Biology subjects

Gebert, D.

Publications and source records attributed to Gebert, D..

8 recordsLinked to original sources

bioRxiv2024

Ribosome abundance, not paralogue composition, is essential for germline development

Ribosomes catalyse all protein synthesis, and mutations altering their levels and function underlie many developmental diseases and cancer. Historically considered to be invariant machines, ribosomes differ in composition between tissues and developmental stages, incorporating a diversity of ribosomal proteins (RP) encoded by duplicated paralogous genes. Here, we use Drosophila to systematically investigate the origins and functions of non-canonical RP paralogues. We show that new paralogues mainly originated through retroposition, and that only a few new copies retain coding capacity over time. Although transcriptionally active non-canonical RP paralogues often present tissue-specific expression, we show that the majority of those are not required for either viability or fertility in Drosophila melanogaster. The only exception, RpS5b, which is required for oogenesis, is functionally interchangeable with its canonical paralogue, indicating that the RpS5b-/- phenotype results from insufficient ribosomes rather than the absence of an RpS5b-specific, functionally-specialised ribosome. Altogether our results provide evidence that, instead of new functions, RP gene duplications provide a means to regulate ribosome levels during development.

developmental biology↗

bioRxiv2024

Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats

The Drosophila genus is ideal for studying genome evolution due to its simple chromosome structure and small genome size, with rearrangements mainly restricted to within chromosome arms. However, work on the rapidly evolving repetitive genomic regions, composed of transposons and tandem repeats, have been hampered by the lack of genus-wide chromosome-level assemblies. Integrating long read genomic sequencing and chromosome capture technology, we produced and annotated 30 chromosome-level genome assemblies within the Drosophila genus. Based on this dataset, we were able to reveal the evolutionary dynamics of genome rearrangements across the Drosophila phylogeny, including the identification of genomic regions that show comparatively high structural stability throughout evolution. Moreover, within the ananassae subgroup, we uncovered the emergence of new chromosome conformations and the rapid expansion of novel satellite DNA sequence families which form large and continuous peri/centromeric domains with higher-order repeat structures that are reminiscent to those observed in the human and Arabidopsis genomes. These chromosome-level genome assemblies present a highly valuable resource for future research, the power of which was demonstrated by our analysis of genome rearrangements and chromosome evolution. In addition, based on our findings, we propose the ananassae subgroup as an ideal model system for studying the evolution of centromere structure.

evolutionary biology↗

bioRxiv2024

Tolerance thresholds underlie responses to DNA damage during germline development

Selfish DNA modules like transposable elements (TEs) are particularly active in the germline, the lineage that passes genetic information across generations. New TE insertions can disrupt genes and impair the functionality and viability of germ cells. However, we find that in P-M hybrid dysgenesis in Drosophila, a sterility syndrome triggered by the P-element DNA transposon, germ cells harbour unexpectedly few new TE insertions, despite accumulating DNA double-strand breaks (DSBs) and inducing cell cycle arrest. Using an engineered CRISPR-Cas9 system, we show that generating DSBs at silenced P-elements or other non-coding sequences is sufficient to induce germ cell loss independently of gene disruption. Indeed, we demonstrate that both developing and adult mitotic germ cells are sensitive to DSBs in a dosage-dependent manner. Following the mitotic-to-meiotic transition, however, germ cells become more tolerant to DSBs, completing oogenesis regardless of the accumulated genome damage. Our findings establish DNA damage tolerance thresholds as crucial safeguards of genome integrity during germline development.

developmental biology↗

bioRxiv2023

Two distinct waves of transcriptome and translatome remodelling drive germline stem cell differentiation

Development and tissue maintenance require a supply of new cells, which are generated by division of stem cells and then specialised to perform their function. The differentiation process requires the tight control of gene expression, but this has been challenging to study in a systematic manner in adult stem cells, which are sparsely distributed in tissues. We have overcome these limitations by establishing a robust protocol to synchronise Drosophila female germline stem cell (GSC) differentiation in vivo, allowing us to perform transcriptome and translatome analyses at high temporal resolution during differentiation. As well as observing dynamic changes in mRNA level, promoter usage and exon inclusion, our data reveal that changing translation efficiency is the predominant regulatory mechanism during GSC differentiation. Indeed, changes in mRNA level are frequently buffered by changes in translation efficiency, including the translational repression of transcripts that will only be translated later during oocyte maturation or embryo development. Contrary to the expected linear accumulation of changes from stem cell to differentiated cell, our data reveal that differentiation occurs through two distinct waves of changes in both the transcriptome and translatome level.

developmental biology↗

bioRxiv2023

Mitotic heritability of DNA methylation at intermediately methylated sites is imprecise

DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.

genetics↗

bioRxiv2019

Widespread selection for high and low secondary structure in coding sequences across all domains of life

Codon composition, GC-content and local RNA secondary structures can have a profound effect on gene expression and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that in some cases selection favors more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and if this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analyzing a set of one million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low secondary structures significantly more often than expected by chance. Together, we demonstrate that selection for high and low secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.

evolutionary biology↗

bioRxiv2018

Conserved and ubiquitous expression of piRNAs and PIWI genes in mollusks antedates the origin of somatic PIWI/piRNA expression to the root of bilaterians

PIWI proteins and a specific class of small non-coding RNAs, termed Piwi interacting RNAs (piRNAs), suppress transposon activity in animals on the transcriptional and post-transcriptional level, thus protecting genomes from detrimental insertion mutagenesis. While in vertebrates the PIWI/piRNA system appears to be restricted to the germline, somatic expression of piRNAs directed against transposons is widespread in arthropods, likely representing the ancestral state for this phylum. Here, we show that somatic expression of PIWI genes and piRNAs directed against transposons is conserved in mollusks, suggesting that somatic PIWI/piRNA expression was already realized in an early bilaterian ancestor. We further describe lineage specific adaptations regarding transposon composition of piRNA clusters and show that different piRNA clusters are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs participate in the ping-pong amplification loop in a tissue specific manner.

evolutionary biology↗

bioRxiv2017

unitas: the universal tool for annotation of small RNAs

BackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.\n\nResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases (currently more than 800). unitas combines high quality annotation and numerous analysis features in a user-friendly manner. A complete annotation can be started with one simple shell command, making unitas particularly useful for researchers not having access to a bioinformatics facility. Noteworthy, the algorithms implemented in unitas are on par or even outperform comparable existing tools for small RNA annotation that base on available ncRNA sequence information.\n\nConclusionsunitas brings together annotation and analysis features that hitherto required the installation of numerous different bioinformatics tools which can pose a challenge for the non-expert user. With this, unitas overcomes the problem of read normalization. Moreover, the high quality of sequence annotation and analysis, paired with the ease of use, make unitas a valuable tool for researchers in all fields connected to small RNA biology.

bioinformatics↗