Isha Walawalkar, MPH
@walawalki.bsky.social
I’m just a girl in an RNA world
[alternative splicing]
MD-PhD student @jacksonlab.bsky.social, @uconnresearch.bsky.social
[alternative splicing]
MD-PhD student @jacksonlab.bsky.social, @uconnresearch.bsky.social
Reposted by Isha Walawalkar, MPH
Reposted by Isha Walawalkar, MPH
KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ
KATMAP infers splicing factor activity and regulatory targets from knockdown data - Nature Biotechnology
A biophysical model uses knockdown or overexpression data to infer splicing factor activity.
go.nature.com
November 4, 2025 at 3:13 PM
KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ
Reposted by Isha Walawalkar, MPH
🧬 Translating lab discoveries into patient care is complex. Early-career scientists often lack access to clinical context, making it challenging to connect research w/ patient outcomes.
Our virtual course offers exposure to clinical decision-making in #PrecisionOncology: www.jax.org/news-and-ins...
Our virtual course offers exposure to clinical decision-making in #PrecisionOncology: www.jax.org/news-and-ins...
New JAX-led course gives early career researchers a front-row seat to personalized cancer care
Genomic tumor boards connect early career researchers with real-world cancer cases and clinical decision-making
www.jax.org
October 29, 2025 at 12:17 PM
🧬 Translating lab discoveries into patient care is complex. Early-career scientists often lack access to clinical context, making it challenging to connect research w/ patient outcomes.
Our virtual course offers exposure to clinical decision-making in #PrecisionOncology: www.jax.org/news-and-ins...
Our virtual course offers exposure to clinical decision-making in #PrecisionOncology: www.jax.org/news-and-ins...
Reposted by Isha Walawalkar, MPH
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Strong promoters are mutationally robust
Mutational robustness is the persistence of a phenotype upon mutation. It facilitates molecular evolution and has been characterized in a variety of biological systems, but studies of prokaryotic prom...
www.biorxiv.org
October 21, 2025 at 8:02 AM
A fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
Connecting research and clinical practice: training the next generation of translational scientists - @jacksonlab.bsky.social @jaxeducation.bsky.social go.nature.com/4qlnjEI
Connecting research and clinical practice: training the next generation of translational scientists - Nature Biotechnology
A virtual course provides an opportunity for early-career researchers to witness the translation of basic and preclinical research to inform clinical decisions related to precision oncology.
go.nature.com
October 21, 2025 at 1:58 PM
Connecting research and clinical practice: training the next generation of translational scientists - @jacksonlab.bsky.social @jaxeducation.bsky.social go.nature.com/4qlnjEI
Reposted by Isha Walawalkar, MPH
Check out the latest work from our lab, led by Arash Latifkar @ara-latifkar.bsky.social , www.biorxiv.org/content/10.1...
mRNA poly(A)-tail length is a battleground for coronavirus–host competition
Most eukaryotic mRNAs contain a poly(A) tail, which in post-embryonic cells enhances their stability. Many cytoplasmic RNA viruses also harbor poly(A) tails on their genomic RNA and mRNAs. Here, we re...
www.biorxiv.org
October 13, 2025 at 7:44 PM
Check out the latest work from our lab, led by Arash Latifkar @ara-latifkar.bsky.social , www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against #PancreaticCancer 🧪 www.biorxiv.org/content/10.1...
Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against pancreatic cancer
Pancreatic ductal adenocarcinoma (PDAC) remains a devastating malignancy characterized by limited therapeutic options for advanced disease. Immunotherapy, in particular, has had dismal success rates i...
www.biorxiv.org
October 15, 2025 at 7:17 PM
Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against #PancreaticCancer 🧪 www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
They have fired the staff of the CDC’s Morbidity and Mortality Weekly Report and 70 Epidemic Intelligence Service officers, who are disease detectives that respond to outbreaks around the world.
I cannot emphasize enough how dangerous it is to dismantle our disease surveillance infrastructure.
I cannot emphasize enough how dangerous it is to dismantle our disease surveillance infrastructure.
October 11, 2025 at 5:21 PM
They have fired the staff of the CDC’s Morbidity and Mortality Weekly Report and 70 Epidemic Intelligence Service officers, who are disease detectives that respond to outbreaks around the world.
I cannot emphasize enough how dangerous it is to dismantle our disease surveillance infrastructure.
I cannot emphasize enough how dangerous it is to dismantle our disease surveillance infrastructure.
Reposted by Isha Walawalkar, MPH
Reposted by Isha Walawalkar, MPH
Happy to share our review on the Interplay between RNA-protein interactions and RNA structures. The open access article can be accessed here: doi.org/10.1002/2211...
FEBS Press
Methodological advances in mapping transcriptome-wide RNA-protein interactions and RNA structures have started to uncover the potential of RNP conformations in gene regulation. Competing RNA–RNA, RNA...
doi.org
September 12, 2025 at 8:30 AM
Happy to share our review on the Interplay between RNA-protein interactions and RNA structures. The open access article can be accessed here: doi.org/10.1002/2211...
Reposted by Isha Walawalkar, MPH
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm. A recent study by the Weis lab shows that intracellular diffusion is enhanced when polysomes are disassembled or when mRNA levels are reduced in eukaryotic cells. More: biol.ethz.ch/en/news-and-...
October 1, 2025 at 10:13 AM
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm. A recent study by the Weis lab shows that intracellular diffusion is enhanced when polysomes are disassembled or when mRNA levels are reduced in eukaryotic cells. More: biol.ethz.ch/en/news-and-...
Reposted by Isha Walawalkar, MPH
Embryonic signatures of intergenerational epigenetic inheritance across paternal environment & genetic background
@jamiehackett.bsky.social et al @embl.org see transcriptome changes in offspring after fertilisation by fathers exposed to gut dysbiosis or western diet
www.embopress.org/doi/full/10....
@jamiehackett.bsky.social et al @embl.org see transcriptome changes in offspring after fertilisation by fathers exposed to gut dysbiosis or western diet
www.embopress.org/doi/full/10....
September 29, 2025 at 10:25 AM
Embryonic signatures of intergenerational epigenetic inheritance across paternal environment & genetic background
@jamiehackett.bsky.social et al @embl.org see transcriptome changes in offspring after fertilisation by fathers exposed to gut dysbiosis or western diet
www.embopress.org/doi/full/10....
@jamiehackett.bsky.social et al @embl.org see transcriptome changes in offspring after fertilisation by fathers exposed to gut dysbiosis or western diet
www.embopress.org/doi/full/10....
Reposted by Isha Walawalkar, MPH
How do cells sort which RNAs to keep or destroy? New preprint from THJ, Brenneke and Plaschka labs shows that export and decay machineries (TREX2/PAXT) both recognise UAP56-bound RNAs. Whether they’re exported or degraded depends on where in the nucleus this happens.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Molecular basis of polyadenylated RNA fate determination in the nucleus
Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs, that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, including prote...
www.biorxiv.org
September 17, 2025 at 10:31 AM
How do cells sort which RNAs to keep or destroy? New preprint from THJ, Brenneke and Plaschka labs shows that export and decay machineries (TREX2/PAXT) both recognise UAP56-bound RNAs. Whether they’re exported or degraded depends on where in the nucleus this happens.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 11:07 AM
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
Reposted by Isha Walawalkar, MPH
This is a fascinating paper that particular types of RNA binding proteins with IDRs that target nuclear speckles also can recruit their own RNAs to nuclear speckles as a negative feedback mechanism for condensation the authors call "interstasis" www.nature.com/articles/s41...
Collective homeostasis of condensation-prone proteins via their mRNAs - Nature
The authors discover a homeostatic process termed interstasis, in which an increased concentration of proteins within RNA–protein condensates induces the sequestration of their own mRNAs.
www.nature.com
September 25, 2025 at 8:24 PM
This is a fascinating paper that particular types of RNA binding proteins with IDRs that target nuclear speckles also can recruit their own RNAs to nuclear speckles as a negative feedback mechanism for condensation the authors call "interstasis" www.nature.com/articles/s41...
Reposted by Isha Walawalkar, MPH
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs
The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...
www.biorxiv.org
September 27, 2025 at 3:39 PM
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Reposted by Isha Walawalkar, MPH
Amazing example of a RNA medicine. Hopefully will be able to be used as a treatment here in the US...
September 24, 2025 at 2:40 PM
Amazing example of a RNA medicine. Hopefully will be able to be used as a treatment here in the US...
Reposted by Isha Walawalkar, MPH
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)
Molecular basis of polyadenylated RNA fate determination in the nucleus
Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs[1][1],[2][2], that are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, in...
www.biorxiv.org
September 22, 2025 at 11:23 PM
How are RNAs sorted for export vs. degradation in the nucleus? In collaboration with @heick.bsky.social’s lab we (@clemensplaschka.bsky.social and @juliusbrennecke.bsky.social labs) discovered a direct mechanistic link between the export and decay machineries: www.biorxiv.org/content/10.1... (1/x)
Reposted by Isha Walawalkar, MPH
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
September 22, 2025 at 10:54 AM
Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
The regulation of most proteins is dominated by different regulatory mechanisms across cell types.
Gratifyingly, this complex regulation defines simple rules ⬇️
www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
Great to see this from @vmetzis.bsky.social & co published
Dissection of CDX2 regulatory elements identifies a repressive element that converts to an enhancer with a nuclear receptor motif switch
www.cell.com/developmenta...
Dissection of CDX2 regulatory elements identifies a repressive element that converts to an enhancer with a nuclear receptor motif switch
www.cell.com/developmenta...
A dual enhancer-attenuator element ensures transient Cdx2 expression during mouse posterior body formation
Amblard et al. dissect the function of cis-regulatory elements regulating transient
Cdx2 expression during mouse caudal body formation. They highlight the requirement
of an attenuator, a transiently r...
www.cell.com
September 22, 2025 at 3:34 PM
Great to see this from @vmetzis.bsky.social & co published
Dissection of CDX2 regulatory elements identifies a repressive element that converts to an enhancer with a nuclear receptor motif switch
www.cell.com/developmenta...
Dissection of CDX2 regulatory elements identifies a repressive element that converts to an enhancer with a nuclear receptor motif switch
www.cell.com/developmenta...
Reposted by Isha Walawalkar, MPH
It is my pleasure to share with you the latest from @jsvejstrup.bsky.social lab, where we look at how the reduction of RNAPII levels has a severe, yet organized transcriptional response in the cell.
September 19, 2025 at 9:15 AM
It is my pleasure to share with you the latest from @jsvejstrup.bsky.social lab, where we look at how the reduction of RNAPII levels has a severe, yet organized transcriptional response in the cell.
Reposted by Isha Walawalkar, MPH
Dream collaboration with the groups of Torben Heick Jensen (@heick.bsky.social; @au.dk) and Clemens Plaschka (@impvienna.bsky.social). Building in part on the incredible work from Ulrich Hohmann on human mRNA export.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A molecular switch orchestrates the nuclear export of human messenger RNA
The nuclear export of messenger RNA (mRNA) is a key step in eukaryotic gene expression ([Köhler and Hurt, 2007][1]). Despite recent insights into the packaging of newly transcribed mRNAs into ribonucl...
www.biorxiv.org
September 17, 2025 at 12:42 PM
Dream collaboration with the groups of Torben Heick Jensen (@heick.bsky.social; @au.dk) and Clemens Plaschka (@impvienna.bsky.social). Building in part on the incredible work from Ulrich Hohmann on human mRNA export.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Isha Walawalkar, MPH
Online Now: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome Online now:
Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome
UPF1 depletion inhibits nonsense-mediated mRNA decay (NMD) and stabilizes direct target transcripts within hours. Boehm et al. use conditional protein degradation and advanced transcriptomics to map the NMD-regulated human transcriptome, highlighting alternative splicing as a major NMD-activating mechanism.
dlvr.it
September 10, 2025 at 3:19 PM
Online Now: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome Online now:
Reposted by Isha Walawalkar, MPH
Excited to share some new work from our group - www.biorxiv.org/content/10.1...
A great collaboration with @kurianlab.bsky.social that began with how an RBP (QKI) controls cardiomyocyte function, and led to uncovering a unique mechanism of direct interaction with U6 & the tri-snRNP at weak 5'SS
A great collaboration with @kurianlab.bsky.social that began with how an RBP (QKI) controls cardiomyocyte function, and led to uncovering a unique mechanism of direct interaction with U6 & the tri-snRNP at weak 5'SS
QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites
During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...
www.biorxiv.org
September 8, 2025 at 4:43 PM
Excited to share some new work from our group - www.biorxiv.org/content/10.1...
A great collaboration with @kurianlab.bsky.social that began with how an RBP (QKI) controls cardiomyocyte function, and led to uncovering a unique mechanism of direct interaction with U6 & the tri-snRNP at weak 5'SS
A great collaboration with @kurianlab.bsky.social that began with how an RBP (QKI) controls cardiomyocyte function, and led to uncovering a unique mechanism of direct interaction with U6 & the tri-snRNP at weak 5'SS
Reposted by Isha Walawalkar, MPH
Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5ʹ splice sites
During organogenesis, precise pre-mRNA splicing is essential to assemble tissue architecture. Many developmentally essential exons bear weak 5'splice sites (5'SS) yet are spliced with high precision, ...
www.biorxiv.org
September 8, 2025 at 6:12 AM
Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...