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Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.

التفاصيل البيبلوغرافية
العنوان: Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.
المؤلفون: Zhaorong Ma, Michael J Axtell
المصدر: PLoS ONE, Vol 8, Iss 12, p e83721 (2013)
بيانات النشر: Public Library of Science (PLoS), 2013.
سنة النشر: 2013
المجموعة: LCC:Medicine
LCC:Science
مصطلحات موضوعية: Medicine, Science
الوصف: Conserved plant microRNAs (miRNAs) modulate important biological processes but little is known about conserved cis-regulatory elements (CREs) surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA)-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10-20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA) from multiple species that currently don't have a full genome assembly available.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1932-6203
Relation: http://europepmc.org/articles/PMC3869802?pdf=render; https://doaj.org/toc/1932-6203
DOI: 10.1371/journal.pone.0083721
URL الوصول: https://doaj.org/article/1ce567179cf54a78842c57bd48acdef4
رقم الأكسشن: edsdoj.1ce567179cf54a78842c57bd48acdef4
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:19326203
DOI:10.1371/journal.pone.0083721