"Our findings uncovered a species survival strategy in which telomerase RNA extends telomeres for the next generation by hitchhiking on introns of germline-expressed genes." 🤯
#Celegans 🧪
#Celegans 🧪
Nematode telomerase RNA hitchhikes on introns of germline–up-regulated genes
Telomerase is a ribonucleoprotein complex that elongates telomeric DNA, ensuring germline immortality. In this study, we identified the Caenorhabditis elegans telomerase RNA component 1 (terc-1), as t...
www.science.org
October 23, 2025 at 10:16 PM
"Our findings uncovered a species survival strategy in which telomerase RNA extends telomeres for the next generation by hitchhiking on introns of germline-expressed genes." 🤯
#Celegans 🧪
#Celegans 🧪
This study @science.org finds what appears to be the long-lost RNA subunit of C. elegans telomerase. The TERC RNA is encoded within an intron of a germline-upregulated gene, nmy-2🪱🔬🧬Nematode telomerase RNA hitchhikes on introns of germline–up-regulated genes | Science www.science.org/doi/10.1126/...
October 23, 2025 at 9:38 PM
This study @science.org finds what appears to be the long-lost RNA subunit of C. elegans telomerase. The TERC RNA is encoded within an intron of a germline-upregulated gene, nmy-2🪱🔬🧬Nematode telomerase RNA hitchhikes on introns of germline–up-regulated genes | Science www.science.org/doi/10.1126/...
Amazing relatedness of telomerase with a bacterial anti-phage immunity system, from a new tree of reverse transcriptase. Group II introns are there too. Some of the most fascinating biological creatures have reverse transcriptase at their core.
Great stuff for my upcoming undergrad genome lectures!
Great stuff for my upcoming undergrad genome lectures!
7/10 We teamed up with RT aficionado @pentamorfico.bsky.social from the Rafa Pinilla-Redondo lab to build a new phylogenetic tree of RTs across all domains of life.
Remarkably, this revealed that the DRT enzymes are bacterial homologs of TERT.
Remarkably, this revealed that the DRT enzymes are bacterial homologs of TERT.
October 18, 2025 at 9:02 AM
Amazing relatedness of telomerase with a bacterial anti-phage immunity system, from a new tree of reverse transcriptase. Group II introns are there too. Some of the most fascinating biological creatures have reverse transcriptase at their core.
Great stuff for my upcoming undergrad genome lectures!
Great stuff for my upcoming undergrad genome lectures!
"DNA synthesis is solved"
"We can just print any sequence"
"Biology and biotech are solved fields"
"Sequence-agnostic synthesis is on the horizon"
*plant introns enter the chat*
Humbug.
"We can just print any sequence"
"Biology and biotech are solved fields"
"Sequence-agnostic synthesis is on the horizon"
*plant introns enter the chat*
Humbug.
October 13, 2025 at 10:09 PM
"DNA synthesis is solved"
"We can just print any sequence"
"Biology and biotech are solved fields"
"Sequence-agnostic synthesis is on the horizon"
*plant introns enter the chat*
Humbug.
"We can just print any sequence"
"Biology and biotech are solved fields"
"Sequence-agnostic synthesis is on the horizon"
*plant introns enter the chat*
Humbug.
You’re analyzing 10x Genomics single-cell RNA-seq and notice lots of intronic reads.
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
October 10, 2025 at 1:15 PM
You’re analyzing 10x Genomics single-cell RNA-seq and notice lots of intronic reads.
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
Wait—wasn’t this a 3′ UMI-based assay for mature mRNA?
Let’s unpack why introns show up—and why they matter. 🧵
Splicing in phage and jumbophage genomes!
Great discovery pipeline and new paper from Liana Merk and @cryptogenomicon.bsky.social highlights wide-spread use of Group II introns in phages:
academic.oup.com/nar/article/...
Great discovery pipeline and new paper from Liana Merk and @cryptogenomicon.bsky.social highlights wide-spread use of Group II introns in phages:
academic.oup.com/nar/article/...
Presence of group II introns in phage genomes
Abstract. Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic e
academic.oup.com
September 16, 2025 at 7:54 PM
Splicing in phage and jumbophage genomes!
Great discovery pipeline and new paper from Liana Merk and @cryptogenomicon.bsky.social highlights wide-spread use of Group II introns in phages:
academic.oup.com/nar/article/...
Great discovery pipeline and new paper from Liana Merk and @cryptogenomicon.bsky.social highlights wide-spread use of Group II introns in phages:
academic.oup.com/nar/article/...
Glenn Li, Bartel lab - ~10% of introns in yeast get stabilized under nutrition depletion. found they're protected by a specific splicosome complex.
discovered other proteins involved.
discovered other proteins involved.
October 24, 2024 at 12:42 PM
Glenn Li, Bartel lab - ~10% of introns in yeast get stabilized under nutrition depletion. found they're protected by a specific splicosome complex.
discovered other proteins involved.
discovered other proteins involved.
Okay, what search engine do you use? I goggled “how did yeast lose its introns?” And the entire first page was AI’s explanation of the spliceosome.
May 26, 2024 at 9:38 PM
Okay, what search engine do you use? I goggled “how did yeast lose its introns?” And the entire first page was AI’s explanation of the spliceosome.
GC content on the frequencies of synonymous triplets, particularly stop codons, revealing a bias for such triplets near splice sites in introns across various clades, with maximum Shannon information observed at 43.3% GC content. doi.org/10.1038/s415...
January 9, 2024 at 2:49 PM
GC content on the frequencies of synonymous triplets, particularly stop codons, revealing a bias for such triplets near splice sites in introns across various clades, with maximum Shannon information observed at 43.3% GC content. doi.org/10.1038/s415...
Now: Asa Ben-Hur: Deep chromatin state models as foundation models for genomics: a case study in predicting retained introns #ISMB2024 💻🧬🧪
July 15, 2024 at 8:41 PM
Now: Asa Ben-Hur: Deep chromatin state models as foundation models for genomics: a case study in predicting retained introns #ISMB2024 💻🧬🧪
RESEARCH PAPER: ELAV mediates circular RNA biogenesis in neurons
By Alfonso-Gonzalez et al.
➡️ https://tinyurl.com/gd352670
#circRNA #neuroscience #RNAbindingprotein #Drosophila #embryos #neurons #mRNA #introns #splicing
By Alfonso-Gonzalez et al.
➡️ https://tinyurl.com/gd352670
#circRNA #neuroscience #RNAbindingprotein #Drosophila #embryos #neurons #mRNA #introns #splicing
September 9, 2025 at 3:03 PM
RESEARCH PAPER: ELAV mediates circular RNA biogenesis in neurons
By Alfonso-Gonzalez et al.
➡️ https://tinyurl.com/gd352670
#circRNA #neuroscience #RNAbindingprotein #Drosophila #embryos #neurons #mRNA #introns #splicing
By Alfonso-Gonzalez et al.
➡️ https://tinyurl.com/gd352670
#circRNA #neuroscience #RNAbindingprotein #Drosophila #embryos #neurons #mRNA #introns #splicing
4/
What You Gain with Introns
Including intronic reads increases:
+59% median genes per cell
+48% total UMI counts
Detection of genes with no exonic reads
That’s more power, not more noise.
What You Gain with Introns
Including intronic reads increases:
+59% median genes per cell
+48% total UMI counts
Detection of genes with no exonic reads
That’s more power, not more noise.
October 10, 2025 at 1:15 PM
4/
What You Gain with Introns
Including intronic reads increases:
+59% median genes per cell
+48% total UMI counts
Detection of genes with no exonic reads
That’s more power, not more noise.
What You Gain with Introns
Including intronic reads increases:
+59% median genes per cell
+48% total UMI counts
Detection of genes with no exonic reads
That’s more power, not more noise.
And, for those of you who are interested in making gRNAs against gene introns for NHEJ-mediated knock-in, we also made lists guidelines and genome-wide lists of gRNAs for human and mouse. For more details, please visit rnabio.naist.jp/atlas/
October 23, 2025 at 12:35 AM
And, for those of you who are interested in making gRNAs against gene introns for NHEJ-mediated knock-in, we also made lists guidelines and genome-wide lists of gRNAs for human and mouse. For more details, please visit rnabio.naist.jp/atlas/
Most of the genes are interrupted by +1 non-coding regions (introns). Very few genes exist as a continuous sequence #wop_genetics
November 25, 2024 at 8:55 AM
Most of the genes are interrupted by +1 non-coding regions (introns). Very few genes exist as a continuous sequence #wop_genetics
New study by Chan et al. reveals the evolutionary dynamics of self-splicing introns in mitochondrial genomes of Epichloë fungi. Results support rapid intron loss and evolution of homing suppressors.
Link: doi.org/10.1093/molb...
#NewPaperAlert #genomics #fungi #mitochondria
Link: doi.org/10.1093/molb...
#NewPaperAlert #genomics #fungi #mitochondria
An alternative self-splicing intron lifecycle revealed by dynamic intron turnover in Epichloë endophyte mitochondrial genomes
Abstract. Self-splicing group I and II introns are selfish genetic elements that are widely yet patchily distributed across the tree of life. Their selfish
doi.org
April 11, 2025 at 2:02 PM
New study by Chan et al. reveals the evolutionary dynamics of self-splicing introns in mitochondrial genomes of Epichloë fungi. Results support rapid intron loss and evolution of homing suppressors.
Link: doi.org/10.1093/molb...
#NewPaperAlert #genomics #fungi #mitochondria
Link: doi.org/10.1093/molb...
#NewPaperAlert #genomics #fungi #mitochondria
A eukaryote without tRNA introns https://www.biorxiv.org/content/10.1101/2025.06.17.660180v1
June 18, 2025 at 4:34 AM
A eukaryote without tRNA introns https://www.biorxiv.org/content/10.1101/2025.06.17.660180v1
Phylogenetic and evolutionary insights from 30 newly-assembled Onygenales Mitochondrial Genomes: co-evolution of introns and HEGs shapes mitogenome size variation https://pubmed.ncbi.nlm.nih.gov/40717938/
July 29, 2025 at 5:25 AM
Phylogenetic and evolutionary insights from 30 newly-assembled Onygenales Mitochondrial Genomes: co-evolution of introns and HEGs shapes mitogenome size variation https://pubmed.ncbi.nlm.nih.gov/40717938/
KS: hypothesis, cis-regulatory elements in flanking introns control splicing regulation. CRISPR-cas9 deletions confirm that upstream intron retention is regulated by elements, but downstream intron retention is controlled by something else, maybe RNA structures.
December 3, 2024 at 11:29 AM
KS: hypothesis, cis-regulatory elements in flanking introns control splicing regulation. CRISPR-cas9 deletions confirm that upstream intron retention is regulated by elements, but downstream intron retention is controlled by something else, maybe RNA structures.
Definitely retained introns containing TEs are activating sensors, or at least that has been seen with various splicing inhibitors. Curious if inhibiting this SOS splicing would do the same thing, certainly think it would, but might come down to the abundance of the RNAs that are spliced this way.
February 19, 2025 at 10:31 PM
Definitely retained introns containing TEs are activating sensors, or at least that has been seen with various splicing inhibitors. Curious if inhibiting this SOS splicing would do the same thing, certainly think it would, but might come down to the abundance of the RNAs that are spliced this way.
Crick's weird pal Georg Kreisel on the discovery of introns/exons and repetitive DNA in 1977: "First, molecular biology made a splash because of the apparent astonishing simplicity. Now it continues to be exciting for the opposite reason. It couldn’t be better if it had all been planned."
April 23, 2025 at 9:35 AM
Crick's weird pal Georg Kreisel on the discovery of introns/exons and repetitive DNA in 1977: "First, molecular biology made a splash because of the apparent astonishing simplicity. Now it continues to be exciting for the opposite reason. It couldn’t be better if it had all been planned."
2/
Internal Poly-A Priming
Poly(dT) primers don’t only bind the 3′ poly-A tail.
They sometimes bind internal poly-A stretches in introns—especially in pre-mRNA.
Introns have ~21× more poly-A 7-mers than exons
Internal Poly-A Priming
Poly(dT) primers don’t only bind the 3′ poly-A tail.
They sometimes bind internal poly-A stretches in introns—especially in pre-mRNA.
Introns have ~21× more poly-A 7-mers than exons
June 7, 2025 at 1:45 PM
2/
Internal Poly-A Priming
Poly(dT) primers don’t only bind the 3′ poly-A tail.
They sometimes bind internal poly-A stretches in introns—especially in pre-mRNA.
Introns have ~21× more poly-A 7-mers than exons
Internal Poly-A Priming
Poly(dT) primers don’t only bind the 3′ poly-A tail.
They sometimes bind internal poly-A stretches in introns—especially in pre-mRNA.
Introns have ~21× more poly-A 7-mers than exons
By carrying out 130000 GWAS along with millions of splice-site usage measures, we could infer that hexamer sequences surrounding the splice-sites form a rank order that could mostly explain the choices! By chaning hexamers, we could modify introns for desirable outcomes (4/10)
October 20, 2025 at 11:28 PM
By carrying out 130000 GWAS along with millions of splice-site usage measures, we could infer that hexamer sequences surrounding the splice-sites form a rank order that could mostly explain the choices! By chaning hexamers, we could modify introns for desirable outcomes (4/10)
@nickywhiffin.bsky.social - HAVANA group here - sorry no reference comes immediately to mind. But we'll do some digging as its a good question! As @iansudbery.bsky.social says, assumption has been that introns in UTR are no different to introns in CDS. 1/2
December 11, 2024 at 2:13 PM
@nickywhiffin.bsky.social - HAVANA group here - sorry no reference comes immediately to mind. But we'll do some digging as its a good question! As @iansudbery.bsky.social says, assumption has been that introns in UTR are no different to introns in CDS. 1/2
Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain https://www.biorxiv.org/content/10.1101/2023.10.05.560965v1
Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain https://www.biorxiv.org/content/10.1101/2023.10.05.560965v1
Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to r
www.biorxiv.org
October 6, 2023 at 3:18 AM
Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain https://www.biorxiv.org/content/10.1101/2023.10.05.560965v1