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Eric Strobel

@estrobel.bsky.social
744 followers 261 following 24 posts

Transcriptional acrobatics. Assistant Professor at the University at Buffalo.

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Eric Strobel @estrobel.bsky.social · 06/06/2025
Check out our new preprint in which we teamed up with the Walter and Chen labs to determine how transcription coordinates the folding and function of a tandem aptamer glycine riboswitch from B. subtilis: www.biorxiv.org/content/10.1...
biorxiv.org
Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch
Riboswitches are non-coding RNA motifs that regulate gene expression in response to ligand binding. The glycine tandem riboswitch (GTR) is notable because it comprises two distinct glycine aptamers th...
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Eric Strobel @estrobel.bsky.social · 05/06/2025
Importantly, all the materials needed to perform this assay are commercially available, so the method is broadly accessible.
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Eric Strobel @estrobel.bsky.social · 05/06/2025
This has implications for the ability of pseudoknots to stabilize transcription pauses, which the Walter lab previously showed is possible (www.sciencedirect.com/science/arti...).
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Eric Strobel @estrobel.bsky.social · 05/06/2025
In addition to validating the method by assessing five RNA folding transitions in three RNA targets, we unexpectedly observed at least three pseudoknot base pairs forming within the RNA exit channel of RNAP.
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Eric Strobel @estrobel.bsky.social · 05/06/2025
This strategy is distinct from previous methods (Cotranscriptional SHAPE-Seq, SPET-Seq, TECprobe-VL), which measure cotranscriptionally folded RNA, but not cotranscriptional RNA folding - in our new approach, we directly assess how RNA structure changes as RNAP transcribes downstream.
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Eric Strobel @estrobel.bsky.social · 05/06/2025
In this study (www.nature.com/articles/s41...) we used a reversible transcription roadblocking strategy developed by the Lafontaine lab to sequentially position E. coli RNAP at two or three positions within a DNA template so that we can take fractions of the reaction for chemical probing.
nature.com
Sequential structure probing of cotranscriptional RNA folding intermediates - Nature Communications
Cotranscriptional RNA folding pathways often involve the sequential formation of folding intermediates as RNA emerges from an RNA polymerase. Here the authors develop an RNA chemical probing method th...
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Eric Strobel @estrobel.bsky.social · 05/06/2025
Our paper describing a method for measuring cotranscriptional RNA folding using high-throughput RNA chemical probing is out @natcomms.nature.com!
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Eric Strobel @estrobel.bsky.social · 01/05/2025
Actually, I was off on the year of Opiate, so only Fear Inoculum counts (better album IMHO)
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Eric Strobel @estrobel.bsky.social · 01/05/2025
Tool - 10,000 Days and Fear Inoculum both qualify.
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Reposted by Eric Strobel
Leo Schärfen @leoschaerfen.bsky.social · 26/03/2025
Here is our paper showing in vivo folding of nascent RNA right after synthesis, published now in @cp-molcell.bsky.social! With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social www.cell.com/molecular-ce...
cell.com
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
Schärfen et al. develop a method to measure the structure of nascent RNAs during their synthesis by RNA polymerases. Base pairing occurs rapidly in cells, revealing the strong regulatory potential of ...
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Reposted by Eric Strobel
Karla Neugebauer @karlaneugebauer.bsky.social · 26/03/2025
I'm excited to share our latest publication on co-transcriptional RNA folding in a eukaryote! Great work by Leo Schärfen with collaboration from Isaac Vock and Matt Simon! @leoschaerfen.bsky.social @mattdsimon.bsky.social Take a peek here authors.elsevier.com/a/1kpxo_Oylr...
authors.elsevier.com
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Reposted by Eric Strobel
Karla Neugebauer @karlaneugebauer.bsky.social · 26/03/2025
I'm excited to share our latest publication on co-transcriptional RNA folding in a eukaryote! Great work by Leo Schärfen with collaboration from Isaac Vock and Matt Simon! @leoschaerfen.bsky.social @mattdsimon.bsky.social Here is the link that works! authors.elsevier.com/a/1kpxo_Oylr...
authors.elsevier.com
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Eric Strobel @estrobel.bsky.social · 14/03/2025
Yup. I use SABIAN cymbals and inquired about getting some prototypes through SABIAN's Sound Check program in January. I was told that the program was on hold for the US until the uncertainty regarding tariffs is resolved. Glad I'm already set up with all the catalog cymbals I want for now...
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Reposted by Eric Strobel
Nell Henderson @nellhenderson.bsky.social · 13/03/2025
BOOM! US tariffs could crash the market for North American drummers, writes PIIE's Cullen Hendrix www.piie.com/blogs/realti...
piie.com
US tariffs could crash the market for North American drummers
North America’s two largest cymbal producers share a family lineage and approaches to cymbal making. What they don’t share is a country of origin. One is US-based, the other Canadian. The similarities...
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Eric Strobel @estrobel.bsky.social · 10/03/2025
Our paper describing our Transcription Elongation Complex Display platform for high-throughput cotranscriptional RNA functional assays is now online at @naturecomms.bsky.social: www.nature.com/articles/s41.... We used TECdisplay to assess the activity of >1M ZTP riboswitch variants!
nature.com
Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display - Nature Communications
Understanding how RNA folds into functional structures requires methods that can systematically assess how sequence perturbations affect RNA structure and function. Here, the authors develop a broadly...
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Reposted by Eric Strobel
Dave Shechner @shechnerlab.bsky.social · 21/11/2024
It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture. If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
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Reposted by Eric Strobel
Catherine Eichhorn @cdeichhorn.bsky.social · 18/11/2024
I haven't seen a nucleic acids starter pack yet, so I started one! Please reach out if I missed you! go.bsky.app/NxKgUY5
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Eric Strobel @estrobel.bsky.social · 29/12/2023
Have you watched Twin Peaks?
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Eric Strobel @estrobel.bsky.social · 28/12/2023
More or less sense than using pipes as the primary means of transit?
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Eric Strobel @estrobel.bsky.social · 28/12/2023
Apparently since the beginning!
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Eric Strobel @estrobel.bsky.social · 27/12/2023
Thanks!
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Eric Strobel @estrobel.bsky.social · 26/12/2023
We designed the TECdisplay platform to be broadly accessible and easy to use, so our hope is that this approach democratizes the development and application of high-throughput RNA biochemical assays.
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Eric Strobel @estrobel.bsky.social · 26/12/2023
We applied this to a ZTP riboswitch variant library to investigate the mechanisms by which variants that match the consensus sequence and structure misfold. Panel c illustrates the ZMP-mediated antitermination response for the 32,768 variants in the library!
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Eric Strobel @estrobel.bsky.social · 26/12/2023
Our first TECdisplay assay measures transcription termination efficiency: TECs are tethered to a bead by the nascent RNA and DNA is released from the bead if transcription is terminated, but retained on the bead if RNA polymerase bypasses the terminator.
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Eric Strobel @estrobel.bsky.social · 26/12/2023
It also avoids the technical biases of RNA sequencing library preparation and is compatible with assays that destroy the RNA, since sequence information is recovered from DNA.
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Eric Strobel @estrobel.bsky.social · 26/12/2023
The activity of each RNA variant is then measured as the distribution of template DNA between fractions. In principle this approach can be applied to any RNA function that can be used to fractionate a TEC library.
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Eric Strobel @estrobel.bsky.social · 26/12/2023
About 6 years ago, I had an idea for measuring RNA function by using the activity of cotransciptionally displayed RNA to fractionate a transcription elongation complex (TEC) library. After fractionation, DNA would be recovered, barcoded, pooled back together, and sequenced
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Eric Strobel @estrobel.bsky.social · 26/12/2023
Our latest preprint, led by Skyler Kelly: we developed a platform for high-throughput cotranscriptional RNA biochemistry called Transcription Elongation Complex display. www.biorxiv.org/content/10.1...
biorxiv.org
Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Eric Strobel @estrobel.bsky.social · 29/11/2023
The final version of our article describing a modernized procedure for cotranscriptional RNA structure probing is online! www.nature.com/articles/s41...
nature.com
Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing ...
RNA begins to fold as the nascent transcript emerges from a transcribing RNA polymerase. Here, the authors develop a concise method for mapping RNA folding pathways that couples in vitro transcription...
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Eric Strobel @estrobel.bsky.social · 19/09/2023
Paper data for an assay I dreamed up in 2018 👀
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