High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera.

BMC Genomics
Erica MicaDavid S Horner

Abstract

MicroRNAs are short (approximately 21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families. Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts. Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing...Continue Reading

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Jul 25, 2013·The Plant Cell·Kestrel Rogers, Xuemei Chen
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May 18, 2021·Frontiers in Plant Science·Lilian P Matallana-RamirezKitt G Payn
Dec 27, 2021·Genomics·Behzad Hajieghrari, Naser Farrokhi

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Datasets Mentioned

BETA
SRS005164
GSE13801

Methods Mentioned

BETA
Illumina sequencing
size fractionation
oligonucleotide
454 sequencing
RNA-Seq
oligonucleotide array
PCR

Software Mentioned

PYTHON
Blast
Scanarray Express
Microarray Imager ( CombiMatrix )
microHarvester
MatPlotLib
TCM
custom
SPIDEY
Combimatrix

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