Publications

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. Mechanism for local attenuation of DNA replication at double-strand breaks. Nature. PMID: 39972127

Quintanilla I, Azeroglu B, Sagar MAK, Stracker TH, Lazzerini Denchi E, Pegoraro G. Optical pooled screening for the discovery of regulators of the Alternative Lengthening of Telomeres pathway. bioRxivorg. 2025 PMCID: PMC11844499

Sood V, Holewinski R, Andresson T, Larson DR, Misteli T. Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens. Mol Cell. PMID: 39978338

Azeroglu B, Khurana S, Wang SC, Tricola GM, Sharma S, Jubelin C, Cortolezzis Y, Pegoraro G, Miller KM, Stracker TH, Lazzerini Denchi E. Identification of modulators of the ALT pathway through a native FISH-based optical screen. Cell Rep. 2025 Jan 28;44(1):115114. PMCID: PMC11844024

Keikhosravi A, Guin K, Pegoraro G, Misteli T. Simulation and quantitative analysis of spatial centromere distribution patterns. bioRxiv. 2025. PMCID: PMC11785228

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. Chromosome mis-segregation triggers cell cycle arrest through a mechanosensitive nuclear envelope checkpoint. Nat Cell Biol. 2025;27(1):73–86. PMCID: PMC11735390

Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G.  High-throughput image processing software for the study of nuclear architecture and gene expression. Sci Rep. 2024.

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. Predictive prioritization of enhancers associated with pancreas disease risk. bioRxiv. 2024. PMCID: PMC11418953

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. Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells. bioRxiv. 2024 PMCID: PMC11451594

Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol. 2024

Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters Mol Biol Cell. 2024.

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. A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate Genes Dev. 2024.

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. The homeobox transcription factor DUXBL controls exit from totipotency Nat Genet. 2024.

Stavreva DA, Varticovski L, Raziuddin R, Pegoraro G, Schiltz RL, Hager GL Novel biosensor for high-throughput detection of progesterone receptor-interacting endocrine disruptors. Sci Rep. 2024.

Gadkari M, Sun J, Carcamo A, Fraser I, Franco LM, Pegoraro G. HcHCR: High-throughput single-cell imaging of RNA in human primary immune cells Methods Mol Biol. 2024.

Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E. Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway. Methods Mol Biol. 2024

Shilo A, Pegoraro G, Misteli T. High-throughput RNA-HCR-FISH detection of endogenous pre-mRNA splice variants.  Methods Mol Biol.

Thakur BL, Kusi NA, Mosavarpour S, Zhu R, Redon CE, Fu H, Dhall A, Pongor LS, Sebastian R, Indig FE, Aladjem MI. SIRT1 prevents R-loops during chronological aging by modulating DNA replication at rDNA loci Cells. 2023 Nov 15;12(22):2630

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. Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression Gene. 2023

Vidak S, Serebryannyy LA, Pegoraro G, Misteli T. Activation of endoplasmic reticulum stress in premature aging via the inner nuclear membrane protein SUN2. Cell Rep. 2023

Schibler AC, Jevtic P, Pegoraro G, Levy DL, Misteli T. Identification of epigenetic modulators as determinants of nuclear size and shape. Elife 2023.

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. The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. J Cell 2023.

Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E. Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway Methods in Cell Biology. Academic Press; 2022.

Shilo A, Pegoraro G, Misteli T. HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms. Nucleic Acids Res [Internet]. 2022 Oct 16;dx.doi.org/10.1093/nar/gkac869 PMID: 36243969

Finn EH, Misteli T. Nuclear position modulates long-range chromatin interactions. PLoS Genet. 2022 Oct;18(10): e1010451. PMCID: PMC9581366

Gadkari M, Sun J, Carcamo A, Alessi H, Hu Z, Fraser IDC, Pegoraro G, Franco LM. High-throughput imaging of mRNA at the single-cell level in human primary immune cells. RNA. 2022 Sep;28(9):1263–1278. PMCID: PMC9380748

Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res. 2022 Aug 12;50(14):7906–7924. PMCID: PMC9371915

Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell. 2022 Jul 1;33(8):ar72. PMCID: PMC9635277

Schibler A, Jevtic P, Pegoraro G, Levy DL, Misteli T. Identification of epigenetic modulators as determinants of nuclear size and shape. [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

Vidak S, Serebryannyy LA, Pegoraro G, Misteli T. Activation of endoplasmic reticulum stress via clustering of the inner nuclear membrane protein SUN2.  bioRxiv. 2022 [cited 2022 Dec 21]. p. 2021.09.14.460295. Available from: https://www.biorxiv.org/content/10.1101/2021.09.14.460295v2

Gallant K, Bektas A, Kaileh M, Lustig A, Ferrucci L, Pegoraro G, Misteli T. HiIDDD: a high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells Sci Rep. Nature Publishing Group; 2022 Apr 15;12(1):6335. PMCID: PMC9022135

Fons NR, Kines RC, Thompson CD, Day PM, Lowy DR, Schiller JT. Chondroitin Sulfate Proteoglycans Are De Facto Cellular Receptors for Human Papillomavirus 16 under High Serum Conditions J Virol. 2022 Apr 13;96(7): e0185721. PMCID: PMC9006963

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. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation Sci Adv. 2022 Apr;8(13): eabj8360. PMCID: PMC8967222

Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR MYC amplifies gene expression through global changes in transcription factor dynamics Cell Rep. 2022 Jan 25;38(4):110292. PMCID: PMC8849550

Finn E, Misteli T, Pegoraro G High-Throughput DNA FISH (hiFISH) n: Sexton T, editor. Spatial Genome Organization: Methods and Protocols. New York, NY: Springer US; 2022. p. 245–274.

Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner Sci Adv. 2021 Oct;7(40): eabg8306. PMID: 34597136

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 CTCF is a barrier for 2C-like reprogramming Nat Commun. Nature Publishing Group; 2021 Aug 11;12(1):4856. PMCID: PMC8358036

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 Mapping multiple endocrine disrupting activities in Virginia rivers using effect-based assays Sci Total Environ. 2021 Jun 15; 773:145602. PMCID: PMC8026610

Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection Cell. 2021 May 27;184(11):2878–2895.e20. PMCID: PMC8183334

Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors  Mol Cell. 2021 Apr 1;81(7):1484–1498.e6. PMCID: PMC9258326

Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T Self-assembly of multi-component mitochondrial nucleoids via phase separation EMBO J. 2021 Mar 15;40(6): e107165. PMCID: PMC7957436

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

Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability Mol Cell. 2020 Sep 3;79(5):836–845.e7. PMCID: PMC7483679