Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the heterochromatic short interfering rna pathway is largely conserved in land plants

Ceyda Coruh, Sung Hyun Cho, Saima Shahida, Qikun Liu, Andrzej Wierzbicki, Michael Axtell

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.

Original languageEnglish (US)
Pages (from-to)2148-2162
Number of pages15
JournalPlant Cell
Volume27
Issue number8
DOIs
StatePublished - Aug 1 2015

Fingerprint

Bryopsida
Embryophyta
Physcomitrella patens
embryophytes
small interfering RNA
Small Interfering RNA
RNA
loci
Nucleotides
nucleotides
Angiosperms
DNA methylation
DNA Methylation
Angiospermae
Plant RNA
RNA Sequence Analysis
Bryophyta
Intergenic DNA
Nucleic Acid Repetitive Sequences
DNA-Directed RNA Polymerases

All Science Journal Classification (ASJC) codes

  • Plant Science
  • Cell Biology

Cite this

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abstract = "Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.",
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Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the heterochromatic short interfering rna pathway is largely conserved in land plants. / Coruh, Ceyda; Cho, Sung Hyun; Shahida, Saima; Liu, Qikun; Wierzbicki, Andrzej; Axtell, Michael.

In: Plant Cell, Vol. 27, No. 8, 01.08.2015, p. 2148-2162.

Research output: Contribution to journalArticle

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AU - Coruh, Ceyda

AU - Cho, Sung Hyun

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AU - Wierzbicki, Andrzej

AU - Axtell, Michael

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