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📜 ALL PUBLICATIONS _

2025
SP140–RESIST pathway regulates interferon mRNA stability and antiviral immunity Witt KC, Dziulko A, An J, Pekovic F, Cheng AX, Liu GY, Lee OV, Turner DJ, Lari A, Gaidt MM, Chavez R, Fattinger SA, Abraham P, Dhaliwal H, Lee AY, Kotov DI, Coscoy L, Glaunsinger BA, Valkov E, Chuong EB, Vance RE. Nature 2025.
2024
Regulation of human interferon signaling by transposon exonization Pasquesi GIM*, Allen H*, Ivancevic A*, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Cell 2024.

An ancient piece of viral DNA called an Alu element gets spliced into the human IFNAR2 gene, creating a shortened version of this key immune receptor. The resulting "decoy" protein is secreted from cells and intercepts interferon signals, acting as a natural brake on the immune response.

2024
Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer Ivancevic A, Simpson DM, Joyner OM, Bagby SM, Nguyen LL, Bitler BG, Pitts TM, Chuong EB. Science Advances 2024.

Ancient retroviruses called LTR10 elements stay silent in healthy cells but reawaken in colorectal cancer, where they act as rogue gene switches driven by the MAPK signaling pathway. Treating tumors with MEK inhibitor drugs shuts these viral switches back off, pointing to a possible new therapeutic angle.

๐Ÿ“ฐ CU Boulder Today ยท NCI Cancer Currents ยท Medscape ยท USNews
2024
Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes in rhabdomyosarcoma Hsieh J, Danis EP, Owens CR, Parrish JK, Nowling NL, Wolin AR, Purdy SC, Rosenbaum SR, Ivancevic AM, Chuong EB, Ford HL, Jedlicka P. Oncogene 2024.
2024
EHMT1/2 Inhibition Promotes Regression of Therapy-Resistant Ovarian Cancer Tumors Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, Jeong AD, Guntupalli SR, Behbakht K, Gbaja V, Arnoult N, Chuong EB*, Bitler B*. Molecular Cancer Research 2024.

Blocking the gene-silencing enzymes EHMT1 and EHMT2 causes therapy-resistant ovarian tumors to shrink. The drugs work by reawakening tumor suppressor genes that the cancer had switched off to evade treatment.

2024
An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140 Dziulko AK, Allen H, Chuong EB. Human Molecular Genetics 2024.

An ancient retrovirus embedded in the human genome acts as a hidden gene switch that turns on the immune regulator SP140 specifically in tumors. The finding adds SP140 to a growing list of cancer-relevant genes hijacked by reactivated viral DNA.

2024
Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Nguyen LL, Watson ZL, Ortega R, Woodruff ER, Jordan KR, Iwanaga R, Yamamoto TM, Bailey CA, To F, Jeong AD, Guntupalli SR, Behbakht K, Gibaja V, Arnoult N, Cocozaki A, Chuong EB*, Bitler BG*. Molecular Cancer Therapeutics 2024.

Pairing EHMT inhibitors (which target gene-silencing enzymes) with PARP inhibitors (which block DNA repair) kills therapy-resistant ovarian cancer cells far better than either drug alone. The combination could help patients whose tumors have stopped responding to standard PARP inhibitor treatment.

2023
An intronic LINE-1 regulates IFNAR1 expression in human immune cells Buttler CA, Ramirez D, Dowell RD, Chuong EB. Mobile DNA 2023.

A LINE-1 transposon sitting inside the IFNAR1 gene helps control how much of this interferon receptor immune cells produce. The work shows that even "parasitic" DNA insertions can be domesticated to fine-tune neighboring immune genes.

2023
Mouse B2 SINE elements function as IFN-inducible enhancers Horton I*, Kelly CJ*, Dziulko A, Simpson DM, Chuong EB. eLife 2023.

Short repetitive DNA elements called B2 SINEs, found only in rodent genomes, were co-opted as gene enhancers that fire up during the antiviral immune response in mice. This mirrors similar discoveries in primates and cattle, suggesting that different mammals have independently repurposed different transposable elements to wire up their immune systems.

2023
ATF6-Mediated Signaling Contributes to PARP Inhibitor Resistance in Ovarian Cancer McMellen A, Yamamoto TM, Qamar L, Sanders BE, Nguyen LL, Ortiz Chavez D, Bapat J, Berning A, Post MD, Johnson J, Behbakht K, Nurmemmedov E, Chuong EB, Bitler BG. Molecular Cancer Research 2023.
2022
Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity Kelly CJ, Chitko-McKown C, Chuong EB. Genome Research 2022.

Transposable elements unique to cattle and their relatives โ€” LINE-2 and Bov-A3 โ€” were repurposed as immune gene switches that activate during viral infection. The finding extends transposon co-option as a regulatory innovation beyond primates and rodents to a third major mammalian lineage.

2022
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells Pasquesi GIM, Kelly CJ, Ordonez AD, Chuong EB. Mobile DNA 2022.

Transposable elements in bat genomes are dynamically switched on and off during the interferon antiviral response. Because bats tolerate many viruses without getting sick, these regulatory changes may help explain their unusual immune resilience.

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2018
Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA. Genome Biology 2018.
2017
Molecular conservation of marsupial and eutherian placentation and lactation Guernsey MW, Chuong EB, Cornelis G, Renfree MB*, Baker JC*. eLife 2017.
2016
Regulatory evolution of innate immunity through co-option of endogenous retroviruses Chuong EB, Elde NC*, Feschotte C*. Science 2016.

Ancient retroviruses from the MER41 family carry built-in binding sites for immune transcription factors, and were co-opted as gene enhancers that turn on innate immune genes like AIM2 and APOL1 during interferon signaling. Deleting these viral remnants with CRISPR shuts off the immune response at their target genes โ€” proving they are essential regulators, not junk DNA.

2016
Disruption of promoter memory by a long noncoding RNA Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ. PNAS 2016.
2014
Copy number variation is a fundamental aspect of the placental genome Hannibal RL, Chuong EB, Mulia JR, Gilbert DM, Valouev A, Baker JC. PLOS Genetics 2014.
2014
2013
Evolutionary perspectives into placental biology and disease Chuong EB, Hannibal RL, Green SL, Baker JC. Applied & Translational Genomics 2013.

A review of how evolutionary perspectives illuminate placental biology and pregnancy-related disease. Highlights how rapid placental innovation and genetic conflicts between mother and fetus shape both normal pregnancy and its complications.

2013
Endogenous retroviruses function as species-specific enhancer elements in the placenta Chuong EB, Rumi MA, Soares MJ, Baker JC. Nature Genetics 2013.

Endogenous retroviruses embedded in mammalian genomes function as species-specific gene enhancers in the placenta. This may help explain why the placenta is one of the most rapidly evolving organs across mammals โ€” viral DNA provides a ready supply of regulatory variation.

2010
Maternal-fetal conflict: Rapidly evolving proteins in the rodent placenta Chuong EB, Tong W, Hoekstra HE. Molecular Biology and Evolution 2010.

Proteins expressed at the interface between mother and fetus in rodents evolve at unusually fast rates. The pattern fits the theory of parent-offspring genetic conflict, where maternal and paternal interests over fetal resource allocation drive an evolutionary arms race.

2011
HEB and E2A function as SMAD/FOXH1 cofactors Yoon SJ, Wills AE, Chuong EB, Gupta R, Baker JC. Genes & Development 2011.
2011
Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs Kim SW*, Yoon SJ*, Chuong EB*, Oyolu CB, Wills AE, Gupta R, Baker JC. Developmental Biology 2011.

Maps how chromatin โ€” the protein packaging of DNA โ€” and transcription factor binding change across early vertebrate development. The dataset reveals how regulatory landscapes are reorganized as embryos lay down their body plan.

2008
Comparative analysis of testis protein evolution in rodents Turner LM, Chuong EB, Hoekstra HE. Genetics 2008.
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2017
Regulatory activities of transposable elements: from conflicts to benefits Chuong EB, Elde NC, Feschotte C. Nature Reviews Genetics 2017.

A comprehensive review synthesizing evidence that transposable elements โ€” long dismissed as genomic parasites โ€” are a major source of new regulatory DNA across animal genomes. Covers TE-derived enhancers, promoters, and insulators, and the evolutionary forces that turn parasitic sequences into functional control elements.

2021
Emerging roles for endogenous retroviruses in immune epigenetic regulation Buttler CA, Chuong EB. Immunological Reviews 2021.

Reviews how endogenous retroviruses serve as platforms for epigenetic regulation of immune genes. Walks through the mechanisms by which retrovirus-derived chromatin marks and binding sites tune immune cell behavior.

2020
Transposable elements teach T cells new tricks Ivancevic A, Chuong EB. PNAS 2020.

A commentary on new work showing that transposable elements provide critical binding sites for the transcription factors that establish T cell identity. Highlights how the immune system has been built, in part, on a foundation of parasitic DNA.

2018
The placenta goes viral: retroviruses control gene expression in pregnancy Chuong EB. PLOS Biology 2018.

A perspective on how endogenous retroviruses โ€” relics of ancient infections in our ancestors โ€” became domesticated into essential regulators of placental gene expression. Argues that placental biology is fundamentally a story of host-virus integration.

2013
Retroviruses facilitate the rapid evolution of the mammalian placenta Chuong EB. Bioessays 2013.

Argues that endogenous retroviruses have been a major driving force behind placental evolution by donating species-specific regulatory elements to host genomes. Provides a framework for understanding why the placenta differs so dramatically across mammals.

2013
Transposons up the dosage Chuong EB, Feschotte C. Science 2013.

A commentary on new work showing that transposable elements contribute to X chromosome dosage compensation โ€” the cellular mechanism that balances gene expression from the two sex chromosomes. Another example of how parasitic DNA gets repurposed for fundamental cellular functions.