Biology subjects

Battistini, F.

Publications and source records attributed to Battistini, F..

5 recordsLinked to original sources

bioRxiv2026

Structural and functional basis of the non-canonical human Dicer-tRNA complex

Human Dicer (hDicer) is a key enzyme in the RNA interference (RNAi) pathway that generates [~]21-22 nt micro-RNA (miRNAs) and small interfering RNAs (siRNAs). We have previously shown that hDicer also generates tRNA-derived small RNAs (tsRNAs), which mediate nuclear gene silencing and regulate hundreds of disease-associated genes. As powerful and evolutionarily conserved cellular regulators, tsRNAs emerged as an important class of small RNAs. Therefore, it is essential to understand their biogenesis. However, the molecular and structural basis of tRNA cleavage by hDicer, as well as the role of chemical modifications such as 5-methylcytosine (m5C), in this process, remain unknown. Here, we present the first structural insights into hDicer in complex with tRNA, obtained by cryo-electron microscopy (cryo-EM), selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and molecular dynamics (MD) simulations. Our results reveal that tRNAs adopt alternative conformations that are recognized and processed by hDicer. Furthermore, we show that tRNA cleavage by hDicer is facilitated by the m5C modification deposited by Nop2/SUN RNA methyltransferase 2 (NSUN2). Collectively, our findings redefine tRNAs as bona fide hDicer substrates and uncover a modification-dependent biogenetic pathway that reshapes the current understanding of the origins and regulation of human small RNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/744379v1_ufig1.gif" ALT="Figure 1000"> View larger version (24K): org.highwire.dtl.DTLVardef@14a8682org.highwire.dtl.DTLVardef@1c4d0daorg.highwire.dtl.DTLVardef@6bc433org.highwire.dtl.DTLVardef@11e27e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Regulatory landscape of widespread stop codon readthrough in Drosophila

In stop codon readthrough (SCR), ribosomes continue to translate past the stop. While programmed SCR is rare in mammals, it appears remarkably widespread in insects, yet its regulation and biological significance remain poorly understood. Here, we systematically characterize SCR in Drosophila melanogaster by integrating ribosome profiling, comparative genomics, proteomics, and functional screening. We identify [~]1,400 SCR genes, reveal sequence features associated with programmed SCR, and distinguish constitutive and tissue-restricted modes. We identify conserved cis-elements sufficient to stimulate constitutive SCR and demonstrate that many remain functional in mammalian cells. Unexpectedly, the major distinction between insect and mammalian cells was not termination efficiency, but insect responsiveness to SCR-promoting regulatory elements. SCR was further associated with increased overall protein output, suggesting a function beyond proteome diversification. Our results establish SCR as a pervasive regulatory mechanism in Drosophila and provide a new framework for its study through the Drosophila Stop Codon Readthrough Atlas.

genomics↗

bioRxiv2022

The Pseudo-Torsional Space of RNA

The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a big variety of conformations. These backbone conformations can be depicted by pseudo-torsional angles linking RNA backbone atoms, from which Ramachandran-like plots can be built. We explored here different definitions of these pseudo-torsional angles, finding that the most accurate ones are the traditional {eta} (eta) and {theta} (theta) angles, which represent the relative position of RNA backbone atoms P and C4. We explore the distribution of {eta}-{theta} in known experimental structures, comparing the pseudo-torsional space generated with structures determined exclusively by one experimental technique. We found that the complete picture only appears when combining data from different sources. The maps provide a quite comprehensive representation of the RNA accessible space, which can be used in RNA-structural prediction. Finally, our results highlight that protein interactions leads to significant changes in the population of the {eta}-{theta} space, pointing towards the role of induced-fit mechanisms in protein-RNA recognition.

bioinformatics↗

bioRxiv2020

THE IMPACT OF THE HYDROXYMETHYLCYTOSINE EPIGENETIC SIGNATURE ON DNA STRUCTURE AND FUNCTION

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties not too different to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methyl-cytosine (mC) and 5-hydroxymethyl-cytosine (hmC) generally lead to more rigid duplexes with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). On the contrary, our simulations suggest that methylated-DNA binding domains (MBD), associated with repression activities, are very sensitive to the substitution d(mCpG)[->] d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) [->] d(hmCpG) change. Overall, while changes in gene activity due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

biochemistry↗

bioRxiv2019

Colibactin DNA damage signature indicates causative role in colorectal cancer

Colibactin, a potent genotoxin of Escherichia coli, causes DNA double strand breaks (DSBs) in human cells. We investigated if colibactin creates a particular DNA damage signature in infected cells by identifying DSBs in colon cells after infection with pks+ E.coli. Interestingly, genomic contexts of DSBs were enriched for AT-rich penta-/hexameric sequence motifs, exhibiting a particularly narrow minor groove width and extremely negative electrostatic potential. This corresponded with the binding characteristics of colibactin to double-stranded DNA, as elucidated by docking and molecular dynamics simulations. A survey of somatic mutations at the colibactin target sites of several thousand cancer genomes revealed significant enrichment of the identified motifs in colorectal cancers. Our work provides direct evidence for a role of colibactin in the etiology of human cancer.\n\nOne sentence summaryWe identify a mutational signature of colibactin, which is significantly enriched in human colorectal cancers.

microbiology↗