Vikram Paralkar
@paralkarlab.bsky.social
Physician-Scientist | University of Pennsylvania | Pol I, rRNA, Ribosomes, Chromatin, Transcription | Hematopoiesis and Leukemia | 🩸🔬🧪🧬
https://paralkarlab.med.upenn.edu
https://paralkarlab.med.upenn.edu
Delighted to present our work on Pol I in hematopoiesis at the @cshlnews.bsky.social meeting on Eukaryotic Transcription. Thanks to Mustafa Mir (my collaborator in the Penn Epigenetics Institute @pennepigenetics.bsky.social) for his lab's amazing single molecule imaging platform, and for this photo!
August 27, 2025 at 2:17 PM
Delighted to present our work on Pol I in hematopoiesis at the @cshlnews.bsky.social meeting on Eukaryotic Transcription. Thanks to Mustafa Mir (my collaborator in the Penn Epigenetics Institute @pennepigenetics.bsky.social) for his lab's amazing single molecule imaging platform, and for this photo!
Given the ChatGPT "Blueberry" discussion, here's what I got when I ran this question with ChatGPT o4-mini (my account isn't yet updated to GPT-5 - they seem to be rolling it out in phases). It seems to have got it right...
August 8, 2025 at 3:07 AM
Given the ChatGPT "Blueberry" discussion, here's what I got when I ran this question with ChatGPT o4-mini (my account isn't yet updated to GPT-5 - they seem to be rolling it out in phases). It seems to have got it right...
We previously published custom genomes for rDNA mapping. We reanalyzed published scATAC datasets, and found that rDNA accessibility trends match rRNA transcription. This indicates that the hundreds of rDNA repeats in human and mouse genomes dynamically open and close during hematopoiesis. (14/x)
August 2, 2025 at 5:50 PM
We previously published custom genomes for rDNA mapping. We reanalyzed published scATAC datasets, and found that rDNA accessibility trends match rRNA transcription. This indicates that the hundreds of rDNA repeats in human and mouse genomes dynamically open and close during hematopoiesis. (14/x)
The REALLY SURPRISING thing is that cells have an excess of 28S rRNA (60S subunit) compared to 18S rRNA (40S subunit). This is particularly striking in the myeloid lineage, where cells have 60-80% EXCESS 28S compared to 18S! (12/x)
August 2, 2025 at 5:50 PM
The REALLY SURPRISING thing is that cells have an excess of 28S rRNA (60S subunit) compared to 18S rRNA (40S subunit). This is particularly striking in the myeloid lineage, where cells have 60-80% EXCESS 28S compared to 18S! (12/x)
Normal hematopoietic cells contain ~100K to 1.2 million ribosome subunits per cell. But that is not the surprising thing. (11/x)
August 2, 2025 at 5:50 PM
Normal hematopoietic cells contain ~100K to 1.2 million ribosome subunits per cell. But that is not the surprising thing. (11/x)
We also performed FISH-Flow on mouse cell lines. In parallel, we isolated and analyzed total RNA from exactly 5 million cells from both lines, allowing us to carefully measure absolute per cell 18S and 28S molecule numbers (thus measuring number of 40S and 60S subunits respectively). (10/x)
August 2, 2025 at 5:50 PM
We also performed FISH-Flow on mouse cell lines. In parallel, we isolated and analyzed total RNA from exactly 5 million cells from both lines, allowing us to carefully measure absolute per cell 18S and 28S molecule numbers (thus measuring number of 40S and 60S subunits respectively). (10/x)
We used a Flt3-ITD/Dnmt3a-KO AML mouse model to demonstrate that AML progenitors have higher rRNAs than stage-matched normal counterparts. Critically, less proliferative cells within the AML (like AML-CMP, AML-MPP) have higher rRNA levels than more proliferative normal cell types (GMP). (9/x)
August 2, 2025 at 5:50 PM
We used a Flt3-ITD/Dnmt3a-KO AML mouse model to demonstrate that AML progenitors have higher rRNAs than stage-matched normal counterparts. Critically, less proliferative cells within the AML (like AML-CMP, AML-MPP) have higher rRNA levels than more proliferative normal cell types (GMP). (9/x)
Overall, while there is some correlation between nascent & mature rRNA, the precision of our measurements allow us to identify multiple cell types with similar nascent but different mature rRNA levels (& vice versa), suggesting cell-type-specific variations in ribosome processing or half life. (7/x)
August 2, 2025 at 5:50 PM
Overall, while there is some correlation between nascent & mature rRNA, the precision of our measurements allow us to identify multiple cell types with similar nascent but different mature rRNA levels (& vice versa), suggesting cell-type-specific variations in ribosome processing or half life. (7/x)
Strikingly, rRNA levels also don't really correlate with cell cycling. There are multiple cell types with similar cycling parameters, but different nascent and mature rRNA levels. Overall, there is poor correlation between rRNA transcription/levels and percent cells in S/G2/M. (6/x)
August 2, 2025 at 5:50 PM
Strikingly, rRNA levels also don't really correlate with cell cycling. There are multiple cell types with similar cycling parameters, but different nascent and mature rRNA levels. Overall, there is poor correlation between rRNA transcription/levels and percent cells in S/G2/M. (6/x)
Importantly, these levels don't always correlate with protein translation - HSCs have plenty of ribosomes, but low translation rates. This was pointed out by @signerlab.bsky.social in his 2014/2016 work; he was kind enough to share with us raw data from his in vivo translation quantification. (5/x)
August 2, 2025 at 5:50 PM
Importantly, these levels don't always correlate with protein translation - HSCs have plenty of ribosomes, but low translation rates. This was pointed out by @signerlab.bsky.social in his 2014/2016 work; he was kind enough to share with us raw data from his in vivo translation quantification. (5/x)
There is substantial variation in nascent and mature rRNA levels across hematopoiesis, with moderate levels in stem cells, high levels in progenitors, and variably moderate-to-low levels in mature cells of different lineages. (4/x)
August 2, 2025 at 5:50 PM
There is substantial variation in nascent and mature rRNA levels across hematopoiesis, with moderate levels in stem cells, high levels in progenitors, and variably moderate-to-low levels in mature cells of different lineages. (4/x)
We used rRNA FISH-Flow to quantify the abundance of nascent 47S and mature 18S and 28S rRNAs in the mouse hematopoietic tree, with a particular focus on stem and progenitor cells, and on myeloid and erythroid lineages. 18S rRNA levels correspond to 40S subunit abundance, and 28S to 60S. (3/x)
August 2, 2025 at 5:50 PM
We used rRNA FISH-Flow to quantify the abundance of nascent 47S and mature 18S and 28S rRNAs in the mouse hematopoietic tree, with a particular focus on stem and progenitor cells, and on myeloid and erythroid lineages. 18S rRNA levels correspond to 40S subunit abundance, and 28S to 60S. (3/x)
At the FASEB Heme Malignancies meeting with old friends and new - Pam Sung, Peter Van Galen (@vangalenlab.bsky.social), Julia Maxson (@juliamaxson.bsky.social), Johnathon Shafer. Trying out ales at the @treehousebrewing.bsky.social! #HEMSRC
July 30, 2025 at 7:02 PM
At the FASEB Heme Malignancies meeting with old friends and new - Pam Sung, Peter Van Galen (@vangalenlab.bsky.social), Julia Maxson (@juliamaxson.bsky.social), Johnathon Shafer. Trying out ales at the @treehousebrewing.bsky.social! #HEMSRC
Charles Antony from our group presents work on live cell imaging of RNA Pol I and ribosomal RNA transcription in AML at the FASEB Heme Malignancies meeting. #HEMSRC. This work is part of an incredibly fruitful collaboration with my colleague Mustafa Mir in @pennepigenetics.bsky.social!
July 28, 2025 at 4:09 PM
Charles Antony from our group presents work on live cell imaging of RNA Pol I and ribosomal RNA transcription in AML at the FASEB Heme Malignancies meeting. #HEMSRC. This work is part of an incredibly fruitful collaboration with my colleague Mustafa Mir in @pennepigenetics.bsky.social!
Progress takes all of us! Support the #Fight4Hematology and help fuel the next breakthrough. Donate Now!
donate.hematology.org/s/
donate.hematology.org/s/
July 15, 2025 at 5:57 PM
Progress takes all of us! Support the #Fight4Hematology and help fuel the next breakthrough. Donate Now!
donate.hematology.org/s/
donate.hematology.org/s/
Many thanks to Nancy Speck for chairing Aishwarya's thesis committee, and to Kathrin Bernt, Liling Wan, and Alessandro Gardini for their guidance over the years on the committee. Delighted to celebrate this moment with current and former members of the Paralkar lab.
June 30, 2025 at 11:01 PM
Many thanks to Nancy Speck for chairing Aishwarya's thesis committee, and to Kathrin Bernt, Liling Wan, and Alessandro Gardini for their guidance over the years on the committee. Delighted to celebrate this moment with current and former members of the Paralkar lab.
Congratulations to DOCTOR Aishwarya Pawar @aishwarya2510.bsky.social (of @cambupenn.bsky.social Cancer Biology graduate group) for defending her thesis with flying colors, and for her first-author paper in press in @genesdev.bsky.social! We are so proud of you!
June 30, 2025 at 11:01 PM
Congratulations to DOCTOR Aishwarya Pawar @aishwarya2510.bsky.social (of @cambupenn.bsky.social Cancer Biology graduate group) for defending her thesis with flying colors, and for her first-author paper in press in @genesdev.bsky.social! We are so proud of you!
More candid photos, including @karlaneugebauer.bsky.social, @merlinnithyag.bsky.social, Esther Obeng, Craig Forrester, @ykanglab.bsky.social, Hojun Li, @hewittlab.bsky.social, Eugene Khandros, Velia Fowler
June 12, 2025 at 6:54 PM
More candid photos, including @karlaneugebauer.bsky.social, @merlinnithyag.bsky.social, Esther Obeng, Craig Forrester, @ykanglab.bsky.social, Hojun Li, @hewittlab.bsky.social, Eugene Khandros, Velia Fowler
Delighted to present work from our lab at the Gordon Conference on Red Cells in Newport, RI! Also, delighted to attend this meeting with friends and colleagues from Penn.
June 12, 2025 at 3:36 AM
Delighted to present work from our lab at the Gordon Conference on Red Cells in Newport, RI! Also, delighted to attend this meeting with friends and colleagues from Penn.
Random storefront sighting! 🫣
June 7, 2025 at 6:09 PM
Random storefront sighting! 🫣
Looking forward to your Penn Genetics talk, @harmitmalik.bsky.social! I will try to get on your calendar, but I'm sure it's packed already! 😀
May 12, 2025 at 9:19 PM
Looking forward to your Penn Genetics talk, @harmitmalik.bsky.social! I will try to get on your calendar, but I'm sure it's packed already! 😀
Rounding with our amazing Leukemia Inpatient team (we all coordinated to wear blue). Heme-Onc fellow Henry Litt in the center, with Internal Medicine residents Isabella Conde, Pearl Subramanian, and Jack Stylli. I tried my best to recruit the residents to careers in oncology!
April 25, 2025 at 9:31 PM
Rounding with our amazing Leukemia Inpatient team (we all coordinated to wear blue). Heme-Onc fellow Henry Litt in the center, with Internal Medicine residents Isabella Conde, Pearl Subramanian, and Jack Stylli. I tried my best to recruit the residents to careers in oncology!
I have interesting neighbors...
April 9, 2025 at 9:27 AM
I have interesting neighbors...
Ominous message in the dentist's office! 😂
February 18, 2025 at 4:12 PM
Ominous message in the dentist's office! 😂