Positions

1. Postdoctoral position to study the evolution of alternative transcriptional termination in yeast

Date: Oct 20 2022. State: open. Reference: postdoc-dRNA-AEI

Mar Albà, ICREA Research Professor, Evolutionary Genomics Group, Hospital del Mar Medical Research Institute (IMIM) – Barcelona Biomedical Research Park (PRBB), Barcelona.

Description

We are looking to recruit one postdoctoral researcher to investigate the evolutionary dynamics of transcription termination and alternative polyadenylation in Saccharomyces cerevisiae and related species.

Many genes contains alternative termination and polyadenylation sites, which can produce transcripts with different 3’UTRs and sometimes also affect the coding sequence. Alternative transcription termination impacts post-transcriptional regulation of gene expression and generates transcript and protein diversity upon which natural selection can act, shaping the evolution of genes. In this project we will investigate alternative transcriptional termination in different yeast species using Nanopore native RNA sequencing data. We will identify complete single mRNA molecules, including the 3’UTR and poly(A) tail, obtaining a unique view into the transcriptional diversity of the species. The effects at the level of translation of early transcription termination events will be investigated using Ribo-Seq data from the same species. Furthermore, by using data from different Saccharomyces yeasts we will be able to identify conserved as well as species-specific events, obtaining a picture of the evolutionary dynamics of alternative transcription termination in this eukaryotic model system.

Requirements

• Research experience in comparative genomics and transcriptomics
• Expertise in at least one programming language
• Expertise in a programmatic statistics language (ideally R)
• Interest in molecular evolution
• Excellent verbal and written communication skills in English

Related Publications:

Montañés, J.C., Huertas, M., Moro, S.G., Blevins, W.R., Carmona, M., Ayté, J., Hidalgo, E., Albà, M.M. (2022). Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms. Genome Research, 32:1215-1227.

Blevins, W.R., Ruiz-Orera, J., Messeguer, X., Blasco-Moreno, B., Villanueva-Cañas, J.L., Espinar, L., Díez, J., Carey, L.B., Albà, M.M. (2021). Uncovering de novo gene birth in yeast using deep transcriptomics. Nature Communications, vol. 12: 604.

Location: We are located at the Barcelona Biomedical Research Park (PRBB), one of the most vibrant interdisciplinary research centers in Southern Europe hosting 1400 scientists and research support staff. The researchers will have access to state-of-the-art computational resources and a wide range of training opportunities.

Funding: The position is funded by Agencia Estatal de Investigación (Spanish Government) project PID2021-122726NB-I00. The contract will initially be for two years. Gross salary 30.951,44 – 33.899,38 Eur per year depending on experience. Flexible starting date.

Contact: Please send an email to Mar Albà (malba@imim.es) quoting “postdoc-dRNA-AEI” and including a CV and a motivation letter, together with the name of two contacts for references.

2. PhD fellowship applications through the La Caixa INPhINIT website are now open!

DOCTORAL INPhINIT FELLOWSHIPS PROGRAMME – INCOMING

Position
1. Project Title/ Job Position title: Study of the transcriptome diversity across individuals using new RNA sequencing technologies
2. Area of Knowledge:
• LIFE SCIENCES

3. Group of disciplines:
Human Biology, Microbiology, Molecular Biology, Genetics, Cellular Biology, Genomics and Proteomics, Biochemistry

4. Research project/ Research Group description (max. 2.000 characters)
One important source of phenotypic variation across individuals is at the level of gene expression, including transcripts that are only expressed under certain conditions and/or in certain individuals. Studying these differences has become easier with the development of long reads, such as Nanopore transcriptome technologies (Workman et al., 2019). In contrast to Illumina reads, which have a maximum size of about 300 bp, long reads can be several kilobases long. With these techniques it is possible to accurately identify splicing variants and differentiate between highly similar paralogous copies.
The project will leverage short and long read technologies to investigate transcriptome diversity in humans and other organisms. We have recently developed a method to build transcriptomes from ONT RNA-Seq data (cDNA and direct RNA) that does not require a reference genome and that could be used to recover chimeric transcripts in highly rearranged genomes such as those of cancer cells (de la Rubia et al., 2022). We will use this and other recently developed methods to identify novel isoforms and non-annotated transcripts across individuals and in different disease conditions. Direct RNA sequencing preserves the orientation of the original molecule and provides poly(A) length and information on RNA modifications. We will use this information to obtain a catalog of alternative transcript 3’end and poly(A) events and investigate these events from an evolutionary perspective, using available data from different yeast species.
The results of the project are expected to open new avenues of research into transcriptome diversity in health and disease.
Job position description (max. 2.000 characters)
We are seeking candidates to apply for a PhD studentship from the INPhINIT “La Caixa” Fellowship Programme. The student should be highly motivated to do a PhD in the field of Computational Genomics, with a special emphasis in transcriptomics. The fellowship will have a duration of 3 years.
The pre-doctoral researcher will use computational tools to reconstruct the transcriptome of different human tissues and cell lines using short and long read RNA-Seq data. She/he will also develop new computational approaches to predict alternative polyadenylation events using direct RNA sequencing data.
The research group is part of the Research Programme on Biomedical Informatics (GRIB, IMIM-UPF), and is located at the Barcelona Biomedical Research Park (PRBB), which offers a vibrant scientific and social atmosphere for PhD students. Research in the group is funded by several National projects as well as an ERC advanced Grant.
Group Leader
1. Title: ICREA Research Professor
2. Full name: Mar Albà
3. Email: malba@imim.es
4. Research project/ Research Group website (Url): evolutionarygenomics.imim.es
5. Website description: Evolutionary Genomics Group
Additional website (optional, max. 5 websites)
1. Url: https://scholar.google.es/citations?hl=ca&user=K3Y_DHkAAAAJ
2. Website description: Publications Mar Albà in Google Scholar