Like bacteria, phages use sRNAs to regulate gene expression! Out today in @cp-trendsmicrobiol.bsky.social, @mvelascogomariz.bsky.social and I highlight a recent RIL-seq study from the @saharmelamed.bsky.social lab that looked into posttranscriptional regulation of lambda!
tinyurl.com/lambda-RIL-seq
tinyurl.com/lambda-RIL-seq
Unraveling posttranscriptional regulatory networks in phage infection
Phages employ sophisticated transcriptional regulatory networks to optimize replication. Recently, Silverman et al. used RIL-seq (RNA interaction by l…
tinyurl.com
February 26, 2026 at 1:29 PM
Like bacteria, phages use sRNAs to regulate gene expression! Out today in @cp-trendsmicrobiol.bsky.social, @mvelascogomariz.bsky.social and I highlight a recent RIL-seq study from the @saharmelamed.bsky.social lab that looked into posttranscriptional regulation of lambda!
tinyurl.com/lambda-RIL-seq
tinyurl.com/lambda-RIL-seq
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 19, 2025 at 6:43 AM
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT
Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv
doi.org
December 27, 2025 at 2:06 PM
RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1
April 8, 2025 at 4:20 AM
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1
Small RNAs are key players in how bacteria adapt to changing environments. Tools like RIL-seq uncover complex sRNA-RNA networks, paving the way for innovative approaches to fight bacterial infections. Check our review in Springer Nature Protocols:
link.springer.com/protocol/10....
link.springer.com/protocol/10....
November 18, 2024 at 8:11 AM
Small RNAs are key players in how bacteria adapt to changing environments. Tools like RIL-seq uncover complex sRNA-RNA networks, paving the way for innovative approaches to fight bacterial infections. Check our review in Springer Nature Protocols:
link.springer.com/protocol/10....
link.springer.com/protocol/10....
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle: Molecular Cell www.cell.com/molecular-ce...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 18, 2025 at 6:44 PM
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle: Molecular Cell www.cell.com/molecular-ce...
Congratulations to the Papenfort group and collaborators for this intriguing work uncovering the role of ProQ and its associated sRNAs in Vibrio motility! Grateful for the opportunity to be part of this discovery!
academic.oup.com/nar/article-...
#RNA
#RIL-seq
#Motility
academic.oup.com/nar/article-...
#RNA
#RIL-seq
#Motility
ProQ-associated small RNAs control motility in Vibrio cholerae
Abstract. Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important
academic.oup.com
December 31, 2024 at 5:21 AM
Congratulations to the Papenfort group and collaborators for this intriguing work uncovering the role of ProQ and its associated sRNAs in Vibrio motility! Grateful for the opportunity to be part of this discovery!
academic.oup.com/nar/article-...
#RNA
#RIL-seq
#Motility
academic.oup.com/nar/article-...
#RNA
#RIL-seq
#Motility
Some say, important sRNAs can be recognized by having their own “sponge” 🧽. Well, here comes InvS: a sponge of PinT (and vice versa). Congrats to @kooshapour.bsky.social and @ginlaca.bsky.social on their great work! doi.org/10.1101/2025...
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT
Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular survival, respectively. There has been increasing evidence ...
doi.org
April 10, 2025 at 8:06 AM
Some say, important sRNAs can be recognized by having their own “sponge” 🧽. Well, here comes InvS: a sponge of PinT (and vice versa). Congrats to @kooshapour.bsky.social and @ginlaca.bsky.social on their great work! doi.org/10.1101/2025...
RIL-seq revealing sRNA-mediated phage-host dialogue! What a cool finding. Big congrats on the Molecular Cell paper!
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 19, 2025 at 12:35 PM
RIL-seq revealing sRNA-mediated phage-host dialogue! What a cool finding. Big congrats on the Molecular Cell paper!
A new RIL-seq experiment, now to study host-pathigen interactions! Congrats to the @westermannlab.bsky.social and colleagues!
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1
April 9, 2025 at 10:14 AM
A new RIL-seq experiment, now to study host-pathigen interactions! Congrats to the @westermannlab.bsky.social and colleagues!
Cool work by @microberna.bsky.social & Kai Papenfort, presenting the first RNA-RNA map in C. crescentus using RIL-seq, revealing an RNA sponge that controls the transition from nutrient abundance to starvation; new insights into RNA networks and stress responses!
#RNA
www.nature.com/articles/s41...
#RNA
www.nature.com/articles/s41...
An RNA sponge directs the transition from feast to famine in Caulobacter crescentus - Nature Communications
In bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone Hfq to modulate gene expression at the post-transcriptional level. Here, the authors identify global Hfq-mediated RNA-R...
www.nature.com
October 30, 2025 at 1:43 PM
Cool work by @microberna.bsky.social & Kai Papenfort, presenting the first RNA-RNA map in C. crescentus using RIL-seq, revealing an RNA sponge that controls the transition from nutrient abundance to starvation; new insights into RNA networks and stress responses!
#RNA
www.nature.com/articles/s41...
#RNA
www.nature.com/articles/s41...
valuable comparison of RIL-seq and iRIL-seq methods developed by @saharmelamed.bsky.social @yjchao.bsky.social
December 14, 2025 at 4:34 AM
valuable comparison of RIL-seq and iRIL-seq methods developed by @saharmelamed.bsky.social @yjchao.bsky.social
I never expected horses 🐎 in my RNA research, but here we are 😁
In our new perspective, Simon Dove and I discuss how RIL-seq maps transcriptome-wide sRNA networks in vivo and how iRIL-seq expands the RNA–RNA interaction toolbox.
journals.asm.org/doi/10.1128/...
@hebrewuniversity.bsky.social
In our new perspective, Simon Dove and I discuss how RIL-seq maps transcriptome-wide sRNA networks in vivo and how iRIL-seq expands the RNA–RNA interaction toolbox.
journals.asm.org/doi/10.1128/...
@hebrewuniversity.bsky.social
mGem: Horses for courses in mapping bacterial small RNA interaction networks | mBio
Small RNAs (sRNAs) are bacterial RNA species that are anywhere between 50 and 500
nucleotides in length. Many sRNAs employ a short sequence (as few as 6 nucleotides),
known as the seed sequence, to ba...
journals.asm.org
March 6, 2026 at 2:54 PM
I never expected horses 🐎 in my RNA research, but here we are 😁
In our new perspective, Simon Dove and I discuss how RIL-seq maps transcriptome-wide sRNA networks in vivo and how iRIL-seq expands the RNA–RNA interaction toolbox.
journals.asm.org/doi/10.1128/...
@hebrewuniversity.bsky.social
In our new perspective, Simon Dove and I discuss how RIL-seq maps transcriptome-wide sRNA networks in vivo and how iRIL-seq expands the RNA–RNA interaction toolbox.
journals.asm.org/doi/10.1128/...
@hebrewuniversity.bsky.social
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings reveal a previously unrecognized RNA-level regulatory layer in phage-host interactions and highlight the role of post-transcriptional control in promoting phage infection.
dlvr.it
December 20, 2025 at 4:19 PM
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Unraveling posttranscriptional regulatory networks in phage infection
Unraveling posttranscriptional regulatory networks in phage infection
Phages employ sophisticated transcriptional regulatory networks to optimize replication. Recently, Silverman et al. used RIL-seq (RNA interaction by ligation and sequencing) to reveal an additional layer of regulation and uncovered the Hfq-mediated posttranscriptional regulon of the model phage lambda.
dlvr.it
February 27, 2026 at 12:37 AM
Unraveling posttranscriptional regulatory networks in phage infection
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1
April 8, 2025 at 4:20 AM
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT https://www.biorxiv.org/content/10.1101/2025.04.07.647523v1
...and here is a reference
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
April 3, 2026 at 10:53 AM
...and here is a reference
In the @narjournal.bsky.social paper “Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT,” Hoda discovered a small RNA that blocks the activity of PinT, a molecule associated with Salmonella virulence: academic.oup.com/nar/article/...
(2/3)
(2/3)
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT
Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv
academic.oup.com
May 5, 2026 at 2:58 PM
In the @narjournal.bsky.social paper “Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT,” Hoda discovered a small RNA that blocks the activity of PinT, a molecule associated with Salmonella virulence: academic.oup.com/nar/article/...
(2/3)
(2/3)
Authors used RAW 264.7 from @cellosaurus.bsky.social in their study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT
www.biorxiv.org
April 10, 2025 at 12:03 PM
Authors used RAW 264.7 from @cellosaurus.bsky.social in their study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #reproducibility
Low-cost RNA-Seq combined with parental whole-genome sequencing achieved genomic prediction accuracy of 0.73-0.78 in barley RILs, outperforming 50K SNP arrays for five of eight traits. The consensus SNP dataset showed particular advantage in inter-population predictions.
Assessment of genomic prediction capabilities of transcriptome data in a barley multi-parent RIL population
rdcu.be
March 20, 2026 at 10:30 PM
Low-cost RNA-Seq combined with parental whole-genome sequencing achieved genomic prediction accuracy of 0.73-0.78 in barley RILs, outperforming 50K SNP arrays for five of eight traits. The consensus SNP dataset showed particular advantage in inter-population predictions.
BSA-seq and linkage mapping identified qPCB03, a novel large-effect QTL on chromosome B03 explaining 11-13% of protein variation. A validated KASP marker increased protein concentration by 1.23-1.57 percentage points in RIL populations, facilitating marker-assisted breeding.
Identification and utilization of a novel large-effect QTL and linked markers for enhancing protein concentration in peanut
rdcu.be
March 16, 2026 at 12:29 AM
BSA-seq and linkage mapping identified qPCB03, a novel large-effect QTL on chromosome B03 explaining 11-13% of protein variation. A validated KASP marker increased protein concentration by 1.23-1.57 percentage points in RIL populations, facilitating marker-assisted breeding.
EFTA02524895.jpg
#epsteinweb #efta02524895
https://epsteinweb.org
Available in the iOS app store now!
https://apps.apple.com/us/app/epstein-web/id6758880661
#epsteinweb #efta02524895
https://epsteinweb.org
Available in the iOS app store now!
https://apps.apple.com/us/app/epstein-web/id6758880661
April 12, 2026 at 12:28 PM
EFTA02524895.jpg
#epsteinweb #efta02524895
https://epsteinweb.org
Available in the iOS app store now!
https://apps.apple.com/us/app/epstein-web/id6758880661
#epsteinweb #efta02524895
https://epsteinweb.org
Available in the iOS app store now!
https://apps.apple.com/us/app/epstein-web/id6758880661