Biology subjects

Veronezi, G. M. B.

Publications and source records attributed to Veronezi, G. M. B..

3 recordsLinked to original sources

bioRxiv2022

Nucleation and spreading rejuvenate polycomb domains every cell cycle

Gene repression by the polycomb pathway is essential for proper development in metazoans. Polycomb domains, characterized by trimethylation of histone H3 (H3K27me3), carry the memory of repression through successive cell divisions, and hence, need to be maintained to counter dilution during replication of parental H3K27me3 with unmodified nascent H3. Yet, how locus-specific H3K27me3 is maintained through replication is unknown. To understand H3K27me3 recovery post-replication, we first defined nucleation sites within each polycomb domain in mouse embryonic stem cells. Then, to track H3K27me3 dynamics in unperturbed cells during replication, we developed CUT&Flow, which maps H3K27me3 domains as a function of the cell cycle stage. Using CUT&Flow, we show that post-replication rejuvenation of polycomb domains occurs by nucleation and spreading, using the same nucleation sites used during de novo domain formation. By using subunit-specific inhibitors of the PRC2 complex, we find that PRC2 need not rely on pre-existing H3K27me3 to target nucleation sites post-replication. The timing of nucleation relative to the cell cycle reflects the combination of replication timing and H3K27me3 deposition kinetics derived from de novo domain formation. Thus, competition between H3K27me3 deposition and nucleosome turnover drives both de novo domain formation and maintenance during every cell cycle.

molecular biology↗

bioRxiv2021

Nematode Small RNA Pathways in the Absence of piRNAs

Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited. Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that are associated with secondary 5-triphosphate small RNAs (22-24G-RNAs). These Ascaris WAGOs and their small RNAs target repetitive sequences (WAGO-1, WAGO-2, WAGO-3, and NRDE-3) or mature mRNAs (CSR-1, NRDE-3, and WAGO-3) and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Ascaris CSR-1 likely functions to "license" gene expression in the absence of an Ascaris piRNA pathway. Ascaris ALG-4 and its associated 26G-RNAs target and appear to repress specific mRNAs during meiosis in the testes. Notably, Ascaris WAGOs (WAGO-3 and NRDE-3) small RNAs change their targets between repetitive sequences and mRNAs during spermatogenesis or in early embryos illustrating target plasticity of these WAGOs. We provide a unique and comprehensive view of mRNA and small RNA expression throughout nematode spermatogenesis that illustrates the dynamics and flexibility of small RNA pathways. Overall, our study provides key insights into the conservation and divergence of nematode small RNA pathways.

genomics↗

bioRxiv2020

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

Germline and somatic genomes are typically the same in a multicellular organism. However, in some organisms including the parasitic nematode Ascaris, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematode Ascaris demonstrated that programmed DNA elimination encompasses high fidelity chromosomal breaks at specific genome locations and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of the 120 bp repeats, the breaks regions, and the eliminated genes remained unknown. Here, we used PacBio long-read sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes of Ascaris germline and somatic genomes, enabling a complete chromosomal view of DNA elimination. Surprisingly, we found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All new Ascaris somatic chromosome ends are recapped by de novo telomere healing. We provide an ultrastructural analysis of DNA elimination and show that Ascaris eliminated DNA is incorporated into many double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that germline chromosome fusions occurred forming Ascaris sex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.

genomics↗