Nascent Transcription Affected by RNA Polymerase IV in<i>Zea mays</i>

Erhard, Karl F.; Talbot, Joy-El; Deans, Natalie C.; McClish, Allison E.; Hollick, Jay B.

doi:10.1534/genetics.115.174714

Cited by 69 publications

(90 citation statements)

References 85 publications

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“…Loss of 24-nt siRNAs in rmr6-1 caused relatively low numbers of TEs to become transcriptionally de-repressed, confirming previous findings in mop1-1 and rmr6 (Jia et al, 2009;Madzima et al, 2014;Erhard et al, 2015) and supporting the hypothesis that RdDM is generally dispensable for stable silencing of the vast majority of TEs (Matzke et al, 2015). It was recently demonstrated that at RdDM loci, mop1-1 decreases DNA methylation in all C contexts but does not completely remove CHH methylation (Gent et al, 2014): lower levels of residual CHH methylation might still be sufficient to ensure DNA silencing at most RdDM loci.…”

Section: Putative Direct and Indirect Rddm Targets In Maizesupporting

confidence: 88%

“…In addition, we found that the smaller numbers of genes that are down-regulated in the rmr6-1 background also show the same loss of gene-proximal siRNAs. Together, these data support the current model by which the geneflanking 24-nt siRNAs in maize primarily function to reinforce transcriptional silencing of TEs located near active genes, avoiding the spreading of euchromatin into the close TEs (Gent et al, 2013(Gent et al, , 2014Erhard et al, 2015;Li et al, 2015). The similar occupancy of RMR6-dependent, gene-flanking, 24-nt siRNA loci found for protein-coding genes and lncRNAs suggests that the CHH island system of RdDM is engaged near active genes independently of their coding or noncoding nature.…”

Section: Long-term Abiotic Stresses Affect Accumulation Of Very Few Msupporting

confidence: 79%

“…The enrichment of RdDM-associated siRNAs near maize genes (Wang et al, 2009;Gent et al, 2013;Gent et al, 2014;Xin et al, 2014) has been suggested to ensure the continuous silencing of potentially deleterious TEs and TE-like sequences in an active and accessible chromatin environment required for the Pol II transcription of close genes (Gent et al, 2014). In maize, gene expression can be influenced by gene-proximal TEs and repeats (Erhard et al, 2013), and both genes and TEs can be regulated by the direct competition between Pol IV and Pol II occupancy at their promoters Erhard et al, 2015). At the genome-wide level, the expression of maize genes positively correlates with the accumulation levels of upstream 24-nt siRNAs (Gent et al, 2013).…”

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confidence: 99%

“…At the genome-wide level, the expression of maize genes positively correlates with the accumulation levels of upstream 24-nt siRNAs (Gent et al, 2013). In the absence of Pol IV-dependent siRNAs, Pol II transcription globally decreases around the transcription start site and increases at 39 end of genes (Erhard et al, 2015), and gene-proximal TEs lose DNA methylation (Li et al, 2015). Thus, the available data suggest that Pol IV-dependent 24-nt siRNAs in maize primarily serve to mark and enforce boundaries between areas of transcriptionally active euchromatin and transcriptionally repressed heterochromatin.…”

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confidence: 99%

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Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

et al. 2016

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(A.L., M.J.A.) Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.

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Section: Putative Direct and Indirect Rddm Targets In Maizesupporting

confidence: 88%

Section: Long-term Abiotic Stresses Affect Accumulation Of Very Few Msupporting

confidence: 79%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

et al. 2016

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“…Recent results show that maize Pol IV also has more general effects on gene regulation, possibly unrelated to RdDM (Erhard et al, 2015). Loss of RPD1 function results in strong developmental defects, possibly explained by the ectopic expression of specific genes (Parkinson et al, 2007;Erhard et al, 2013Erhard et al, , 2015.…”

Section: Diverse Roles For Multiple Dna-dependent Rna Polymerasesmentioning

confidence: 99%

Trans-Homolog Interactions Facilitating Paramutation in Maize

Giacopelli

Hollick

2015

Plant Physiol.

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ORCID IDs: 0000-0001-9846-3473 (B.J.G.); 0000-0001-9250-4836 (J.B.H.).Paramutations represent locus-specific trans-homolog interactions affecting the heritable silencing properties of endogenous alleles. Although examples of paramutation are well studied in maize (Zea mays), the responsible mechanisms remain unclear. Genetic analyses indicate roles for plant-specific DNA-dependent RNA polymerases that generate small RNAs, and current working models hypothesize that these small RNAs direct heritable changes at sequences often acting as transcriptional enhancers. Several studies have defined specific sequences that mediate paramutation behaviors, and recent results identify a diversity of DNA-dependent RNA polymerase complexes operating in maize. Other reports ascribe broader roles for some of these complexes in normal genome function. This review highlights recent research to understand the molecular mechanisms of paramutation and examines evidence relevant to small RNA-based modes of transgenerational epigenetic inheritance.Transgenerational epigenetic changes affecting gene regulation have been implicated in agricultural performance, human disease, and evolution (Groszmann et al., 2013;Jablonka, 2013;Heard and Martienssen, 2014). Paramutation represents one well-studied mechanism for generating and establishing such changes (Hollick, 2010). Alexander Brink first applied the term paramutation to describe directed, yet reversible, changes in maize (Zea mays) kernel pigment patterns resulting from trans-homolog interactions (THI) of certain red1 (r1) alleles (Brink, 1958). Mottled pigmentation conditioned by the R-r:standard (R-r) allele is invariably suppressed after exposure to R-stippled (R-st) in heterozygotes (Brink, 1956). The suppressed R-r state (denoted R-rʹ ) is meiotically heritable, induces a similar change to naive R-r (secondary paramutation), and gradually reverts back to an R-r reference state when maintained in hemizygous conditions (Styles and Brink, 1969). These behaviors classify R-r as an epiallele having variable silencing properties influenced by THI. This type of nonMendelian inheritance has remained a great unsolved mystery of genetics research and is a topic of considerable interest.Paramutation has a genetic definition intended for invariable occurrences of heritable, although potentially reversible, changes of an allele when heterozygous with another specific allele of the same gene (Brink, 1958). Used in the same sense originally assigned to mutation, paramutation represents both the process and outcome of these THI without reference to specific molecular features. Alleles inducing paramutation, such as R-st and R-rʹ, are termed paramutagenic. Alleles susceptible to paramutation, like R-r, are paramutable, and alleles neither paramutagenic nor paramutable are termed neutral. Some neutral alleles, similar to deficiencies, facilitate the reversion of an existing paramutation to the paramutable reference state, while others do not . These behaviors can generate and maintain wide phenotypi...

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Application of nucleoside or nucleotide analogues in RNA dynamics and RNA‐binding protein analysis

et al. 2022

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Cellular RNAs undergo dynamic changes during RNA biological processes, which are tightly orchestrated by RNA-binding proteins (RBPs). Yet, the investigation of RNA dynamics is hurdled by highly abundant steady-state RNAs, which make the signals of dynamic RNAs less detectable. Notably, the exert of nucleoside or nucleotide analogue-based RNA technologies has provided a remarkable platform for RNA dynamics research, revealing diverse unnoticed features in RNA metabolism. In this review, we focus on the application of two types of analogue-based RNA sequencing, antigen-/antibody-and click chemistry-based methodologies, and summarize the RNA dynamics features revealed. Moreover, we discuss emerging single-cell newly transcribed RNA sequencing methodologies based on nucleoside analogue labeling, which provides novel insights into RNA dynamics regulation at single-cell resolution. On the other hand, we also emphasize the identification of RBPs that interact with polyA, non-polyA RNAs, or newly transcribed RNAs and also their associated RNA-binding domains at genomewide level through ultraviolet crosslinking and mass spectrometry in different contexts. We anticipated that further modification and development of these analogue-based RNA and RBP capture technologies will aid in obtaining an unprecedented understanding of RNA biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Methods > RNA Analyses in Cells Meifeng Zheng and Yingying Lin contributed equally to this study.

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Nascent Transcription Affected by RNA Polymerase IV inZea mays

Cited by 69 publications

References 85 publications

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

Trans-Homolog Interactions Facilitating Paramutation in Maize

Application of nucleoside or nucleotide analogues in RNA dynamics and RNA‐binding protein analysis

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