1
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

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

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Most cited references55

          • Record: found
          • Abstract: found
          • Article: not found

          Initial sequencing and analysis of the human genome.

          The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            High-resolution profiling of histone methylations in the human genome.

            Histone modifications are implicated in influencing gene expression. We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. Typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions are identified. The monomethylations of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylations of H3K27, H3K9, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Chromosome banding patterns are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Mobile elements: drivers of genome evolution.

              Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.
                Bookmark

                Author and article information

                Journal
                Genome Res
                Genome Res
                genome
                genome
                GENOME
                Genome Research
                Cold Spring Harbor Laboratory Press
                1088-9051
                1549-5469
                September 2019
                : 29
                : 9
                : 1402-1414
                Affiliations
                [1 ]Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
                [2 ]Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
                [3 ]Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
                Author notes
                Author information
                http://orcid.org/0000-0002-2027-1313
                http://orcid.org/0000-0001-9106-3573
                http://orcid.org/0000-0002-3032-7966
                Article
                9509184
                10.1101/gr.249789.119
                6724667
                31413151
                0dd0cc98-0b43-4aab-a8a7-4fc61de8d5d1
                © 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/.

                History
                : 22 February 2019
                : 24 July 2019
                Page count
                Pages: 13
                Funding
                Funded by: National Institutes of Health (NIH), open-funder-registry 10.13039/100000002;
                Award ID: U24-HG009446
                Funded by: NIH , open-funder-registry 10.13039/100000002;
                Award ID: U54-HG004557
                Categories
                Research

                Comments

                Comment on this article