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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.

This study discovered a new molecular pathway that controls how cells fight off viruses. The protein SP140 partners with a complex called RESIST to protect antiviral messenger RNAs from being destroyed, keeping the immune defense active. This mechanism is essential for cells to mount an effective response against viral infections.

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 viral DNA fragment (Alu element) embedded in our genome creates a decoy version of a key immune receptor called IFNAR2. This truncated protein is secreted from cells and intercepts interferon signals, acting as a built-in brake on the immune system. The discovery reveals that "junk DNA" parasites have been repurposed to fine-tune human immunity.

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 viral DNA sequences called LTR10 elements, normally kept silent, become reactivated in colorectal cancer and function as rogue gene switches. These cancer-specific switches are driven by the MAPK signaling pathway and can be turned off with MEK inhibitor drugs, suggesting a new therapeutic strategy.

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.

This study examined how a cancer-driving protein in a childhood muscle cancer depends on another protein called ETS1 to access DNA. Understanding this dependency could reveal new drug targets for rhabdomyosarcoma, a rare but aggressive pediatric cancer.

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 enzymes EHMT1 and EHMT2, which chemically modify DNA-packaging proteins, caused therapy-resistant ovarian cancer tumors to shrink. This approach works by reactivating genes that suppress tumor growth, offering a potential strategy for cancers that no longer respond to standard treatments.

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 gene SP140 specifically in tumors. This finding shows how viral relics can be co-opted to drive cancer-specific gene expression patterns.

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.

Combining two drug classes โ€” one targeting epigenetic enzymes (EHMT inhibitors) and one targeting DNA repair (PARP inhibitors) โ€” proved more effective at killing therapy-resistant ovarian cancer cells than either drug alone. This dual approach could help overcome treatment resistance in advanced ovarian cancer.

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 transposable element sitting inside the IFNAR1 gene โ€” which encodes a critical interferon receptor โ€” helps regulate how much of that receptor immune cells produce. This shows that "parasitic" DNA insertions can be domesticated to control the expression of neighboring immune genes.

2023
Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines Ramirez D, Chuong EB, Dowell RD. BMC Research Notes 2023.

This study profiled the very earliest gene expression changes when human and rhesus macaque immune cells are stimulated with interferon, providing a resource for understanding species differences in antiviral responses.

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, are activated as gene enhancers during the immune response to viruses. This parallel discovery in mice mirrors similar findings in primates and cattle, revealing that different mammals independently co-opted different transposable elements to boost their immune defenses.

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.

The stress-response protein ATF6 helps ovarian cancer cells survive treatment with PARP inhibitor drugs by activating protective cellular pathways. Targeting ATF6 alongside PARP inhibitors could help overcome this common form of drug resistance.

2022
Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity Kelly CJ, Chitko-McKown C, Chuong EB. Genome Research 2022.

DNA parasites unique to cattle and their relatives have been repurposed as immune gene switches that activate in response to viral infection. This shows that the co-option of transposable elements for immunity is a widespread evolutionary phenomenon, not limited to primates.

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 activated during the interferon antiviral response, suggesting bats โ€” known for their unusual tolerance of viruses โ€” may use these elements to regulate immune signaling differently from other mammals.

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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.

By mapping the three-dimensional folding of chromosomes, this study identified transposable elements that physically contact and potentially regulate distant host genes, revealing a new layer of TE-mediated gene control.

2017
Molecular conservation of marsupial and eutherian placentation and lactation Guernsey MW, Chuong EB, Cornelis G, Renfree MB*, Baker JC*. eLife 2017.

Despite 160 million years of independent evolution, marsupials and placental mammals share remarkably similar gene expression programs during pregnancy and lactation, suggesting deep conservation of reproductive biology.

2016
Regulatory evolution of innate immunity through co-option of endogenous retroviruses Chuong EB, Elde NC*, Feschotte C*. Science 2016.

Endogenous retroviruses โ€” ancient viral DNA embedded in our genome โ€” were co-opted as immune gene switches that turn on in response to interferon signaling. Deleting these elements with CRISPR abolished the immune activation of nearby genes, proving they are essential regulatory components.

2016
Disruption of promoter memory by a long noncoding RNA Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ. PNAS 2016.

A long non-coding RNA can erase the "memory" of gene activation at a promoter, allowing cells to reset their transcriptional state. This reveals a mechanism by which non-coding transcripts influence gene regulation.

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.

The placenta naturally accumulates large-scale gains and losses of DNA segments during development, making it one of the most genetically variable tissues in the body โ€” a feature that may facilitate rapid placental evolution.

2014
Dissecting the transcriptional network of early embryogenesis in a model vertebrate Wills AE, Gupta R, Chuong EB, Baker JC. Methods 2014.

This study describes methods for dissecting transcriptional networks during early vertebrate embryogenesis, providing a framework for understanding how gene regulatory programs are established during development.

2013
Genomic imprinting and placental evolution in mammals Chuong EB, Hannibal RL, Green SL, Baker JC. Applied & Translational Genomics 2013.

This study examines the relationship between genomic imprinting and placental evolution across mammals, exploring how parent-of-origin gene expression patterns shape reproductive biology.

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

Ancient retroviruses embedded in mammalian genomes function as species-specific gene switches in the placenta, helping drive the rapid evolutionary changes in this organ across different mammals.

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

Genes at the interface between mother and fetus in the rodent placenta evolve at unusually rapid rates, consistent with an evolutionary arms race driven by conflicting genetic interests between parent and offspring.

2011
wnt signaling and the polarity of the primary body axis Yoon SJ, Wills AE, Chuong EB, Gupta R, Baker JC. Genes and Development 2011.

This study investigates the role of Wnt signaling in establishing the primary body axis during vertebrate embryogenesis, revealing how early patterning signals organize the developing embryo.

2011
Chromatin and transcription factor interactions during vertebrate early development Kim SW*, Yoon SJ*, Chuong EB*, Oyolu CB, Wills AE, Gupta R, Baker JC. Developmental Biology 2011.

This study examines how chromatin structure and transcription factor binding interact during early vertebrate development, providing insights into the regulation of gene expression programs that drive embryogenesis.

2008
Comparative analysis of testis protein evolution in rodents Turner LM, Chuong EB, Hoekstra HE. Genetics 2008.

This comparative analysis of testis-expressed proteins in rodents reveals rapid molecular evolution driven by sexual selection and reproductive competition, providing insights into the evolutionary forces shaping male reproductive biology.

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2017
Regulatory activities of transposable elements: from conflicts to benefits Chuong EB, Elde NC, Feschotte C. Nature Reviews Genetics 2017.

This comprehensive review synthesizes evidence that transposable elements โ€” once dismissed as genomic parasites โ€” are a major source of gene regulatory innovation, contributing enhancers, promoters, and other control elements across animal genomes.

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

This review explores how endogenous retroviruses influence immune cell function through epigenetic mechanisms, acting as platforms for chromatin regulation that can both activate and silence nearby immune genes.

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

This commentary highlights new research showing that transposable elements provide binding sites for transcription factors critical in T cell development, expanding our understanding of how immune cell identity is shaped by parasitic DNA.

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

This perspective piece discusses how retroviruses that infected our ancestors millions of years ago now play essential roles in placental development and pregnancy, blurring the line between parasite and partner.

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

This review argues that endogenous retroviruses have been a driving force behind the rapid and diverse evolution of the mammalian placenta, providing ready-made regulatory elements for species-specific gene expression.

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

This commentary discusses how transposable elements contribute to X chromosome dosage compensation, highlighting yet another way genomic parasites have been repurposed for essential biological functions.