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Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate it...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899811/ https://www.ncbi.nlm.nih.gov/pubmed/27278669 http://dx.doi.org/10.1038/srep27722 |
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author | Fonville, Natalie C. Velmurugan, Karthik Raja Tae, Hongseok Vaksman, Zalman McIver, Lauren J. Garner, Harold R. |
author_facet | Fonville, Natalie C. Velmurugan, Karthik Raja Tae, Hongseok Vaksman, Zalman McIver, Lauren J. Garner, Harold R. |
author_sort | Fonville, Natalie C. |
collection | PubMed |
description | The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. |
format | Online Article Text |
id | pubmed-4899811 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-48998112016-06-13 Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome Fonville, Natalie C. Velmurugan, Karthik Raja Tae, Hongseok Vaksman, Zalman McIver, Lauren J. Garner, Harold R. Sci Rep Article The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. Nature Publishing Group 2016-06-09 /pmc/articles/PMC4899811/ /pubmed/27278669 http://dx.doi.org/10.1038/srep27722 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Fonville, Natalie C. Velmurugan, Karthik Raja Tae, Hongseok Vaksman, Zalman McIver, Lauren J. Garner, Harold R. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title | Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title_full | Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title_fullStr | Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title_full_unstemmed | Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title_short | Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
title_sort | genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899811/ https://www.ncbi.nlm.nih.gov/pubmed/27278669 http://dx.doi.org/10.1038/srep27722 |
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