Research results obtained for the defined objectives:
1. During the action, genomics data in clonal, F1 hybrid female mouse neural progenitor cells (NPCs) established in the hosting group were generated, to determine the transcriptional status of genes, DNA accessible regions and the presence of enhancers. As the NPC clones were derived from crosses of distant mouse species this enabled the bioinformatics analysis of the data in an allele-specific manner, to distinguish the signal originating from the Xi or Xa chromosomes. These data were used to identify enriched TF binding motifs in regulatory regions of the Xi chromosome. The motif corresponding to the architectural protein, CTCF, was detected in this analysis. As part of a collaboration in the group, genomics data to delineate CTCF binding in the X chromosomes were generated, as well as, cell lines to assess the impact of CTCF depletion in the expression of escapees. Notably, CTCF has been suggested to play a role in the process of escape since years and this work is contributing to identify its exact functions in this process.
2. The variability of expression from the Xi chromosome was also investigated using the genomics data of NPC clones. Although the transcriptional data used for this analysis were only derived from NPC samples, there was high variability in the number of escapees between clones and no strong correlation between the frequency of escape and level of expression was observed.
A manuscript summarizing some of the results obtained is currently being drafted, and we expect to submit this to a peer-reviewed journal in the next months.
Concomitant to the research activities, Dr Pérez-Rico improved her data analysis skills with the R and python programming languages and gained knowledge in machine learning methods. Importantly, she learnt to implement bioinformatic pipelines using a workflow manager, which increases analysis reproducibility, in line with the objectives of the Data Management Plan. In addition, Dr Pérez-Rico participated in training offered by EMBL administration and the Heidelberg International Professional (HIP) Women’s Forum to hone transferable skills, in particular, communication and leadership. These skills proved extremely useful during the supervision of a master student during one semester and the dissemination of results.
Project results were communicated both as poster talks in conferences with expert audiences and with the general public. Outreach activities included talks with high school students and professional women of the Heidelberg Area, participation as jury in science fairs and a pen pal program. These activities were broadly communicated in my Twitter account and with a blog entry (
https://emblpenpals.wordpress.com/2020/05/16/how-to-fulfill-our-social-responsibility-as-scientists(s’ouvre dans une nouvelle fenêtre)). The fellow is particularly grateful for having had the opportunity to interact with young students in developing countries (Mexico and Nigeria) that often lack access to outreach activities, as she experienced during her childhood.
