Chromatin accessibility landscape and transcription changes in recognition memory after visual imprinting in chicks

Project Information

CHARM-Vis

Grant agreement ID: 867429

DOI

10.3030/867429

Project closed

EC signature date 25 April 2019

Start date 1 July 2019

End date 30 June 2021

Funded under

• SPREADING EXCELLENCE AND WIDENING PARTICIPATION

Total cost

€ 137 391,36

EU contribution

€ 137 391,36

Coordinated by

ILIA STATE UNIVERSITY
Georgia

Periodic Reporting for period 1 - CHARM-Vis (Chromatin accessibility landscape and transcription changes in recognition memory after visual imprinting in chicks)

Reporting period: 2019-07-01 to 2021-06-30

Summary of the context and overall objectives of the project

CHARM-Vis aimed at studying the formation of memory in vertebrates, an important, yet not-well-understood biological process. Particularly, the project focused on identifying changes in the chromatin landscape – and gene transcription – in chick brain following visual imprinting.
During visual imprinting, visually naïve chicks come to recognize an object by being exposed to it. This phenomenon can be peformed in tightly controlled conditions, thus offering an ideal model for the study of memory formation.
Samples from the intermediate and medial mesopallium (IMM), a chick forebrain region previously recognized as of crucial importance for visual imprinting, were analysed using Assay for Transposase-Accessible Chromatin (ATAC) and single nuclei (sn) RNA sequencing, and the resulting data were analyzed for identifying molecular changes associated with imprinting.
By the end of the action, the use of these two technologies ensured the identification of dozens of memory-related molecular events at an unprecedented level of resolution. An independent validation of our findings is currently undergoing. Once confirmed, our findings will allow to achieve a better characterization of the molecular mechanisms involved in memory formation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Several activities were required for achieving the objective of the project. First, we produced the snRNA-seq and ATAC-seq data related to memory formation in chicks. This step required formulating and optimizing an experimental protocol specific for preparing nuclei suspensions suitable for snRNA-seq from frozen chick brain tissue. This first activity was performed in collaboration with the SciLifeLab facilities in Stockholm, Sweden.
The data production activity produced more than 350 GB of raw data, which required advanced bioinformatics software pipelines for being analyzed. The analyses detected several significant changes in gene expression levels and chromatin openess, and the results are currently undergoing further validation studies.
Alongside the production and study of the ATAC- and snRNA-seq data, we further investigated proteins and circular RNAs changes in the IMM associated with imprinting. These additional studies underlined the presence of even more molecular mechanisms possibly involved in memory formation.
Our results are being disseminated through scientific publications (one accepted, two under preparation), while the CHARM-Vis projects has been presented to groups of interests in several fora, including the EU Conference “Making the Most of Georgia’s Association to Horizon 2020” (November 2019, Tbilisi, Georgia).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This is the first time that molecular changes associated to imprinting in chicks are investigated at the single cell level. We expect the results of our action to shed light on the biological processes related to memory formation in vertebrates, with potential impact on the treatment of mental illnesses, particularly amnesia.

Expression levels of the MEF2C gene between good learner and untrained chicks across cell clusters