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Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Source :
- Genome Research. 29:1402-1414
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
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.
- Subjects :
- Transposable element
Sequence analysis
Alu element
RNA polymerase II
Computational biology
RNA polymerase III
Evolution, Molecular
Histones
03 medical and health sciences
0302 clinical medicine
Alu Elements
Genetics
Humans
Enhancer
Gene
Genetics (clinical)
030304 developmental biology
0303 health sciences
Whole Genome Sequencing
biology
Sequence Analysis, RNA
Research
Computational Biology
RNA Polymerase III
Molecular Sequence Annotation
Enhancer Elements, Genetic
ComputingMethodologies_PATTERNRECOGNITION
Gene Expression Regulation
biology.protein
Human genome
Transcription Initiation Site
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 15495469 and 10889051
- Volume :
- 29
- Database :
- OpenAIRE
- Journal :
- Genome Research
- Accession number :
- edsair.doi.dedup.....49afde1af47edcc9ea8a086f40391f68