scholarly journals Broad noncoding transcription suggests genome surveillance by RNA polymerase V

2020 ◽  
Vol 117 (48) ◽  
pp. 30799-30804
Author(s):  
Masayuki Tsuzuki ◽  
Shriya Sethuraman ◽  
Adriana N. Coke ◽  
M. Hafiz Rothi ◽  
Alan P. Boyle ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
De Novo ◽  
Genome Integrity ◽  
Biological Functions ◽  
Pol V ◽  
Low Levels ◽  
Interfering Rna ◽  
Eukaryotic Genomes ◽  
Transcribed Sequences ◽  
Pervasive Transcription

Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. InArabidopsis thaliana, RNA polymerase V (Pol V) produces noncoding transcripts, which base pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets, Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of nonconserved sequences may serve an essential role in maintenance of genome integrity.

scholarly journals Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Lauren Gibilisco ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Early Development ◽  
Defense Mechanisms ◽  
De Novo ◽  
Genome Integrity ◽  
Selfish Dna ◽  
Mutational Burden ◽  
Y Chromosomes ◽  
Genome Wide ◽  
Eukaryotic Genomes

Abstract Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs (‘toxic’ Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different ages. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE expression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the ‘toxic’ Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.

scholarly journals Small RNA-Mediated De Novo Silencing of Ac/Ds Transposons Is Initiated by Alternative Transposition in Maize

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 393-406 ◽  
Author(s):  
Dafang Wang ◽  
Jianbo Zhang ◽  
Tao Zuo ◽  
Meixia Zhao ◽  
Damon Lisch ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
De Novo ◽  
Inverted Repeats ◽  
Small Interfering Rnas ◽  
Major Fraction ◽  
First Case ◽  
Transposon Silencing ◽  
Alternative Transposition ◽  
Interfering Rna ◽  
Eukaryotic Genomes

Although transposable elements (TEs) comprise a major fraction of many higher eukaryotic genomes, most TEs are silenced by host defense mechanisms. The means by which otherwise active TEs are recognized and silenced remains poorly understood. Here we analyzed two independent cases of spontaneous silencing of the active maize Ac/Ds transposon system. This silencing is initiated by alternative transposition, a type of aberrant transposition event that engages the termini of two nearby separate TEs. Alternative transposition during DNA replication can generate Composite Insertions that contain inverted duplications of the transposon sequences. We show that the inverted duplications of two Composite Insertions are transcribed to produce double-stranded RNAs that trigger the production of two distinct classes of small interfering RNAs: a 24-nt class complementary to the TE terminal inverted repeats and noncoding subterminal regions, and a 21- to 22-nt class corresponding to the TE transcribed regions. Plants containing these small interfering RNA-generating Composite Insertions exhibit decreased levels of Ac transcript and heritable repression of Ac/Ds transposition. Further, we demonstrate that Composite Insertions can heritably silence otherwise active elements in trans. This study documents the first case of transposon silencing induced by alternative transposition and may represent a general initiating mechanism for silencing of DNA transposons.

scholarly journals The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

2021 ◽  
Vol 118 (30) ◽  
pp. e2100709118
Author(s):  
Kezhi Zheng ◽  
Lili Wang ◽  
Longjun Zeng ◽  
Dachao Xu ◽  
Zhongxin Guo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Histone Modifications ◽  
Noncoding Rna ◽  
De Novo ◽  
Noncoding Rnas ◽  
Reproductive Development ◽  
Small Interfering Rnas ◽  
Pol V ◽  
Specific Manner

RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V–independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V–dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V–dependent loci but not on Pol V–independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

scholarly journals Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males

2020 ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Lauren Gibilisco ◽  
Doris Bachtrog
Keyword(s):  
Y Chromosome ◽  
Early Development ◽  
Defense Mechanisms ◽  
De Novo ◽  
Genome Integrity ◽  
Selfish Dna ◽  
Mutational Burden ◽  
Y Chromosomes ◽  
Genome Wide ◽  
Eukaryotic Genomes

AbstractLarge portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity in Drosophila. Repeat-rich Y chromosomes can act as reservoirs for TEs (‘toxic’ Y effect), and incomplete epigenomic defenses during early development can lead to deleterious TE mobilization. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE misexpression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger Y chromosome. The repeat-rich Y of D. miranda still contains many actively transcribed genes, which compromise the formation of silencing heterochromatin. Elevated TE expression results in more de novo insertions of repeats in males compared to females. This lends support to the idea that the ‘toxic’ Y chromosome can create a mutational burden in males when genome-wide defense mechanisms are compromised, and suggests a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA.

scholarly journals Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae

2021 ◽  
Vol 7 (3) ◽  
pp. 41
Author(s):  
Emma Lesage ◽  
Jorge Perez-Fernandez ◽  
Sophie Queille ◽  
Christophe Dez ◽  
Olivier Gadal ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Tandem Repeats ◽  
Chromatin State ◽  
Rrna Genes ◽  
Rdna Genes ◽  
Regulatory Pathways ◽  
Chromatin States ◽  
Non Coding Rnas ◽  
Pervasive Transcription

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

Mechanism for De Novo RNA Synthesis and Initiating Nucleotide Specificity by T7 RNA Polymerase

2007 ◽  
Vol 370 (2) ◽  
pp. 256-268 ◽  
Author(s):  
William P. Kennedy ◽  
Jamila R. Momand ◽  
Y. Whitney Yin
Keyword(s):  
Rna Polymerase ◽  
Rna Synthesis ◽  
De Novo ◽  
T7 Rna Polymerase ◽  
Nucleotide Specificity

Identification of RNA polymerase III-transcribed genes in eukaryotic genomes

2013 ◽  
Vol 1829 (3-4) ◽  
pp. 296-305 ◽  
Author(s):  
Giorgio Dieci ◽  
Anastasia Conti ◽  
Aldo Pagano ◽  
Davide Carnevali
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Polymerase Iii ◽  
Eukaryotic Genomes

DNA methylation in 5-aza-2'-deoxycytidine-resistant variants of C3H 10T1/2 C18 cells

1984 ◽  
Vol 4 (10) ◽  
pp. 2098-2102
Author(s):  
E Flatau ◽  
F A Gonzales ◽  
L A Michalowsky ◽  
P A Jones
Keyword(s):  
Cell Line ◽  
Cytosine Methylation ◽  
De Novo ◽  
Lethal Dose ◽  
Cytotoxic Effects ◽  
Drug Treatments ◽  
A Cell ◽  
Mouse Cells ◽  
Low Levels ◽  
Dna Cytosine Methylation

A cell line (T17) was derived from C3H 10T1/2 C18 cells after 17 treatments with increasing concentrations of 5-aza-2'-deoxycytidine. The T17 cell line was very resistant to the cytotoxic effects of 5-aza-2'-deoxycytidine, and the 50% lethal dose for 5-aza-2'-deoxycytidine was ca. 3 microM, which was 30-fold greater than that of the parental C3H 10T1/2 C18 cells. Increased drug resistance was not due to a failure of the T17 cell line to incorporate 5-aza-2'-deoxycytidine into DNA. The cells were also slightly cross-resistant to 5-azacytidine. The percentage of cytosines modified to 5-methylcytosine in T17 cells was 0.7%, a 78% decrease from the level of 3.22% in C3H 10T1/2 C18 cells. The DNA cytosine methylation levels in several clones isolated from the treated lines were on the order of 0.7%, and clones with methylation levels lower than 0.45% were not obtained even after further drug treatments. These highly decreased methylation levels appeared to be unstable, and DNA modification increased as the cells divided in the absence of further drug treatment. The results suggest that it may not be possible to derive mouse cells with vanishingly low levels of 5-methylcytosine and that considerable de novo methylation can occur in cultured lines.

scholarly journals Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

2021 ◽  
Author(s):  
Jincheng Long ◽  
James Walker ◽  
Wenjing She ◽  
Billy Aldridge ◽  
Hongbo Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Small Rnas ◽  
Nurse Cell ◽  
De Novo ◽  
Epigenetic Inheritance ◽  
Genome Integrity ◽  
Nurse Cells ◽  
Male Germline ◽  
Methylation Patterns

AbstractThe plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and facilitates meiosis. Why reprogramming is limited to the germline and how specific genes are chosen is unknown. Here, we demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by germline-specific siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the tapetum-specific chromatin remodeler CLASSY3. Remarkably, tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Finally, we demonstrate that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal that tapetal niRNAs are sufficient to reconstitute germline methylation patterns and drive extensive, functional methylation reprogramming analogous to piRNA-mediated reprogramming in animal germlines.

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