Postdoctoral researcher | @BrandesLab | Long non-coding RNAs, epigenetics and chromatin in the cardiovascular system @UofGlasgow alumnus 🏴
Frankfurt on the Main, Germany
Joined September 2020
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This work was made possible with support from @GoetheUni, @CPI_Cluster, @dfg_public, and @DZHK_de.
Special thanks to co-authors: @tim_warwick @Kat_Pimpi @CristianPG_mlg @KurianLab @Ralf_Gilsbach @TheMarcelSchulz @iDikic2 @Ralf_P_Brandes and everyone else involved!
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Importantly, enhancers lost after lncRNA depletion could be mapped with Hi-C to the promoters of differentially expressed genes.
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We next identified the top SWI/SNF-sensitive open chromatin regions using a SWI/SNF PROTAC and ATAC-seq. Enhancers 'lost' after PROTAC also corresponded to enhancers lost after lncRNA depletion.
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Remarkably, depletion of SWI/SNF-bound lncRNAs using an siRNA library followed by CUT&RUN revealed a LOSS of SWI/SNF binding at enhancers and a relative GAIN of binding at promoters.
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iCLIP revealed lncRNAs as the most positively enriched class of SWI/SNF-bound RNA. Binding of lncRNAs to SWI/SNF occurred at a higher frequency than would be expected.
The top candidate lncRNAs were mostly trans-acting in nature, based on RedChIP data.
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SWI/SNF lacks a DNA recognition motif yet achieves precise enhancer targeting.
Using RedChIP and CUT&RUN approaches, we show that RNA-DNA interactions are enriched with SWI/SNF.
The majority of these RNAs are trans-acting and bind cell type-specific enhancers.
(2/7)
New year, new paper 🚨
How does a chromatin remodeling complex, conserved across species and expressed in all cells, find cell type-specific enhancers?
Read our @NatureComms paper to see how #lncRNAs play a fundamental role:
🔗 nature.com/articles/s41467-0…
(1/7)
Honoured to have been a part of this huge effort and to have developed such strong scientific collaborations along the way 🙌🏻. Congratulations @CristianPG_mlg, @iDikic2 and everyone else involved 🎉🎊
It is finally out! My first @ScienceMagazine paper is online and it does not seem real😃. I am Incredibly happy! Really thanks to all my coauthors and special mention to my incredible supervisor @iDikic2 for all the support and trust ! 🫶. Science science.org/doi/10.1126/scie…
James A. Oo retweeted
Now online! Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells dlvr.it/TG6t4q
James A. Oo retweeted
Do you want to detect #RNA-#DNA interactions from RADICL-seq, Red-C or GRID-seq, but lack a reliable method? Then try RADIAnT, our new statistical framework for calling robust, consistent interactions from RNA-DNA ligation methods biorxiv.org/content/10.1101/…
James A. Oo retweeted
Online Now: Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle dlvr.it/T5GfWv
Thanks to @CPI_ExStra @trr267 @goetheuni @dfg_public @dzhk_germany and @BrandesLab for supporting the project! – at Frankfurt on the Main, Germany
Thanks to those involved so far @tim_warwick @Kat_Pimpi @CristianPG_mlg @KurianLab @Ralf_Gilsbach @TheMarcelSchulz @iDikic2 @mixmue @Ralf_P_Brandes – at Frankfurt on the Main, Germany
Happy to share our pre-print on #lncRNA recruitment of SWI/SNF to cell type-specific #enhancers.
We performed several sequencing experiments to reveal the mechanism for how the highly conserved and ubiquitously expressed SWI/SNF finds its DNA targets genome-wide. – at Frankfurt on the Main, Germany
Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers biorxiv.org/cgi/content/shor… #bioRxiv
James A. Oo retweeted
A method for genome scale lncRNA screening using CasRx was developed by Ronald Rad, Juan Montero and colleagues @DKFZ, @TU_Muenchen.
nature.com/articles/s41592-0…
James A. Oo retweeted
Are you a developmental biologist studying cardiac cell fate decisions with an interest in RNA biology looking for a post-doc position?
Join us at our new lab at Goethe University Frankfurt
@UK_Frankfurt
@ERC_Research
Please RT🙏
Thanks again to all involved. @BrandesLab @Ralf_P_Brandes @iDikic2 @CiesekSandra – at Frankfurt on the Main, Germany
Absolutely thrilled to have received the 2022 Rudi Busse award from the medical faculty of @goetheuni for my #PhD thesis on #lncRNA maintenance of #gene expression and #genome stability. Very nice ceremony tonight at the Dies Academicus in Frankfurt. – at Frankfurt on the Main, Germany
