Honors & Awards

  • Postdoctoral Fellowship, American Italian Cancer Association (2021-2022)
  • 4-year PhD Fellowship, Wellcome Trust (2016-2020)

Professional Education

  • PhD, University of Manchester, Quantitative and Biophysical Biology (2021)
  • MSc, University of Nottingham, Mathematical Medicine and Biology (2016)
  • BS, UniversitĂ  degli Studi di Firenze, Mathematics (2015)

Stanford Advisors

All Publications

  • Developmental Regulation of Alternative Polyadenylation in an Adult Stem Cell Lineage. bioRxiv : the preprint server for biology Gallicchio, L., R Matias, N., Morales-Polanco, F., Nava, I., Stern, S., Zeng, Y., Fuller, M. T. 2024


    Co-transcriptional alternate processing of nascent mRNA molecules can make major contributions to cell type specific gene expression programs as proliferating precursor cells initiate terminal differentiation. Alternative Cleavage and Polyadenylation (APA) can result in the production of mRNA isoforms from the same gene locus with either longer or shorter 3'UTRs. In Drosophila spermatogenesis, approximately 500 genes undergo APA as proliferating spermatogonia differentiate into spermatocytes, producing transcript isoforms with shortened 3'UTRs, and resulting in profound stage specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that PCF11 and Cbc, the two components of Cleavage factor II (CFII), orchestrate APA switching during Drosophila spermatogenesis. Knockdown of PCF11 or cbc in spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Although PCF11 is widely expressed, cbc is strongly upregulated in spermatocytes. Our findings reveal a developmental mechanism where changes in activity of specific cleavage factors can direct cell type specific APA at selected genes, presenting CFII as a key developmental regulator of APA during spermatogenesis.

    View details for DOI 10.1101/2024.03.18.585561

    View details for PubMedID 38562704

  • Cell-type-specific interacting proteins collaborate to regulate the timing of Cyclin B protein expression in male meiotic prophase. Development (Cambridge, England) Baker, C. C., Gallicchio, L., Matias, N. R., Porter, D. F., Parsanian, L., Taing, E., Tam, C., Fuller, M. T. 2023


    During meiosis, germ cell and stage-specific components impose additional layers of regulation on the core cell cycle machinery to set up an extended G2 period termed meiotic prophase. In Drosophila males, meiotic prophase lasts 3.5 days, during which spermatocytes upregulate of over 1800 genes and grow 25-fold. Previous work showed that the cell cycle regulator Cyclin B (CycB) is subject to translational repression in immature spermatocytes, mediated by the RNA-binding protein Rbp4 and its partner Fest. Here we show that the spermatocyte-specific protein Lut is required for translational repression of cycB in an 8-hour window just before spermatocytes are fully mature. In males mutant for rbp4 or lut, spermatocytes enter and exit meiotic division 6-8 hours earlier than in wild-type. In addition, spermatocyte-specific isoforms of Syncrip (Syp) are required for expression of CycB protein in mature spermatocytes and normal entry into the meiotic divisions. Lut and Syp interact with Fest independent of RNA. Thus a set of spermatocyte-specific regulators choreograph the timing of expression of CycB protein during male meiotic prophase.

    View details for DOI 10.1242/dev.201709

    View details for PubMedID 37882771

  • Regulation and function of alternative polyadenylation in development and differentiation. RNA biology Gallicchio, L., Olivares, G. H., Berry, C. W., Fuller, M. T. 2023; 20 (1): 908-925


    Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.

    View details for DOI 10.1080/15476286.2023.2275109

    View details for PubMedID 37906624

  • Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage. Genes & development Berry, C. W., Olivares, G. H., Gallicchio, L., Ramaswami, G., Glavic, A., OlguĂ­n, P., Li, J. B., Fuller, M. T. 2022


    Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3' cleavage site, resulting in the production of mRNA isoforms with different length 3' UTRs. Although widespread, the role of APA in the biology of cells, tissues, and organisms has been controversial. We identified >500 Drosophila genes that express mRNA isoforms with a long 3' UTR in proliferating spermatogonia but a short 3' UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3' end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3' UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed >250 genes where the long 3' UTR versus short 3' UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3' end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.

    View details for DOI 10.1101/gad.349689.122

    View details for PubMedID 36175033

  • miR-9a regulates levels of both rhomboid mRNA and protein in the early Drosophila melanogaster embryo. G3 (Bethesda, Md.) Gallicchio, L., Griffiths-Jones, S., Ronshaugen, M. 2022


    MicroRNAs can have subtle and combinatorial effects on the levels of the targets and pathways they act on. Studying the consequences of a single microRNA knockout often proves difficult as many such knockouts exhibit phenotypes only under stress conditions. This has often led to the hypothesis that microRNAs buffer the effects of intrinsic and environmental stochasticity on gene expression. Observing and understanding this buffering effect entails quantitative analysis of microRNA and target expression in single cells. To this end, we have employed single molecule fluorescence in situ hybridization, immunofluorescence, and high-resolution confocal microscopy to investigate the effects of miR-9a loss on the expression of the serine-protease Rhomboid in Drosophila melanogaster early embryos. Our single-cell quantitative approach shows that spatially, the rhomboid mRNA pattern is identical in WT and miR-9a knockout embryos. However, we find that the number of mRNA molecules per cell is higher when miR-9a is absent, and the level and temporal accumulation of rhomboid protein shows a more dramatic increase in the miR-9a knockout. Specifically, we see accumulation of rhomboid protein in miR-9a mutants by stage 5, much earlier than in WT. The data therefore show that miR-9a functions in the regulation of rhomboid mRNA and protein levels. While further work is required to establish whether rhomboid is a direct target of miR-9 in Drosophila, our results further establish the miR-9 family microRNAs as conserved regulators of timing in neurogenic processes. This work shows the power of single-cell quantification as an experimental tool to study phenotypic consequences of microRNA mis-regulation.

    View details for DOI 10.1093/g3journal/jkac026

    View details for PubMedID 35143618

  • Single-cell visualization of mir-9a and Senseless co-expression during Drosophila melanogaster embryonic and larval peripheral nervous system development G3-GENES GENOMES GENETICS Gallicchio, L., Griffiths-Jones, S., Ronshaugen, M. 2021; 11 (1)


    The Drosophila melanogaster peripheral nervous system (PNS) comprises the sensory organs that allow the fly to detect environmental factors such as temperature and pressure. PNS development is a highly specified process where each sensilla originates from a single sensory organ precursor (SOP) cell. One of the major genetic orchestrators of PNS development is Senseless, which encodes a zinc finger transcription factor (Sens). Sens is both necessary and sufficient for SOP differentiation. Senseless expression and SOP number are regulated by the microRNA miR-9a. However, the reciprocal dynamics of Senseless and miR-9a are still obscure. By coupling single-molecule FISH with immunofluorescence, we are able to visualize transcription of the mir-9a locus and expression of Sens simultaneously. During embryogenesis, we show that the expression of mir-9a in SOP cells is rapidly lost as Senseless expression increases. However, this mutually exclusive expression pattern is not observed in the third instar imaginal wing disk, where some Senseless-expressing cells show active sites of mir-9a transcription. These data challenge and extend previous models of Senseless regulation and show complex co-expression dynamics between mir-9a and Senseless. The differences in this dynamic relationship between embryonic and larval PNS development suggest a possible switch in miR-9a function. Our work brings single-cell resolution to the understanding of dynamic regulation of PNS development by Senseless and miR-9a.

    View details for DOI 10.1093/g3journal/jkaa010

    View details for Web of Science ID 000651851700005

    View details for PubMedID 33561238

    View details for PubMedCentralID PMC7849905