Biology subjects

Mick, S. T.

Publications and source records attributed to Mick, S. T..

3 recordsLinked to original sources

bioRxiv2024

mRNA initiation and termination are spatially coordinated

The expression of a precise mRNA transcriptome is crucial for establishing cell identity and function, with dozens of alternative isoforms produced for a single gene sequence. The regulation of mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processing mechanisms across a gene. Decisions involved in mRNA initiation and termination underlie the largest extent of mRNA isoform diversity, but little is known about any relationships between decisions at both ends of mRNA molecules. Here, we systematically profile the joint usage of mRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues and species. Using both short and long read RNA-seq data, we observe that mRNAs preferentially using upstream TSSs also tend to use upstream PASs, and congruently, the usage of downstream sites is similarly paired. This observation suggests that mRNA 5 end choice may directly influence mRNA 3 ends. Our results suggest a novel "Positional Initiation-Termination Axis" (PITA), in which the usage of alternative terminal sites are coupled based on the order in which they appear in the genome. PITA isoforms are more likely to encode alternative protein domains and use conserved sites. PITA is strongly associated with the length of genomic features, such that PITA is enriched in longer genes with more area devoted to regions that regulate alternative 5 or 3 ends. Strikingly, we found that PITA genes are more likely than non-PITA genes to have multiple, overlapping chromatin structural domains related to pairing of ordinally coupled start and end sites. In turn, PITA coupling is also associated with fast RNA Polymerase II (RNAPII) trafficking across these long gene regions. Our findings indicate that a combination of spatial and kinetic mechanisms couple transcription initiation and mRNA 3 end decisions based on ordinal position to define the expression mRNA isoforms.

genomics↗

bioRxiv2023

evopython: a Python package for feature-focused, comparative genomic data exploration

MotivationSoftware such as LiftOver allows for the intra- and inter-species conversion of genomic coordinates between genome assemblies, but this coordinate-centric workflow is naive to sequence alterations underling the conversion. For instance, it does not clarify the location of any insertions or deletions that might have occurred. ResultsTo facilitate inter-species, sequence-based analyses, we developed evopython, a simple, object-oriented Python package that enables the sequence-aware resolution of genomic coordinates directly from pairwise and multiple whole-genome alignment data. The output is a Python dictionary storing all information relevant to the alignment: the participating species names, the position of the alignment in each species genome assembly, and the aligned sequences. Availability and implementationThe source code and documentation are available at https://github.com/fiszbein-lab/evopython. Contactanafisz@bu.edu

bioinformatics↗

bioRxiv2022

Splicing-dependent transcriptional activation

Transcription and splicing are intrinsically coupled. Transcription dynamics regulate splicing, and splicing feeds back to transcription initiation to jointly determine gene expression profiles. A recently described phenomenon called exon-mediated activation of transcription starts (EMATS) shows that splicing of internal exons can regulate transcription initiation and activate cryptic promoters. Here, we present the first complete catalog of human EMATS genes that have a weak alternative promoter located upstream and proximate to an efficiently spliced internal skipped exon. We found that EMATS genes are associated with Mendelian genetic diseases --specifically intellectual development disorders, cardiomyopathy, and immunodeficiency-- and provide a list of EMATS genes with pathological variants. EMATS was originally described as a natural mechanism used during evolution to fine-tune gene expression through punctual genomic mutations that affect splicing. Here, we show that EMATS can be used to manipulate gene expression with therapeutic purposes. We constructed stable cell lines expressing a splicing reporter based on the alternative splicing of exon 7 of SMN2 gene under the regulation of different promoters. Using a small molecule (Risdiplam) and an antisense oligonucleotide (ASO) modeled after Spinraza, we promoted the inclusion of SMN2 exon 7 which triggered an increase in gene expression up to 40-folds by activating transcription initiation. We observed the strongest effects in reporters under the regulation of weak human promoters, where the highest drug doses dramatically increased exon inclusion. Overall, our findings present evidence to develop the first therapeutic strategy to use EMATS to activate gene expression using small molecules and ASOs that affect splicing.

molecular biology↗