Publications and Preprints

2025

Mechanism for local attenuation of DNA replication at double-strand breaks

Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. 

Optical pooled screening for the discovery of regulators of the Alternative Lengthening of Telomeres pathway

Quintanilla I, Azeroglu B, Sagar MAK, Stracker TH, Lazzerini Denchi E, Pegoraro G. bioRxivorg. 2025

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens

Sood V, Holewinski R, Andresson T, Larson DR, Misteli T. Mol Cell.

Identification of modulators of the ALT pathway through a native FISH-based optical screen

Azeroglu B, Khurana S, Wang SC, Tricola GM, Sharma S, Jubelin C, Cortolezzis Y, Pegoraro G, Miller KM, Stracker TH, Lazzerini Denchi E. Cell Rep. 2025 Jan 28;44(1):115114.

Simulation and quantitative analysis of spatial centromere distribution patterns

Keikhosravi A, Guin K, Pegoraro G, Misteli T. bioRxiv. 2025.

Chromosome mis-segregation triggers cell cycle arrest through a mechanosensitive nuclear envelope checkpoint

Hervé S, Scelfo A, Bersano Marchisio G, Grison M, Vaidžiulytė K, Dumont M, Angrisani A, Keikhosravi A, Pegoraro G, Deygas M, P F Nader G, Macé AS, Gentili M, Williart A, Manel N, Piel M, Miroshnikova YA, Fachinetti D. Nat Cell Biol. 2025;27(1):73–86.

2024

High-throughput image processing software for the study of nuclear architecture and gene expression

Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G. Sci Rep. 2024

Allele-level visualization of transcription and chromatin by high-throughput imaging

Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Histochem Cell Biol. 2024

redictive prioritization of enhancers associated with pancreas disease risk

Wang L, Baek S, Prasad G, Wildenthal J, Guo K, Sturgill D, Truongvo T, Char E, Pegoraro G, McKinnon K, Pancreatic Cancer Cohort Consortium, Pancreatic Cancer Case-Control Consortium, Hoskins JW, Amundadottir LT, Arda HE. bioRxiv. 2024. PMCID: PMC11418953

Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells

McCreery KP, Stubb A, Stephens R, Fursova NA, Cook A, Kruse K, Michelbach A, Biggs LC, Keikhosravi A, Nykänen S, Hydén-Granskog C, Zou J, Lackmann JW, Niessen CM, Vuoristo S, Miroshnikova YA, Wickström SA. bioRxiv. 2024 PMCID: PMC11451594

Cell type- and transcription-independent spatial proximity between enhancers and promoters

Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Mol Biol Cell. 2024

A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate

Chavan A, Isenhart R, Nguyen SC, Kotb NM, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M. Genes Dev. 2024.

The homeobox transcription factor DUXBL controls exit from totipotency

Vega-Sendino M, Lüttmann FF, Olbrich T, Chen Y, Kuenne C, Stein P, Tillo D, Carey GI, Zhong J, Savy V, Radonova L, Lu T, Saykali B, Kim KP, Domingo CN, Schüler L, Günther S, Bentsen M, Bosnakovski D, Schöler H, Kyba M, Maity TK, Jenkins LM, Looso M, Williams CJ, Kim J, Ruiz S. Nat Genet. 2024.

Novel biosensor for high-throughput detection of progesterone receptor-interacting endocrine disruptors

Stavreva DA, Varticovski L, Raziuddin R, Pegoraro G, Schiltz RL, Hager GL. Sci Rep. 2024.

HcHCR: High-throughput single-cell imaging of RNA in human primary immune cells

Gadkari M, Sun J, Carcamo A, Fraser I, Franco LM, Pegoraro G. Methods Mol Biol. 2024.

Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway

Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E. Methods Mol Biol. 2024

High-throughput RNA-HCR-FISH detection of endogenous pre-mRNA splice variants

Shilo A, Pegoraro G, Misteli T. Methods Mol Biol.

2023

SIRT1 prevents R-loops during chronological aging by modulating DNA replication at rDNA loci

Thakur BL, Kusi NA, Mosavarpour S, Zhu R, Redon CE, Fu H, Dhall A, Pongor LS, Sebastian R, Indig FE, Aladjem MI. Cells. 2023 Nov 15;12(22):2630

Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression

Ghule PN, Boyd JR, Kabala F, Fritz AJ, Bouffard NA, Gao C, Bright K, Macfarlane J, Seward DJ, Pegoraro G, Misteli T, Lian JB, Frietze S, Stein JL, van Wijnen AJ, Stein GS. Gene. 2023

Activation of endoplasmic reticulum stress in premature aging via the inner nuclear membrane protein SUN2

Vidak S, Serebryannyy LA, Pegoraro G, Misteli T. Cell Rep. 2023

Identification of epigenetic modulators as determinants of nuclear size and shape

Schibler AC, Jevtic P, Pegoraro G, Levy DL, Misteli T. Elife 2023.

The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability

Shrestha RL, Balachandra V, Kim JH, Rossi A, Vadlamani P, Sethi SC, Ozbun L, Lin S, Cheng KCC, Chari R, Karpova TS, Pegoraro G, Foltz DR, Caplen NJ, Basrai MA. J Cell 2023.

2022

Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway

Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E.  Methods in Cell Biology. Academic Press; 2022.

HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms

Shilo A, Pegoraro G, Misteli T.  Nucleic Acids Res [Internet]. 2022 Oct 16;dx.doi.org/10.1093/nar/gkac869 PMID: 36243969

Nuclear position modulates long-range chromatin interactions

Finn EH, Misteli T  PLoS Genet. 2022 Oct;18(10): e1010451. PMCID: PMC9581366

High-throughput imaging of mRNA at the single-cell level in human primary immune cells

Gadkari M, Sun J, Carcamo A, Alessi H, Hu Z, Fraser IDC, Pegoraro G, Franco LM

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP Nucleic Acids Res. 2022 Aug 12;50(14):7906–7924. PMCID: PMC9371915

Large-scale mapping of positional changes of hypoxia-responsive genes upon activation

Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T Mol Biol Cell. 2022 Jul 1;33(8):ar72. PMCID: PMC9635277

Identification of epigenetic modulators as determinants of nuclear size and shape

Schibler A, Jevtic P, Pegoraro G, Levy DL, Misteli T [Internet]. bioRxiv. 2022 [cited 2022 Dec 21]. p. 2022.05.28.493845. Available from:https://www.biorxiv.org/content/biorxiv/early/2022/05/29/2022.05.28.493845

Activation of endoplasmic reticulum stress via clustering of the inner nuclear membrane protein SUN2

Vidak S, Serebryannyy LA, Pegoraro G, Misteli T bioRxiv. 2022 [cited 2022 Dec 21]. p. 2021.09.14.460295. Available from: https://www.biorxiv.org/content/10.1101/2021.09.14.460295v2

HiIDDD: a high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells

Gallant K, Bektas A, Kaileh M, Lustig A, Ferrucci L, Pegoraro G, Misteli T Sci Rep. Nature Publishing Group; 2022 Apr 15;12(1):6335. PMCID: PMC9022135

Chondroitin Sulfate Proteoglycans Are De Facto Cellular Receptors for Human Papillomavirus 16 under High Serum Conditions

Fons NR, Kines RC, Thompson CD, Day PM, Lowy DR, Schiller JT J Virol. 2022 Apr 13;96(7): e0185721. PMCID: PMC9006963

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation

Rinaldi L, Fettweis G, Kim S, Garcia DA, Fujiwara S, Johnson TA, Tettey TT, Ozbun L, Pegoraro G, Puglia M, Blagoev B, Upadhyaya A, Stavreva DA, Hager GL Sci Adv. 2022 Apr;8(13): eabj8360. PMCID: PMC8967222

MYC amplifies gene expression through global changes in transcription factor dynamics

Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR Cell Rep. 2022 Jan 25;38(4):110292. PMCID: PMC8849550

High-Throughput DNA FISH (hiFISH)

Finn E, Misteli T, Pegoraro G In: Sexton T, editor. Spatial Genome Organization: Methods and Protocols. New York, NY: Springer US; 2022. p. 245–274.

2021

The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner

Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S Sci Adv. 2021 Oct;7(40): eabg8306. PMID: 34597136

CTCF is a barrier for 2C-like reprogramming

Olbrich T, Vega-Sendino M, Tillo D, Wu W, Zolnerowich N, Pavani R, Tran AD, Domingo CN, Franco M, Markiewicz-Potoczny M, Pegoraro G, FitzGerald PC, Kruhlak MJ, Lazzerini-Denchi E, Nora EP, Nussenzweig A, Ruiz S Nat Commun. Nature Publishing Group; 2021 Aug 11;12(1):4856. PMCID: PMC8358036

Mapping multiple endocrine disrupting activities in Virginia rivers using effect-based assays

Stavreva DA, Collins M, McGowan A, Varticovski L, Raziuddin R, Brody DO, Zhao J, Lee J, Kuehn R, Dehareng E, Mazza N, Pegoraro G, Hager GL Sci Total Environ. 2021 Jun 15; 773:145602. PMCID: PMC8026610

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection

Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR Cell. 2021 May 27;184(11):2878–2895.e20. PMCID: PMC8183334

An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL Mol Cell. 2021 Apr 1;81(7):1484–1498.e6. PMCID: PMC9258326

Self-assembly of multi-component mitochondrial nucleoids via phase separation

Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T EMBO J. 2021 Mar 15;40(6): e107165. PMCID: PMC7957436

2020

A Deep Learning Pipeline for Nucleus Segmentation

Zaki G, Gudla PR, Lee K, Kim J, Ozbun L, Shachar S, Gadkari M, Sun J, Fraser IDC, Franco LM, Misteli T, Pegoraro G Cytometry A. 2020 Dec;97(12):1248–1264. PMCID: PMC8914348

Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability

Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P Mol Cell. 2020 Sep 3;79(5):836–845.e7. PMCID: PMC7483679