Jack Tierney

Bioinformatician @ EMBL-EBI - Using Ribo-Seq for genome annotation

[Jack Tierney @JackATierney]

Ribo-Seq has unearthed thousands of fascinating cases of translation complexity over the last decade. Through the exploration of Ribo-Seq datasets it became clear that a more accurate representation is required to help us better understand this complexity. #Translation #RiboSeq

[bioRxiv Genomics @biorxiv_genomic]

Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity https://t.co/PDp9UT4X3E #biorxiv_genomic

[Jack Tierney @JackATierney]

@ATinyGreenCell CDS annotations should represent what is believed to be decoded from the RNA into a protein product. First ATG of the CDS open reading frame is reasonable in Eukaryotes.

Human gene CACNAD1 has an annotated CDS that starts with 7 ATGs. 589 genes have CDSs that start with >=2 Ms

[Nature Methods @naturemethods]

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes.

https://t.co/b2uC7C5zvm

[Javier Santoyo @jsantoyo]

Translon: a single term for translated regions. #Translation @naturemethods
https://t.co/irP6ryeAVc

[Jack Tierney @JackATierney]

@ewjwallace @guo_lab Transcript leader is definitely my preferred term for TSS -> CDS region. But any leader of decent length more often than not will contain translons so there is need for more fundamental units if we want to characterise the translation of these RNAs properly

[Jack Tierney @JackATierney]

@guo_lab If you wish haha but I would be interested in hearing a good definition of a 5' untranslated region as the classic definition of region between TSS and CDS is more often a misnomer than not. We played with the idea of a scantron for the scanned rather than translated regions 5'

[Jack Tierney @JackATierney]

@guo_lab The necessity for such a unit of translation became clear during my PhD when we were developing the Ribosome Decision Graph concept

https://t.co/1C8rwS1jhm

[Jack Tierney @JackATierney]

@guo_lab No problem. But like in “exon” vs “expressed region” the -on suffix is the mark of a fundamental unit across science and we want to conceptually establish a unit to allow us to describe what is translated and the relationships between these regions

[Kurian Lab @KurianLab]

There is a lack of general terminology for translated regions that does not depend on the properties of their products or their sequence. Spearheaded by Pavel (Pasha) Baranov, this primer provides a unifying nomenclature for translation units: *Translon*
https://t.co/G78Tmgc21e

[Jack Tierney @JackATierney]

Writing this short correspondence sparked great semantic discussions with leaders of a diverse set of fields and particularly among the primary instigators of this initiative (myself, Michał Świrski, Eivind Valen (@eviledv) and Pasha Baranov)

Full Text:
https://t.co/H3d5McJ3Hb

[Jack Tierney @JackATierney]

Many transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features.

In @naturemethods we propose using "Translon" for any region decoded by the ribosome

[Jack Tierney @JackATierney]

Just as Walter Gilbert's exon/intron terminology ('Why genes in pieces?', Nature 1978) gave us language to discuss and understand gene structure, 'Translon' aims to provide vocabulary to better conceptualise the pervasive, largely still enigmatic, translation revealed by Ribo-Seq

[Jack Tierney @JackATierney]

@Pharma_Pro @princetongb @JackScannell13 Box not Bayes, I believe.

[RiboSeqOrg @RiboSeqOrg]

Ribosome profiling helps to reveal the first example of human mRNA translated in all three reading frames simultaneously: https://t.co/DnlDHmoUu5

[Jack Tierney @JackATierney]

@SendoelLab Very exciting! Congratulations to everyone involved.

Will the code and data be made available upon publication? Apologies if I missed a statement on this somewhere

[Jack Tierney @JackATierney]

@HHorkan Congratulations Helen! Save travels

[Jack Tierney @JackATierney]

@greally Do we know what happened in the case of GMI? I had a quick look but nothing clear jumped out.

[Jack Tierney @JackATierney]

@BroshRan @johnprensner That annotated translated regions can be loaded as a custom track from BigBed.

https://t.co/5IORT5XK4V

Have a look on our UCSC clone for looking at ribo-seq data, GWIPS-viz:

https://t.co/wfjL2mEivs

[Genomics Data Science - SFI CRT @GenomicsCRT]

A big congratulations to @JackATierney who passed his viva today 👏👏👏. Jack's PhD research project was on "Graph based data structures for the representation of protein coding loci" under the supervision of Pasha Baranov @bioucc . Fantastic work Jack and well deserved!

[Biochemistry UCC @bioucc]

We are delighted to introduce Dr. Sebastiaan Van Heesch, Princess Máxima Center for Paediatric Oncology & Oncode Institute, Utrecht-our first research seminar of the academic year next Wednesday- Details below - all welcome!