Biology subjects

Ozpolat, B. D.

Publications and source records attributed to Ozpolat, B. D..

5 recordsLinked to original sources

bioRxiv2024

Molecular profile, source and lineage restriction of stem cells in an annelid regeneration model

Regeneration of missing body parts can be observed in diverse animal phyla, but it remains unclear to which extent these capacities rely on shared or divergent principles. Research into this question requires detailed knowledge about the involved molecular and cellular principles in suitable reference models. By combining single-cell RNA sequencing and mosaic transgenesis in the marine annelid Platynereis dumerilii, we map cellular profiles and lineage restrictions during posterior regeneration. Our data reveal cell-type specific injury responses, re-expression of positional identity factors, and the re-emergence of stem cell signatures in multiple cell populations. Epidermis and mesodermal coelomic tissue produce distinct putative posterior stem cells (PSCs) in the emerging blastema. A novel mosaic transgenesis strategy reveals both developmental compartments and lineage restrictions during regenerative growth. Our work supports the notion that posterior regeneration involves dedifferentiation, and reveals molecular and mechanistic parallels between annelid and vertebrate regeneration.

developmental biology↗

bioRxiv2024

A genome resource for the marine annelid Platynereis dumerilii

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of [~]1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation ([~]3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

genomics↗

bioRxiv2024

Sex-biased gene expression precedes sexual dimorphism in the agonadal annelid Platynereis dumerilii

Gametogenesis is the process by which germ cells differentiate into mature sperm and oocytes, cells essential for sexual reproduction. The sex-specific molecular programs that drive spermatogenesis and oogenesis can also serve as sex identification markers. Platynereis dumerilii is a research organism that has been studied in many areas of developmental biology. However investigations often disregard sex, as P. dumerilii juveniles lack sexual dimorphism. The molecular mechanisms of gametogenesis in the segmented worm P. dumerilii are also largely unknown. In this study, we used RNA sequencing to investigate the transcriptomic profiles of gametogenesis in P. dumerilii juveniles. Our analysis revealed that sex-biased gene expression becomes increasingly pronounced during the advanced developmental stages, particularly during the meiotic phases of gametogenesis. We identified conserved genes associated with spermatogenesis, such as dmrt1, and a novel gene psmt, that is associated with oogenesis. Additionally, putative long non-coding RNAs were upregulated in both male and female gametogenic programs. This study provides a foundational resource for germ cell research in P. dumerilii, markers for sex identification, and offers comparative data to enhance our understanding of the evolution of gametogenesis mechanisms across species. Summary statementThis study provides insights into the mechanisms of gametogenesis in Platynereis dumerilii through comparative transcriptomics, unveiling sex-biased genes, including conserved and novel genes, governing this largely unexplored process.

developmental biology↗

bioRxiv2024

The cost and payout of age on germline regeneration and sexual maturation in Platynereis dumerilii

Regeneration, regrowing lost and injured body parts, is an ability that generally declines with age or developmental transitions (i.e. metamorphosis, sexual maturation) in many organisms. Regeneration is also energetically a costly process, and trade-offs occur between regeneration and other costly processes such as somatic growth, or sexual reproduction. Here we investigate the interplay of regeneration, reproduction, and age in the segmented worm Platynereis dumerilii. P. dumerilii can regenerate its whole posterior body axis, along with its reproductive cells, thereby having to carry out the two costly processes (somatic and germ cell regeneration) after injury. We specifically examine how age affects the success of germ cell regeneration and sexual maturation in developmentally young versus old organisms. We hypothesized that developmentally younger individuals (i.e. lower investment state, with gametes in early mitotic stages) will have higher regeneration success and reach sexual maturation faster than the individuals at developmentally older stages (i.e. higher investment state, with gametes in the process of maturation). Surprisingly, older amputated worms grew faster and matured earlier than younger amputees, even though they had to regenerate more segments and recuperate the more costly germ cells which were already starting to undergo gametogenesis. To analyze germ cell regeneration across stages, we used Hybridization Chain Reaction for the germline marker vasa. We found that regenerated worms start repopulating new segments with germ cell clusters as early as 14 days post amputation. In addition, vasa expression is observed in a wide region of newly-regenerated segments, which appears different from expression patterns during normal growth or regeneration in worms before gonial cluster expansion. Future studies will focus on determining the exact sources of gonial clusters in regeneration. FundingNIGMS 1R35GM138008-01, Hibbitt Fellowship, WashU Startup funds

developmental biology↗

bioRxiv2021

Segment number threshold determines juvenile onset of germline cluster proliferation in Platynereis dumerilii

Many animals rely on sexual reproduction to propagate by using gametes (oocytes and sperm). Development of sexual characters and generation of gametes are tightly coupled with the growth of an organism. Platynereis dumerilii is a marine segmented worm which has been used to study germline development and gametogenesis. Platynereis has 4 Primordial Germ Cells (PGCs) that arise early in development and these cells are thought to give rise to germ cell clusters found across the body in the juvenile worms. The germ cell clusters eventually form the gametes. The stages of germline development and how the 4 PGCs become the numerous germ cell clusters are not well-documented in the juvenile stages. Platynereis, like other segmented worms, grows by adding new segments at its posterior end. The number of segments generally reflect the growth state of the worms and therefore is a useful and easily measurable growth state metric. To understand how growth correlates with development and gametogenesis, we investigated germline development across several developmental stages using germline/multipotency markers. We found that segment number predicted the state of germline development and the abundance of germline clusters. Additionally, we found that keeping worms short in segment number via changing external conditions or via amputations supported segment number threshold requirement for germline development. Finally, we asked if these clusters in Platynereis play a role in regeneration (as similar free-roaming cells are observed in Hydra and planarian regeneration) and found that the clusters were not required for regeneration in Platynereis, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state in juvenile Platynereis when germline proliferation is substantially increased.

developmental biology↗