Timothy Fuqua 🏳🌈
@timothyfuqua.bsky.social
Incoming postdoc in Claudia Bank’s lab. Promoters, emergence, fitness landscapes, dogs 🐶 and triathlon 🏊 🚲 🏃. He/him 🏳🌈.
timothyfuqua.com
timothyfuqua.com
A bittersweet gift from the Wagner lab commemorating my last official day in the group: a gel that either stands for Tim Fuqua or Transcription Factor.
I’ve had some great memories here, sorting cells, and looking at promoters. I think it’s also time to announce where I’m off to next…
I’ve had some great memories here, sorting cells, and looking at promoters. I think it’s also time to announce where I’m off to next…
October 30, 2025 at 5:57 PM
A bittersweet gift from the Wagner lab commemorating my last official day in the group: a gel that either stands for Tim Fuqua or Transcription Factor.
I’ve had some great memories here, sorting cells, and looking at promoters. I think it’s also time to announce where I’m off to next…
I’ve had some great memories here, sorting cells, and looking at promoters. I think it’s also time to announce where I’m off to next…
Forgot to add the graphical abstract :)
October 23, 2025 at 11:19 AM
Forgot to add the graphical abstract :)
(3/4) …promoters emerge ~3 times more readily from random DNA than from genomic DNA. Basically this is because genomic sequences are impoverished in proto-sites for regulatory proteins compared to random DNA.
As always…
As always…
August 28, 2025 at 6:37 AM
(3/4) …promoters emerge ~3 times more readily from random DNA than from genomic DNA. Basically this is because genomic sequences are impoverished in proto-sites for regulatory proteins compared to random DNA.
As always…
As always…
(2/4) …created mutagenesis libraries from 225 genomic sequences and 60 randomly synthesized sequences without promoter activity, and measured their ability to create new promoters using Sort-Seq. We found that…
August 28, 2025 at 6:37 AM
(2/4) …created mutagenesis libraries from 225 genomic sequences and 60 randomly synthesized sequences without promoter activity, and measured their ability to create new promoters using Sort-Seq. We found that…
How do new promoters emerge from genomic DNA vs randomly synthesized DNA? Come see my talk at 15:30 in room 113 (Genomic basis of evolutionary innovations) at #ESEB2025 to find out!
August 19, 2025 at 7:58 AM
How do new promoters emerge from genomic DNA vs randomly synthesized DNA? Come see my talk at 15:30 in room 113 (Genomic basis of evolutionary innovations) at #ESEB2025 to find out!
Come see my poster tomorrow at #ESEB2025 P01.124 "The latent cis-regulatory potential of mobile DNA in Escherichia coli" or just read it here :)
August 17, 2025 at 9:00 AM
Come see my poster tomorrow at #ESEB2025 P01.124 "The latent cis-regulatory potential of mobile DNA in Escherichia coli" or just read it here :)
July 29, 2025 at 3:26 PM
5) "In summary, motif grammar on nucleosomes can differentiate between solo and combinatorial TF binding, which may contribute to cell-type-specific enhancer selectivity."
Check out how pioneer motifs are distributed around the nucleosomes:
Check out how pioneer motifs are distributed around the nucleosomes:
June 4, 2025 at 2:45 PM
5) "In summary, motif grammar on nucleosomes can differentiate between solo and combinatorial TF binding, which may contribute to cell-type-specific enhancer selectivity."
Check out how pioneer motifs are distributed around the nucleosomes:
Check out how pioneer motifs are distributed around the nucleosomes:
4) This technique which they call "Interspecies Point Projection (IPP)" ultimately shows rapid binding-site turnover. Again, I love these MoDISco plots. Really strong evidence for Emma Farley's "Dependency Grammar".
June 4, 2025 at 11:49 AM
4) This technique which they call "Interspecies Point Projection (IPP)" ultimately shows rapid binding-site turnover. Again, I love these MoDISco plots. Really strong evidence for Emma Farley's "Dependency Grammar".
4) Phan and Zender et al use synteny and chromatin signatures, rather than DNA sequence, to identify conserved heart CREs between chickens and mice. This technique identifies many orthologous regulatory sequences that are "indirectly conserved." Check out their reporters:
June 4, 2025 at 11:42 AM
4) Phan and Zender et al use synteny and chromatin signatures, rather than DNA sequence, to identify conserved heart CREs between chickens and mice. This technique identifies many orthologous regulatory sequences that are "indirectly conserved." Check out their reporters:
3) I'm a really big fan of this de-novo human THRB enhancer they identified at the end, and how it acquires these SOX2 and PAX motifs.
There's surprisingly a lot of sequence conservation outside of these motifs though...surely drift would have changed some of these by now?
There's surprisingly a lot of sequence conservation outside of these motifs though...surely drift would have changed some of these by now?
June 4, 2025 at 11:26 AM
3) I'm a really big fan of this de-novo human THRB enhancer they identified at the end, and how it acquires these SOX2 and PAX motifs.
There's surprisingly a lot of sequence conservation outside of these motifs though...surely drift would have changed some of these by now?
There's surprisingly a lot of sequence conservation outside of these motifs though...surely drift would have changed some of these by now?
2) Single-molecule footprinting (SMF) is so cool. Like, you can just use methylation marks to see the silhouettes of where TFs are bound to a DNA sequence:
June 4, 2025 at 9:15 AM
2) Single-molecule footprinting (SMF) is so cool. Like, you can just use methylation marks to see the silhouettes of where TFs are bound to a DNA sequence:
1) I think it's also cool that the TF heirarchy in yeast also looks a lot like the one in E. coli, with many regulators binding single site, and others binding thousands of sites.
June 4, 2025 at 9:08 AM
1) I think it's also cool that the TF heirarchy in yeast also looks a lot like the one in E. coli, with many regulators binding single site, and others binding thousands of sites.
We can explain why promoters emerge at most of these hotspots:
March 5, 2025 at 3:05 PM
We can explain why promoters emerge at most of these hotspots:
TLDR: promoters emerge at hotspots in the transposons:
March 5, 2025 at 3:03 PM
TLDR: promoters emerge at hotspots in the transposons:
