Abstract:Arabidopsis NODULIN HOMEOBOX (NDX) is a nuclear protein described as a regulator of specific euchromatic genes within transcriptionally active chromosome arms. Here we show that NDX is primarily a heterochromatin regulator that functions in pericentromeric regions to control siRNA production and non-CG methylation. Most NDX binding sites coincide with pericentromeric het-siRNA loci that mediate transposon silencing, and are antagonistic with R-loop structures that are prevalent in euchromatic chromosomal arms.… Show more
“…3b–d . (2) The transcriptomes of inflorescence and seedlings 6 , 16 were compared in Col-0 (control) samples (Fig. 4a ), identifying 5555 (17.37%) up- and 5618 (17.56%) downregulated genes in flowers relative to seedlings.…”
Section: Methodsmentioning
confidence: 99%
“…Our analysis identified specific sets of genes differentially expressed in ndx1-4 , as well as noncoding heterochromatic siRNA (het-siRNA) loci whose activity was significantly changed in the absence of NDX. Transcriptomic data obtained from inflorescence were also compared with previously published seedling data 6 , highlighting development-specific changes in gene expression profiles. Fig.…”
Section: Background and Summarymentioning
confidence: 99%
“…The seedling data were published in ref. 6 , which were used for comparison with the flower transcriptomic data generated in this study. …”
Section: Background and Summarymentioning
confidence: 99%
“…The mRNA and sRNA datasets generated from Arabidopsis seedlings can be accessed at GEO under the accession number GSE201841 16 and in Supplementary Data 1–16 accompanying the related paper 6 .…”
Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNA (hetsiRNA) loci/regions whose transcriptional activity was significantly changed in the absence of NDX. In addition, data obtained from inflorescence were compared with seedling transcriptomics data, which revealed development-specific changes in gene expression profiles. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further research on NDX function.
“…3b–d . (2) The transcriptomes of inflorescence and seedlings 6 , 16 were compared in Col-0 (control) samples (Fig. 4a ), identifying 5555 (17.37%) up- and 5618 (17.56%) downregulated genes in flowers relative to seedlings.…”
Section: Methodsmentioning
confidence: 99%
“…Our analysis identified specific sets of genes differentially expressed in ndx1-4 , as well as noncoding heterochromatic siRNA (het-siRNA) loci whose activity was significantly changed in the absence of NDX. Transcriptomic data obtained from inflorescence were also compared with previously published seedling data 6 , highlighting development-specific changes in gene expression profiles. Fig.…”
Section: Background and Summarymentioning
confidence: 99%
“…The seedling data were published in ref. 6 , which were used for comparison with the flower transcriptomic data generated in this study. …”
Section: Background and Summarymentioning
confidence: 99%
“…The mRNA and sRNA datasets generated from Arabidopsis seedlings can be accessed at GEO under the accession number GSE201841 16 and in Supplementary Data 1–16 accompanying the related paper 6 .…”
Arabidopsis NODULIN HOMEOBOX (NDX) is a plant-specific transcriptional regulator whose role in small RNA biogenesis and heterochromatin homeostasis has recently been described. Here we extend our previous transcriptomic analysis to the flowering stage of development. We performed mRNA-seq and small RNA-seq measurements on inflorescence samples of wild-type and ndx1-4 mutant (WiscDsLox344A04) Arabidopsis plants. We identified specific groups of differentially expressed genes and noncoding heterochromatic siRNA (hetsiRNA) loci/regions whose transcriptional activity was significantly changed in the absence of NDX. In addition, data obtained from inflorescence were compared with seedling transcriptomics data, which revealed development-specific changes in gene expression profiles. Overall, we provide a comprehensive data source on the coding and noncoding transcriptomes of NDX-deficient Arabidopsis flowers to serve as a basis for further research on NDX function.
“…In rice experiments based on H3K4me3 chromatin‐associated RNA–DNA interactions followed by paired‐end‐tag sequencing (ChRD‐PET) and ssDRIP‐seq analysis, ~20% of H3K4me3‐associated DNA–RNA interactions were shown to be derived from R‐loops, suggesting that R‐loops are involved in chromatin loop conformations (Figure 3C) (Xiao et al, 2022). Recently, work by Karanyi et al (2022) demonstrated that AtNDX, an R‐loop regulator at the FLC locus, regulated heterochromatin organization (Karanyi et al, 2022). However, it is still unclear whether AtNDX‐mediated (hetero)chromosomal contacts in Arabidopsis are R‐loop dependent, as R‐loop structures were shown to be critical for the integrity of topologically associated domains (TADs) in acute myeloid leukemia (AML) cells (Luo et al, 2022).…”
Section: The Biological Significances Of Plant R‐loopsmentioning
An R‐loop is a three‐stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by‐product of transcription. However, recent genome‐wide data have shown that R‐loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R‐loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R‐loop levels. Here, we summarize our current understanding of the biogenesis and effects of R‐loops, the mechanisms that regulate them, and methods of R‐loop profiling, reviewing recent research advances on R‐loops in plants. Furthermore, we provide perspectives on future research directions for R‐loop biology in plants, which might lead to a more comprehensive understanding of R‐loop functions in plant genome regulation and contribute to future agricultural improvements.
R-loops, composed of DNA–RNA hybrids and displaced single-stranded DNA, are known to pose a severe threat to genome integrity. Therefore, extensive research has focused on identifying regulatory proteins involved in controlling R-loop levels. These proteins play critical roles in preventing R-loop accumulation and associated genome instability. Herein I summarize recent knowledge on R-loop regulators affecting R-loop homeostasis, involving a wide array of R-loop screening methods that have enabled their characterization, from forward genetic and siRNA-based screens to proximity labeling and machine learning. These approaches not only deepen our understanding on R-loop formation processes, but also hold promise to find new targets in R-loop dysregulation associated with human pathologies.
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