The message in the noise: characterisation and quantification of noise in alternative splicing

Nearly all human genes undergo alternative splicing (AS) – the process by which different transcripts are generated from a single gene. AS can generate transcripts with strikingly different functions, either due to truncation of the protein coding sequence or alteration of functional domains. AS is highly regulated during development and across tissues involved in processes such as cell differentiation, migration, and cancer.

We have applied long-read sequencing to the study of AS across scales – from single cells to tissues – to reveal unexpected transcript diversity and have identified thousands of novel transcripts. In most cases, only one or two dominant transcripts represent the bulk of the expression arising from a gene, with the remaining transcripts lowly expressed and considered to be noise.
The characterisation of AS diversity across cells in steady state and during differentiation can provide novel insights on the regulation of this fundamental process. More specifically, we aim to answer a) whether individual cells exhibit the same distribution of transcript expression as seen in bulk, and b) how often does functional switching – from dominant to “noisy” transcript – occur in cell differentiation?

We offer a highly collaborative PhD project between the Haerty (bioinformatics) and Macaulay (molecular biology, technology development) groups. You will work in a rapidly developing field and gain unique expertise in experimental (cell culture, single cell biology) and computational (bioinformatics, transcriptomics, proteomic) biology.

The project will be conducted at the Earlham Institute, a UKRI-BBSRC research centre of excellence for bioinformatics and sequencing technology development, in close collaboration with scientists at the University of Oxford, and Wellcome Trust Sanger Genome Campus. You will have access to training and career development opportunities at EI and on the Norwich Research Park as part of the Norwich Biosciences Doctoral Training Partnership.

References

Wright, D. J. et al. Correction to: Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. BMC Genomics 23, 79 (2022).

Clark, M. B. et al. Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain. Mol. Psychiatry (2019) doi:10.1038/s41380-019-0583-1.

Mincarelli, L. et al. Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells. Commun Biol 6, 558 (2023).

Wan, Y. & Larson, D. R. Splicing heterogeneity: separating signal from noise. Genome Biol. 19, 86 (2018).

Gleeson J, Leger A, Prawer YDJ, Lane TA, Harrison PJ, Haerty W, Clark MB. 2022. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount.
Nucleic Acids Res. 50(4):e19.