🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social
A few highlights below... 🧵👇
A few highlights below... 🧵👇
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
www.science.org
September 10, 2026 at 10:05 PM
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social
A few highlights below... 🧵👇
A few highlights below... 🧵👇
Online today @science.org Noncoding transcription controls the developmental dynamics of long-range gene regulation | Science www.science.org/doi/10.1126/...
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
www.science.org
September 10, 2026 at 6:15 PM
Online today @science.org Noncoding transcription controls the developmental dynamics of long-range gene regulation | Science www.science.org/doi/10.1126/...
1 like = 1 nucleotide substitution in noncoding unannotated DNA of this fish
July 22, 2025 at 11:58 PM
1 like = 1 nucleotide substitution in noncoding unannotated DNA of this fish
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the ...
www.science.org
September 11, 2026 at 5:11 PM
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Noncoding RNA controls the expression of a gene implicated in drug- and stress-induced behaviors.
Learn more in a new #SciencePerspective:
Learn more in a new #SciencePerspective:
A neuronal gene that loops the loop
Noncoding RNA controls the expression of a gene implicated in drug- and stress-induced behaviors
scim.ag
December 27, 2024 at 7:56 PM
Noncoding RNA controls the expression of a gene implicated in drug- and stress-induced behaviors.
Learn more in a new #SciencePerspective:
Learn more in a new #SciencePerspective:
Detailed dissolution of temporal dynamics between noncoding RNA and coding genes. Nice work!👍
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
www.science.org
September 28, 2026 at 2:18 AM
Detailed dissolution of temporal dynamics between noncoding RNA and coding genes. Nice work!👍
Study: Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner.
Published: 11 October 2025
www.nature.com/articles/s41...
Published: 11 October 2025
www.nature.com/articles/s41...
Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner - Nature Communications
Whether paternal pre-conceptual SARS-CoV-2 infection impacts sperm RNA content, or effects offspring phenotypes, has not been previously investigated. Here authors report changes in sperm noncoding RN...
www.nature.com
August 5, 2026 at 6:54 AM
Study: Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner.
Published: 11 October 2025
www.nature.com/articles/s41...
Published: 11 October 2025
www.nature.com/articles/s41...
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
www.biorxiv.org
January 31, 2026 at 1:13 AM
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
April 17, 2025 at 6:26 PM
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Study: SARS-CoV-2 reshapes m6A methylation in long noncoding RNAs of human lung cells
Published: 30 September 2025
academic.oup.com/narmolmed/ar...
Published: 30 September 2025
academic.oup.com/narmolmed/ar...
SARS-CoV-2 reshapes m6A methylation in long noncoding RNAs of human lung cells
Abstract. N6-Methyladenosine (m6A) is a key base modification that regulates RNA stability and translation during viral infection. While m6A methylation of
academic.oup.com
December 17, 2025 at 11:01 PM
Study: SARS-CoV-2 reshapes m6A methylation in long noncoding RNAs of human lung cells
Published: 30 September 2025
academic.oup.com/narmolmed/ar...
Published: 30 September 2025
academic.oup.com/narmolmed/ar...
Loss of DNA Demethylase Enhances Arsenic Resistance Via Reducing of PIN2 Antisense Long Noncoding RNA https://www.biorxiv.org/content/10.64898/2026.09.25.754583v1
September 28, 2026 at 12:00 PM
Loss of DNA Demethylase Enhances Arsenic Resistance Via Reducing of PIN2 Antisense Long Noncoding RNA https://www.biorxiv.org/content/10.64898/2026.09.25.754583v1
It was great working with students Kun and Ryan and
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
www.nature.com
September 8, 2026 at 10:06 AM
It was great working with students Kun and Ryan and
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
A longitudinal analysis of patients with colorectal cancer ties lower development of premalignant polyps to robust adaptive immune surveillance and elevated noncoding RNA—decrypting how the immune microenvironment shapes early carcinogenesis. #ScienceTranslationalMedicine https://scim.ag/49TzEcS
Immune microenvironment and noncoding RNA shape early colorectal carcinogenesis in patients with premalignant lesions
Colorectal polyp risk is associated with adaptive local immune response and noncoding RNA expression.
scim.ag
June 11, 2026 at 3:00 PM
A longitudinal analysis of patients with colorectal cancer ties lower development of premalignant polyps to robust adaptive immune surveillance and elevated noncoding RNA—decrypting how the immune microenvironment shapes early carcinogenesis. #ScienceTranslationalMedicine https://scim.ag/49TzEcS
Study: Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner.
Published: 11 October 2025
www.nature.com/articles/s41...
Published: 11 October 2025
www.nature.com/articles/s41...
Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner - Nature Communications
Whether paternal pre-conceptual SARS-CoV-2 infection impacts sperm RNA content, or effects offspring phenotypes, has not been previously investigated. Here authors report changes in sperm noncoding RNAs in SARS-CoV-2 infected sires and increased anxiety-like behaviors in offspring.
www.nature.com
October 11, 2025 at 10:16 PM
Study: Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner.
Published: 11 October 2025
www.nature.com/articles/s41...
Published: 11 October 2025
www.nature.com/articles/s41...
Mouse model suggests that Covid infections impacts the molecular composition (specifically mRNA) of sperm and may induce changes in the brain of offspring.
🧪 www.nature.com/articles/s41...
🧪 www.nature.com/articles/s41...
Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner - Nature Communications
Whether paternal pre-conceptual SARS-CoV-2 infection impacts sperm RNA content, or effects offspring phenotypes, has not been previously investigated. Here authors report changes in sperm noncoding RN...
www.nature.com
November 1, 2025 at 3:44 PM
Mouse model suggests that Covid infections impacts the molecular composition (specifically mRNA) of sperm and may induce changes in the brain of offspring.
🧪 www.nature.com/articles/s41...
🧪 www.nature.com/articles/s41...
Wow! And in "noncoding" region too... So much for "junk" dna...
June 7, 2024 at 9:47 PM
Wow! And in "noncoding" region too... So much for "junk" dna...
📣 Interested in non-coding disease-causing variants? Check out our review "Mechanisms underlying disease-causing variants in promoters and enhancers". Interesting mechanisms, challenges and future perspectives. Great to work with @wbickmor.bsky.social, Kun and Ryan! www.nature.com/articles/s41...
September 8, 2026 at 5:39 PM
📣 Interested in non-coding disease-causing variants? Check out our review "Mechanisms underlying disease-causing variants in promoters and enhancers". Interesting mechanisms, challenges and future perspectives. Great to work with @wbickmor.bsky.social, Kun and Ryan! www.nature.com/articles/s41...
(If only someone had written a book explaining all this stuff about the complexities of gene regulation, regulatory sequences, noncoding genes etc… A book about "how life works" 😉). /18
January 30, 2026 at 9:56 AM
(If only someone had written a book explaining all this stuff about the complexities of gene regulation, regulatory sequences, noncoding genes etc… A book about "how life works" 😉). /18
Our latest is out in Nature Genetics with
@soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social !
We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects.
www.nature.com/articles/s41...
@soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social !
We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects.
www.nature.com/articles/s41...
Decoding common and rare noncoding variant effects across cellular and developmental contexts - Nature Genetics
This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...
www.nature.com
June 15, 2026 at 3:25 PM
Our latest is out in Nature Genetics with
@soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social !
We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects.
www.nature.com/articles/s41...
@soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social !
We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects.
www.nature.com/articles/s41...
I find it interesting that geneslop only really took off with eukaryogenesis
Prokaryotes need to be sparing and precious with noncoding DNA
Eukaryotes? Massive surplus in energy from mitochondria might have caused “DNA too cheap to meter”
From that miracle, ~all complex life on this planet arose
Prokaryotes need to be sparing and precious with noncoding DNA
Eukaryotes? Massive surplus in energy from mitochondria might have caused “DNA too cheap to meter”
From that miracle, ~all complex life on this planet arose
thinking a lot about slop code lately because it's so extremely different from slop text
is there a real benefit to the code being posted publicly if it's a completely unreadable shitpile of slop?
August 29, 2026 at 6:29 PM
I find it interesting that geneslop only really took off with eukaryogenesis
Prokaryotes need to be sparing and precious with noncoding DNA
Eukaryotes? Massive surplus in energy from mitochondria might have caused “DNA too cheap to meter”
From that miracle, ~all complex life on this planet arose
Prokaryotes need to be sparing and precious with noncoding DNA
Eukaryotes? Massive surplus in energy from mitochondria might have caused “DNA too cheap to meter”
From that miracle, ~all complex life on this planet arose
This year, miRNAs won the Nobel Prize—small non-coding RNAs (smRNAs) have arrived! But the biology of many smRNAs remains a mystery. With Decoy-seq, we’re bringing smRNA genetics into the new decade. @hsnajafabadi.bsky.social www.biorxiv.org/content/10.1...
Decoy-seq unlocks scalable genetic screening for regulatory small noncoding RNAs
Small noncoding RNAs (smRNAs) play critical roles in regulating various cellular processes, including development, stress response, and disease pathogenesis. However, functional characterization of sm...
www.biorxiv.org
January 28, 2025 at 1:12 PM
This year, miRNAs won the Nobel Prize—small non-coding RNAs (smRNAs) have arrived! But the biology of many smRNAs remains a mystery. With Decoy-seq, we’re bringing smRNA genetics into the new decade. @hsnajafabadi.bsky.social www.biorxiv.org/content/10.1...
Kinder männlicher mit SARS-CoV-2 infizierter Mäuse hatten vermehrt Angststörungen und Veränderungen des Hypocampus
Wäre doof wennsich das am Menschen bestätigt
www.nature.com/articles/s41...
Wäre doof wennsich das am Menschen bestätigt
www.nature.com/articles/s41...
Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner - Nature Communications
Whether paternal pre-conceptual SARS-CoV-2 infection impacts sperm RNA content, or effects offspring phenotypes, has not been previously investigated. Here authors report changes in sperm noncoding RNAs in SARS-CoV-2 infected sires and increased anxiety-like behaviors in offspring.
www.nature.com
October 11, 2025 at 2:50 PM
Kinder männlicher mit SARS-CoV-2 infizierter Mäuse hatten vermehrt Angststörungen und Veränderungen des Hypocampus
Wäre doof wennsich das am Menschen bestätigt
www.nature.com/articles/s41...
Wäre doof wennsich das am Menschen bestätigt
www.nature.com/articles/s41...
New preprint 📜 from @AlanMonziani in the lab – EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology www.biorxiv.org/content/10.1... . A🧵
EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology
Mammalian genomes are pervasively transcribed into long noncoding RNAs (lncRNAs), whose functions and modes of action remain poorly understood. EPB41L4A-AS1 is an evolutionary conserved, broadly and h...
www.biorxiv.org
April 10, 2025 at 5:58 AM
New preprint 📜 from @AlanMonziani in the lab – EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology www.biorxiv.org/content/10.1... . A🧵
🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
December 26, 2024 at 3:01 AM
🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.