Biology subjects

Drews, F.

Publications and source records attributed to Drews, F..

4 recordsLinked to original sources

bioRxiv2021

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin our study characterizes the functional epigenomic organisation necessary for gene regulation and proper PolII activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) revealed no narrow peaks but broad domains along gene bodies, whereas intergenic regions were devoid of nucleosomes. Our data implicates H3K4me3 levels inside ORFs to be the main factor to associate with gene expression and H3K27me3 appears to occur as a bistable domain with H3K4me3 in plastic genes. Surprisingly, silent and lowly expressed genes show low nucleosome occupancy suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Due to a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different to other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data implies that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. This could represent a buffer for paused Pol II along ORFs in absence of elongation factors of higher eukaryotes.

genomics↗

bioRxiv2020

Two Piwis with Ago-like functions silence somatic genes at the chromatin level

Most sRNA biogenesis mechanisms involve either RNAseIII cleavage or ping-pong amplification by different Piwi proteins harboring slicer activity. Here, we follow the question why the mechanism of transgene-induced silencing in the ciliate Paramecium needs both Dicer activity and two Ptiwi proteins. This pathway involves primary siRNAs produced from non-translatable transgenes and secondary siRNAs from endogenous remote loci. Our data does not indicate any signatures from ping-pong amplification but Dicer cleavage of long dsRNA. We show that Ptiwi13 and 14 have different preferences for primary and secondary siRNAs but do not load them mutually exclusive. Both Piwis enrich for antisense RNAs and Ptiwi14 loaded siRNAs show a 5'-U signature. Both Ptiwis show in addition a general preference for Uridine-rich sRNAs along the entire sRNA length. Our data indicates both Ptiwis and 2-O-methylation to contribute to strand selection of Dicer cleaved siRNAs. This unexpected function of two distinct vegetative Piwis extends the increasing knowledge of the diversity of Piwi functions in diverse silencing pathways. As both Ptiwis show differential subcellular localisation, Ptiwi13 in the cytoplasm and Ptiwi14 in the vegetative macronucleus, we conclude that cytosolic and nuclear silencing factors are necessary for efficient chromatin silencing.

genetics↗

bioRxiv2020

Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana

Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized HRGP superfamily into three family members: the hyperglycosylated arabinogalactan-proteins, the moderately glycosylated extensins, and the lightly glycosylated proline-rich proteins. However, the mechanism of pollen-specific HRGP expression remains untouched. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences that identified 15 transcriptional cis-regulatory motifs responsible for pollen-specific expression of HRGP in Arabidopsis Thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery with various filters identified 15 conserved promoter elements between Thaliana and Lyrata. Known motif analysis revealed pollen related transcription factors of GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Lastly, we performed a machine learning regression analysis and demonstrated that the identified 15 motifs well captured the HRGP gene expression in pollen (R=0.61). In conclusion, we performed the integrative analysis as the first-of-its-kind study to identify cis-regulatory motifs in pollen-specific HRGP genes and shed light on its transcriptional regulation in pollen.

bioinformatics↗

bioRxiv2019

Differential degradation of RNA species by autophagy related pathways in plants

An important function of the plant vacuole is the recycling of the delivered proteins and RNA by autophagy. We provide the first plant vacuolar small RNome by isolation of intact vacuoles from Barley and Arabidopsis, subsequent RNA purification and Next Generation Sequencing. In these vacuolar sRNomes, all types of cellular RNAs were found including those of chloroplast origin, suggesting a bulk-type of RNA transfer to, and breakdown in vacuoles. ATG5 is a major representative of autophagy genes and the vacuolar RNA composition in corresponding knockout plants differed clearly from controls as most chloroplast derived RNA species were missing. Moreover, the read length distribution of RNAs found in ATG5 mutants differed to control samples, indicating altered RNA processing. In contrast, vacuolar RNA length and composition of plants lacking the vacuolar RNase2 (rns2-2), involved in cellular RNA homeostasis, showed minor alterations, only. Our data therefore suggests that mainly autophagy components are responsible for selective transport and targeting of different RNA species into the vacuole for degradation. In addition, mature miRNAs were detected in all vacuolar preparations, however in ATG5 mutants at much lower frequency, indicating a new biological role for vacuolar miRNAs apart from becoming degraded.

plant biology↗