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Health Sciences staff profiles

Beri Temiz

PositionPhD Student
DepartmentDepartment of Anatomy
QualificationsBSc Molecular Biology and Genetics, MSc Marine Biology and Fisheries
Research summaryInvestigating the mechanisms during whole-body regeneration of a marine colonial chordate
TeachingDemonstrating for GENE221: Molecular and Microbial Genetics and GENE312: Evolutionary Genetics
MembershipsEcology and Evolutionary Biology Society of Turkey


Ascidians are colonial chordates living in the intertidal zone as filter feeders. As the closest relative of the vertebrates, these urochordates include some genera with unique abilities thus became a commonly used marine model organism. Among these groups, botryllid ascidians like Botrylloides diegensis have various interesting characteristics including the ability to undergo whole-body regeneration (WBR), hibernation / aestivation, blastogenesis, metamorphosis, and natural chimerism. A small vascular tissue fragment from a B diegensis colony (~100-200 cells) is enough to create a new fully-functional adult within 8-14 days.

WBR ability is restricted to a small number of species such as hydra and planaria, with botryllids as the only chordates that can undergo this type of regeneration. B. diegensis WBR differs from other WBR examples, notably by the emergence of multiple regeneration niches that involve the clustering of Piwi and Integrin alpha positive haematopoietic progenitor cells. These clusters form a regeneration bud, that go on to form the organ systems of the adult.

Previously, we demonstrated that histone deacetylation (HDAC) activity is essential for the completion of WBR. Histone protein modifications, such as acetylation, regulate transcription factor access to the genomic DNA by changing chromatin structure. To be able to understand this in-depth, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) on control and HDAC inhibited colonial groups during the early stages of regeneration. Over 300 differentially accessible regions were found and the functional annotations linked these regions to genes involved in cell proliferation regulation and differentiation, such as RIG1, NOS1 and DLK1.

In addition to genome-wide studies, the roles of the chromatin remodellers during WBR including histone and chaperone targets are currently being investigated. We hypothesise that rapid changes to chromatin dynamics are essential for early cell differentiation from progenitor aggregates. Thus, I will be doing single-cell transcriptomics in order to understand the cellular origins of this process.