ESR1: Identification of the gene networks that modulate ABCA4 expression
Partner
Telethon Institute of Genetics and Medicine, Naples, Italy (www.telethon.it; www.tigem.it) Supervisor Prof. Dr. S. Banfi |
Karla Alejandra Ruiz-Ceja
My name is Karla, I am Mexican, and I was part of the StarT consortium. I am a biologist who graduated from UNAM. Afterwards, I chose to continue my studies abroad, so I pursued my master's degree in Genomic Medicine at the University of Manchester, where I had my first introduction to personalized medicine, a deep study of inherited diseases and bioinformatics. I came back to Mexico and worked for a couple of years as a genomic/bioinformatics specialist and Project Manager for a couple of biotech companies. I then decided it was time to achieve my Ph.D., and in 2019, I joined the StarT consortium at TIGEM in Italy. This allowed me not only to learn a new language but also to enjoy "la dolce vita" with delicious Italian food (tons of pasta and pizza) while I broadened my knowledge and deeply developed in the bioinformatics field. One of the greatest advantages of the StarT consortium was that belonging to a research network let me engage and share ideas with other ESRs, improving and enriching our research. During my PhD, I delved deeper into the bioinformatics world and expanded my knowledge in the analysis of different data types, leading me to the identification of new transcripts of the IRD genes. I concluded my PhD in Biomolecular Science in June 2023 from the L'Università degli Studi della Campania "Luigi Vanvitelli". My project was focused on the study of the genomic organisation of inherited disease genes and the identification of co-expressed long non-coding RNAs by meta-analysis of human retina transcriptome data. Currently, I am a Postdoc studying the long non-coding RNAs that were found to be co-expressed with IRD genes by using different approaches. Thanks to StarT, we published the work: “Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data” (PMID: 37072692) and are currently working on a second manuscript. Being part of the StarT project gave me the chance to learn from myself and others, inspiring and immersing me in different cultures and situations that led me to personal and scientific growth. |
Abstract
We have recently generated a comprehensive mRNA and microRNA (miRNAs) transcriptome of the human retina and have acquired expertise in co&expression analysis. Here, ESR1 will capitalise on these resources to gain insight into the organisation of the ABCA4 transcriptional unit and into the dissection of the gene networks that participate in the modulation of the expression and function of ABCA4 in human retina. ESR1 will further define the genomic organisation of the ABCA4 gene using our vast RNA&seq dataset to identify and validate the presence of alternative transcript variants. By integrating already available and newly&generated transcriptomics data carried out both in human and in mouse, ESR1 will reconstruct the transcriptional gene networks that modulate ABCA4 expression in photoreceptors in both physiological and pathological conditions. ESR1 will pay particular attention to the contribution of miRNAs and will combine target predictions with our data on miRNA expression in the retina to select candidate miRNAs predicted to regulate ABCA4 and validate their biological relevance using in vitro and in vivo assays.
We have recently generated a comprehensive mRNA and microRNA (miRNAs) transcriptome of the human retina and have acquired expertise in co&expression analysis. Here, ESR1 will capitalise on these resources to gain insight into the organisation of the ABCA4 transcriptional unit and into the dissection of the gene networks that participate in the modulation of the expression and function of ABCA4 in human retina. ESR1 will further define the genomic organisation of the ABCA4 gene using our vast RNA&seq dataset to identify and validate the presence of alternative transcript variants. By integrating already available and newly&generated transcriptomics data carried out both in human and in mouse, ESR1 will reconstruct the transcriptional gene networks that modulate ABCA4 expression in photoreceptors in both physiological and pathological conditions. ESR1 will pay particular attention to the contribution of miRNAs and will combine target predictions with our data on miRNA expression in the retina to select candidate miRNAs predicted to regulate ABCA4 and validate their biological relevance using in vitro and in vivo assays.
