Genome-wide analysis of polymerase III-transcribed elements suggests cell-type-specific enhancer function.

elements are one of the most successful families of transposons in the human genome. A portion of elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because 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 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 elements are transcriptionally repressed, the older, expressed elements may be exapted by the human host to function as cell-type-specific enhancers for their nearby protein-coding genes.