Geoff Faulkner (@Faulkner

Geoff Faulkner

2,186 posts

Geoff Faulkner

@Faulkner_Lab

Professor, University of Queensland. Retrotransposons and genomics. Views my own. Scholar publications: tinyurl.com/3k7r3xvj @faulknerlab.bsky.social

Brisbane, Queensland

Joined July 2017

Pinned
Geoff Faulkner
@Faulkner_Lab
Nov 13, 2023
After years of telling visitors to Brisbane what an awesome place it is for fun* adventures, I've decided to make a list in the order I remember them of my favourite places to go for ease of reference. Here goes ... (*definition of fun may vary)
11K
Geoff Faulkner
@Faulkner_Lab
Jul 28, 2021
Our paper refuting earlier claim of SARS-CoV-2 genomic integration is now online @CellReports The virus does not enter human DNA The same would be true of COVID-19 mRNA vaccines Particular thanks to @UQ_SCMB authors for SARS-CoV-2 experiments @UQ_News doi.org/10.1016/j.celr…
Geoff Faulkner
@Faulkner_Lab
Jan 10, 2023
Recent @CellCellPress study claiming HERVK transcription drives senescence has a fundamental RNA-seq analysis problem. The results don't show HERVK elements with intact Env are derepressed, nor are they differentially expressed in senescent cells. 🧵 1/n
Resurrection of endogenous retroviruses during aging reinforces senescence
From cell.com
238K
Geoff Faulkner
@Faulkner_Lab
May 31, 2021
Our manuscript reporting long-read @nanopore sequencing of SARS-CoV-2 infected HEK293T cells is now available as a preprint. It is work we did with some reluctance but given the context of the global pandemic it seemed obligatory. biorxiv.org/cgi/content/sh…
Geoff Faulkner
@Faulkner_Lab
Oct 8, 2022
I have posted this Contradictory Results to bioRxiv: biorxiv.org/content/10.110… Re-analyzing RNA-seq data from this Neuron paper, I found the claimed L1 upregulation in ataxia telangiectasia (AT) cerebellum is due to an apparent RNA-seq batch effect. 1/n pubmed.ncbi.nlm.nih.gov/36070749/
biorxiv.org
Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect
A recent study (Takahashi et al., Neuron , 2022) concluded LINE-1 (L1) retrotransposon activation drives cerebellar ataxia and neurodegeneration. This position was based on L1 upregulation in ataxia...
Geoff Faulkner
@Faulkner_Lab
Aug 5, 2021
The transposable elements (TEs) field has a steep literature learning curve and it's easy to miss key work (for me too). Kazazian's 2004 Science piece got me into the world of TEs. doi.org/10.1126/scienc… Here's a few of my favourites from the field over the last 5 years ...
science.org
Mobile Elements: Drivers of Genome Evolution
Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and...
Geoff Faulkner
@Faulkner_Lab
Sep 5, 2022
Long-read @nanopore ONT sequencing 👇has lately changed my scientific life. It is an unprecedented tool to study retrotransposons (mobile DNA) and how they are regulated. Here's some examples to show what I mean: 🧵1/n
whatisbiotechnology.org
Nanopore sequencing makes it possible to decode the sequence of DNA and RNA
How nanopore sequencing has revolutionised DNA and RNA sequencing
Geoff Faulkner
@Faulkner_Lab
May 7, 2021
Preprint claiming SARS-CoV-2 integration by L1 RT into human cells has now been contributed to PNAS. pnas.org/content/118/21… The authors have added ONT sequencing data and find an example of a potential SARS-CoV-2 integrant on chrX. Some thoughts about this: 1/n
pnas.org
Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be...
Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely repor...
Geoff Faulkner
@Faulkner_Lab
Nov 12, 2020
Our study published today @MolecularCell uses long read @nanopore sequencing and new analysis tools from @_adamewing to interrogate transposon insertions and methylation in human tissues and cancer authors.elsevier.com/a/1c3ZZ3vVUPDf… @SethCheetham @MaterResearch @QldBrainInst
Geoff Faulkner
@Faulkner_Lab
Mar 7, 2021
Deniz et al (Nat Commun, 2020) is one of the best papers to come out of the TE field in recent years, and an (unusual?) example of work that looks even better when examined closely. It shows how endogenous retrovirus (ERVs) enhance oncogenes in AML. 1/n
nature.com
Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid...
Nature Communications - Transposable elements are a potential source of transcriptional regulators, but how these sequences contribute to oncogenesis remains poorly understood. Here, the authors...
Geoff Faulkner
@Faulkner_Lab
Dec 9, 2020
Our study using @nanopore ONT sequencing to survey transposable element (TE) insertions and methylation landscapes in human tissues is now in print @MolecularCell. Detailed thread 👇 Open access link: sciencedirect.com/science/articl… Work funded by @nhmrc @CSL @materfoundation 1/n
Geoff Faulkner
@Faulkner_Lab
Dec 3, 2022
Our study of endogenous retrotransposition during mouse iPSC generation, why it happens, and how it can be prevented, is now online @NatureComms 🥳🥳 nature.com/articles/s4146… Particular credit to @Patricia_Grds @RichardsonL1Lab @_adamewing @ry_lister Sue Mei Lim and Jose Polo
Geoff Faulkner
@Faulkner_Lab
Jun 6, 2020
For analysing retrotransposon expression using RNA-seq I would recommend TEtranscripts from @MollyHammell. The results are very similar to what I get using my own in house scripts but there is a maintained GitHub github.com/mhammell-labor… and it works well.
GitHub - mhammell-laboratory/TEtranscripts: A package for including transposable elements in...
From github.com
Geoff Faulkner
@Faulkner_Lab
Mar 21, 2022
Is L1 retrotransposon activity in the brain specific to only some neuronal lineages? Check out our new preprint👇where we find L1 is activated by the SOX6 transcriptional program of parvalbumin (PV) GABAergic interneuron development. 1/n
biorxiv.org
LINE-1 retrotransposon activation intrinsic to interneuron development
Transposable elements (TEs) are a reservoir of new transcription factor binding sites for protein-coding genes[1][1]–[3][2]. Developmental programs that activate TE-derived regulatory elements could,...