Education History
| Undergraduate |
Lewis and Clark College |
BS |
|---|---|---|
| Doctoral Training |
Stanford University - Roger Kornberg, PhD |
PhD |
| Postdoctoral Fellowship |
Stanford University - Roger Kornberg, PhD |
Postdoctoral Fellow |
| Postdoctoral Fellowship |
Harvard Medical School - Fred Winston, PhD |
Postdoctoral Fellow |
Selected Publications
Journal Article
- Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns B (2008). Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nature genetics, 40(8), 977-86.
- Hendrickson PG, Cairns B (2016). Tet proteins enhance the developmental hourglass. Nature genetics, 48(4), 345-7.
- Hendrickson PG, Doráis JA, Grow EJ, Whiddon JL, Lim JW, Wike CL, Weaver BD, Pflueger C, Emery BR, Wilcox AL, Nix DA, Peterson CM, Tapscott SJ, Carrell DT, Cairns B (2017). Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nature genetics, 49(6), 925-934.
- Grow EJ, Weaver BD, Smith CM, Guo J, Stein P, Shadle SC, Hendrickson PG, Johnson NE, Butterfield RJ, Menafra R, Kloet SL, van der Maarel SM, Williams CJ, Cairns B (2021). p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models. Nature genetics, 53(8), 1207-1220.
- Zhang H, Roberts DN, Cairns B (2005). Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell, 123(2), 219-31.
- Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns B (2008). DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell, 135(7), 1201-12.
- Rai K, Sarkar S, Broadbent TJ, Voas M, Grossmann KF, Nadauld LD, Dehghanizadeh S, Hagos FT, Li Y, Toth RK, Chidester S, Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones D (2010). DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell, 142(6), 930-42.
- Potok ME, Nix DA, Parnell TJ, Cairns B (2013). Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell, 153(4), 759-72.
- Murphy PJ, Wu SF, James CR, Wike CL, Cairns B (2018). Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Cell, 172(5), 993-1006.e13.
- Kasten MM, Clapier CR, Cairns B (2011). SnapShot: Chromatin remodeling: SWI/SNF. Cell, 144(2), 310.e1.
- Cairns B (2004). Around the world of DNA damage INO80 days. Cell, 119(6), 733-5.
- Rougeot J, Chrispijn ND, Aben M, Elurbe DM, Andralojc KM, Murphy PJ, Jansen PWTC, Vermeulen M, Cairns BR, Kamminga L (2019). Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan. Development (Cambridge, England), 146(19),
- Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang (2011). The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. The EMBO journal, 30(12), 2364-72.
- Oler AJ, Cairns B (2012). PP4 dephosphorylates Maf1 to couple multiple stress conditions to RNA polymerase III repression. The EMBO journal, 31(6), 1440-52.
- Aston KI, Uren PJ, Jenkins TG, Horsager A, Cairns BR, Smith AD, Carrell D (2015). Aberrant sperm DNA methylation predicts male fertility status and embryo quality. Fertility and sterility, 104(6), 1388-97.e1-5.
- Rai K, Chidester S, Zavala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns B (2007). Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes & development, 21(3), 261-6.
- Hammoud SS, Low DH, Yi C, Lee CL, Oatley JM, Payne CJ, Carrell DT, Guccione E, Cairns B (2015). Transcription and imprinting dynamics in developing postnatal male germline stem cells. Genes & development, 29(21), 2312-24.
- Huang F, Ramakrishnan S, Pokhrel S, Pflueger C, Parnell TJ, Kasten MM, Currie SL, Bhachech N, Horikoshi M, Graves BJ, Cairns BR, Bhaskara S, Chandrasekharan M (2015). Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination. The Journal of biological chemistry, 290(48), 28760-77.
- Khoddami V, Yerra A, Cairns B (2015). Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases. Methods in enzymology, 560, 273-96.
- Soutourina J, Bordas-Le Floch V, Gendrel G, Flores A, Ducrot C, Dumay-Odelot H, Soularue P, Navarro F, Cairns BR, Lefebvre O, Werner (2006). Rsc4 connects the chromatin remodeler RSC to RNA polymerases. Molecular and cellular biology, 26(13), 4920-33.
- Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns B (2009). Distinctive chromatin in human sperm packages genes for embryo development. Nature, 460(7254), 473-8.
- Cairns B (2009). The logic of chromatin architecture and remodelling at promoters. Nature, 461(7261), 193-8.
- Clapier CR, Cairns B (2012). Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature, 492(7428), 280-4.
- Jones KB, Barrott JJ, Xie M, Haldar M, Jin H, Zhu JF, Monument MJ, Mosbruger TL, Langer EM, Randall RL, Wilson RK, Cairns BR, Ding L, Capecchi M (2016). The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis. Oncogene, 35(38), 5021-32.
- Nelson AC, Cauceglia JW, Merkley SD, Youngson NA, Oler AJ, Nelson RJ, Cairns BR, Whitelaw E, Potts W (2013). Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression. Proceedings of the National Academy of Sciences of the United States of America, 110(49), 19848-53.
- Khoddami V, Yerra A, Mosbruger TL, Fleming AM, Burrows CJ, Cairns B (2019). Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. Proceedings of the National Academy of Sciences of the United States of America, 116(14), 6784-6789.
- Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen (2019). Structure of the RSC complex bound to the nucleosome. Science (New York, N.Y.), 366(6467), 838-843.
- Wu SF, Zhang H, Cairns B (2011). Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome research, 21(4), 578-89.
- Cakiroglu A, Clapier CR, Ehrensberger AH, Darbo E, Cairns BR, Luscombe NM, Svejstrup J (2019). Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes. Genome research, 29(6), 988-998.
- Nakamura R, Motai Y, Kumagai M, Wike CL, Nishiyama H, Nakatani Y, Durand NC, Kondo K, Kondo T, Tsukahara T, Shimada A, Cairns BR, Aiden EL, Morishita S, Takeda (2021). CTCF looping is established during gastrulation in medaka embryos. Genome research, 31(6), 968-980.
- Wike CL, Guo Y, Tan M, Nakamura R, Shaw DK, Díaz N, Whittaker-Tademy AF, Durand NC, Aiden EL, Vaquerizas JM, Grunwald D, Takeda H, Cairns B (2021). Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome research, 31(6), 981-994.
- Khoddami V, Cairns B (2013). Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nature biotechnology, 31(5), 458-64.
- Roberts DN, Wilson B, Huff JT, Stewart AJ, Cairns B (2006). Dephosphorylation and genome-wide association of Maf1 with Pol III-transcribed genes during repression. Molecular cell, 22(5), 633-44.
- VanDemark AP, Kasten MM, Ferris E, Heroux A, Hill CP, Cairns B (2007). Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Molecular cell, 27(5), 817-28.
- Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns B (2016). Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Molecular cell, 62(3), 453-461.
- Clapier CR, Verma N, Parnell TJ, Cairns B (2020). Cancer-Associated Gain-of-Function Mutations Activate a SWI/SNF-Family Regulatory Hub. Molecular cell, 80(4), 712-725.e5.
- Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen (2021). PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature cell biology, 23(4), 424-436.
- Clapier CR, Iwasa J, Cairns BR, Peterson C (2017). Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nature reviews. Molecular cell biology, 18(7), 407-422.
- Gambini A, Stein P, Savy V, Grow EJ, Papas BN, Zhang Y, Kenan AC, Padilla-Banks E, Cairns BR, Williams C (2020). Developmentally Programmed Tankyrase Activity Upregulates ß-Catenin and Licenses Progression of Embryonic Genome Activation. Developmental cell, 53(5), 545-560.e7.
- Saha A, Wittmeyer J, Cairns B (2005). Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nature structural & molecular biology, 12(9), 747-55.
- Szerlong H, Hinata K, Viswanathan R, Erdjument-Bromage H, Tempst P, Cairns B (2008). The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nature structural & molecular biology, 15(5), 469-76.
- Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns B (2010). Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nature structural & molecular biology, 17(5), 620-8.
- Jenkins TG, Aston KI, Pflueger C, Cairns BR, Carrell D (2014). Age-associated sperm DNA methylation alterations: possible implications in offspring disease susceptibility. PLoS genetics, 10(7), e1004458.
- Murphy PJ, Guo J, Jenkins TG, James ER, Hoidal JR, Huecksteadt T, Broberg DS, Hotaling JM, Alonso DF, Carrell DT, Cairns BR, Aston K (2020). NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure. PLoS genetics, 16(6), e1008756.
- Hammoud SS, Low DH, Yi C, Carrell DT, Guccione E, Cairns B (2014). Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. Cell stem cell, 15(2), 239-53.
- Guo J, Grow EJ, Yi C, Mlcochova H, Maher GJ, Lindskog C, Murphy PJ, Wike CL, Carrell DT, Goriely A, Hotaling JM, Cairns B (2017). Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. Cell stem cell, 21(4), 533-546.e6.
- Guo J, Nie X, Giebler M, Mlcochova H, Wang Y, Grow EJ, DonorConnect., Kim R, Tharmalingam M, Matilionyte G, Lindskog C, Carrell DT, Mitchell RT, Goriely A, Hotaling JM, Cairns B (2020). The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty. Cell stem cell, 26(2), 262-276.e4.
- Guo J, Sosa E, Chitiashvili T, Nie X, Rojas EJ, Oliver E, DonorConnect., Plath K, Hotaling JM, Stukenborg JB, Clark AT, Cairns B (2021). Single-cell analysis of the developing human testis reveals somatic niche cell specification and fetal germline stem cell establishment. Cell stem cell, 28(4), 764-778.e4.
- Guo J, Cairns B (2019). Isolation and Enrichment of Spermatogonial Stem Cells From Human Testis Tissues. Current protocols in stem cell biology, 49(1), e77.
- Varshney D, Vavrova-Anderson J, Oler AJ, Cowling VH, Cairns BR, White R (2015). SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nature communications, 6, 6569.
- Ramakrishnan S, Pokhrel S, Palani S, Pflueger C, Parnell TJ, Cairns BR, Bhaskara S, Chandrasekharan M (2016). Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nature communications, 7, 11949.
- Li J, Mulvihill TS, Li L, Barrott JJ, Nelson ML, Wagner L, Lock IC, Pozner A, Lambert SL, Ozenberger BB, Ward MB, Grossmann AH, Liu T, Banito A, Cairns BR, Jones K (2021). A Role for SMARCB1 in Synovial Sarcomagenesis Reveals That SS18-SSX Induces Canonical BAF Destruction. Cancer discovery, 11(10), 2620-2637.
- Jenkins TG, James ER, Alonso DF, Hoidal JR, Murphy PJ, Hotaling JM, Cairns BR, Carrell DT, Aston K (2017). Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology, 5(6), 1089-1099.
- Parnell TJ, Schlichter A, Wilson BG, Cairns B (2015). The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife, 4, e06073.
- Parnell T J, Schlicter A, Wilson B G, Cairns B (2015). The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife, 4, e06073.
- Schlichter A, Kasten MM, Parnell TJ, Cairns B (2020). Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes. eLife, 9,
- Chen H, Murray E, Sinha A, Laumas A, Li J, Lesman D, Nie X, Hotaling J, Guo J, Cairns BR, Macosko EZ, Cheng CY, Chen (2021). Dissecting mammalian spermatogenesis using spatial transcriptomics. Cell reports, 37(5), 109915.
- Sun W, Guo J, McClellan D, Poeschla A, Bareyan D, Casey MJ, Cairns BR, Tantin D, Engel M (2022). GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia. Molecular cancer research, 20, 501-514.
- Nie X, Munyoki SK, Sukhwani M, Schmid N, Missel A, Emery BR, DonorConnect, Stukenborg JB, Mayerhofer A, Orwig KE, Aston KI, Hotaling JM, Cairns BR, Guo (2022). Single-cell analysis of human testis aging and correlation with elevated body mass index. Developmental cell, 57(9), 1160-1176.e5.
- D'Orazio FM, Balwierz PJ, González AJ, Guo Y, Hernández-Rodríguez B, Wheatley L, Jasiulewicz A, Hadzhiev Y, Vaquerizas JM, Cairns B, Lenhard B, Müller (2021). Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Developmental cell, 56(5), 641-656.e5.
- Tharmalingam MD, Matilionyte G, Wallace WHB, Stukenborg JB, Jahnukainen K, Oliver E, Goriely A, Lane S, Guo J, Cairns B, Jorgensen A, Allen CM, Lopes F, Anderson RA, Spears N, Mitchell R (2020). Cisplatin and carboplatin result in similar gonadotoxicity in immature human testis with implications for fertility preservation in childhood cancer. BMC medicine, 18(1), 374.
- Jenkins TG, Aston KI, Cairns B, Smith A, Carrell D (2018). Paternal germ line aging: DNA methylation age prediction from human sperm. BMC genomics, 19(1), 763.
- Wang X, Cairns BR, Guo (2022). When spermatogenesis meets human aging and elevated body mass. Life medicine, 1(3), 267-269.
- Wamaitha SE, Nie X, Pandolfi EC, Wang X, Yang Y, Stukenborg JB, Cairns BR, Guo J, Clark A (2023). Single-cell analysis of the developing human ovary defines distinct insights into ovarian somatic and germline progenitors. Developmental cell, 58(20), 2097-2111.
- Feng BJ, Kohlmann W, Nix DA, Atkinson A, Boucher KM, Carroll C, Stubben CJ, Kolesar J, Singer EA, Riedlinger G, Edge S, Sahu KK, Churchman M, Graham L, Salhia B, Sanchez A, Zakharia Y, Schneider BP, Jain R, Byrne L, Moskaluk CA, Nepple K, Shabsigh A, Chahoud J, Cairns BR, Gupta (2025). Germline whole-exome sequencing reveals FOXP3-related gene variants conferring urinary cancer susceptibility and associated with immune escape. Journal for immunotherapy of cancer, 13(9),
- Yi C, Kitamura Y, Maezawa S, Namekawa SH, Cairns B (2025). ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network. Nature structural & molecular biology, 32(7), 1213-1226.
- Jiang Q, Cui L, Nie X, Cai H, Zhang W, Lu X, Guo Y, Hotaling JM, Cairns BR, Wang X, Guo (2025). A Single-Cell Transcriptome Atlas Characterizes the Immune Landscape of Human Testes During Aging. Aging cell, 24(6), e70032.
- Cui L, Nie X, Guo Y, Ren P, Guo Y, Wang X, Li R, Hotaling JM, Cairns BR, Guo (2025). Single-cell transcriptomic atlas of the human testis across the reproductive lifespan. Nature aging, 5(4), 658-674.
- Shen Z, Wu Y, Manna A, Yi C, Cairns BR, Evason KJ, Chandrasekharan MB, Tantin (2024). Oct4 redox sensitivity potentiates reprogramming and differentiation. Genes & development, 38(7-8), 308-321.
- Smith CM, Grow EJ, Shadle SC, Cairns B (2023). Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program. bioRxiv,
Review
- Kasten MM, Clapier CR, Cairns B (2011). SnapShot: Chromatin remodeling: SWI/SNF. Cell, 144(2), 310.e.l..
Other
- Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen (2021). Author Correction: PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature cell biology, 23(6), 676.
- Hickey GJ, Wike CL, Nie X, Guo Y, Tan M, Murphy PJ, Cairns B (2022). Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos. eLife, 11,
News & Podcasts
Huntsman Cancer Institute News
- Discovery Innovations Special Edition 2026
- Celebrating Mary Beckerle, a Visionary Huntsman Cancer Institute Leader
- Bradley Cairns, PhD, Begins Tenure as CEO of Huntsman Cancer Institute
- Alana Welm, PhD, Named Chair of Oncological Sciences in the Spencer Fox Eccles School of Medicine at the University of Utah
- Renowned Researcher Bradley R. Cairns, PhD, Elected as a Fellow of the Royal Society
- Three Talented Researchers Recognized as Endowed Chairs
- Grieving the Loss of Your Health
- Talks with Docs: Brad Cairns, Cancer Researcher
- First-Ever Genomic Study of Puberty Yields Insights into Development, Cancer, and Infertility