, genome-wide analysis, integrative analysis
Rights and Permissions
© 2019 Zhang et al.; Published by Cold Spring Harbor Laboratory Press. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
DOI of Published Version
10.1101/gr.249789.119
Source
Genome Res. 2019 Sep;29(9):1402-1414. doi: 10.1101/gr.249789.119. Epub 2019 Aug 14. Link to article on publisher's site
Journal/Book/Conference Title
Genome research
Related Resources
PubMed ID
31413151
Repository Citation
Zhang X, Gingeras TR, Weng Z. (2019). Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Program in Bioinformatics and Integrative Biology Publications and Presentations. https://doi.org/10.1101/gr.249789.119. Retrieved from https://escholarship.umassmed.edu/bioinformatics_pubs/155
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Computational Biology Commons, Genetic Phenomena Commons, Genomics Commons, Integrative Biology Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons