The following publications are from BSPC’s collaborations since 2018. BSPC members are indicated in bold. BSPC Post-baccalaureate fellows are additionally indicated with *

2023

• Campbell K*, Cawley NX, Luke R, Scott KEJ, Johnson N*, Farhat NY, Alexander D, Wassif CA, Li W, Cologna SM, Berry-Kravis E, Do AD, Dale R & Porter FD. (2023). Identification of cerebral spinal fluid protein biomarkers in Niemann-Pick disease, type C1. Biomark Res 11(1). PMID:36721240; doi: 10.1186/s40364-023-00448-x
• Jovanovic M, Mitra A, Besio R, Contento BM, Wong KW, Derkyi A, To M, Forlino A, Dale R & Marini JC. (2023). Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study. Matrix Biol . PMID:37348683
• Anbazhagan R, Kavarthapu R, Dale R, Campbell K*, Faucz FR & Dufau ML. (2023). miRNA Expression Profiles of Mouse Round Spermatids in GRTH/DDX25-Mediated Spermiogenesis: mRNA-miRNA Network Analysis. Cells 12(5). PMID:36899892; doi: 10.3390/cells12050756
• Zheng Q, Qiu H, Zhang H & Hinnebusch AG. (2023). Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes. Nucleic Acids Res 51(8). PMID:36864781; doi: 10.1093/nar/gkad099
• Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale R, Mitchell JA, Petros TJ & Rocha PP. (2023). Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nat Genet 55(2). PMID:36717694; doi: 10.1038/s41588-022-01295-6
• Tanizaki Y, Wang S, Zhang H, Shibata Y & Shi YB. (2023). Liver development during Xenopus tropicalis metamorphosis is controlled by T3-activation of WNT signaling. iScience 26(4). PMID:37153451; doi: 10.1016/j.isci.2023.106301
• Trivellin G, Daly AF, Hernández-Ramírez LC, Araldi E, Tatsi C, Dale R, Fridell G*, Mittal A*, Faucz FR, Iben JR, Li T, Vitali E, Stojilkovic SS, Kamenicky P, Villa C, Baussart B, Chittiboina P, Toro C, Gahl WA, Eugster EA, Naves LA, Jaffrain-Rea ML, de Herder WW, Neggers SJ, Petrossians P, Beckers A, Lania AG, Mains RE, Eipper BA & Stratakis CA. (2023). Germline loss-of-function PAM variants are enriched in subjects with pituitary hypersecretion. Front Endocrinol (Lausanne) 14. PMID:37388215; doi: 10.3389/fendo.2023.1166076
• Petroni E, Esnault C, Tetreault D, Dale R, Storz G & Adams PP. (2023). Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 14(1). PMID:37402717; doi: 10.1038/s41467-023-39576-1
• Wang S, Shibata Y, Tanizaki Y, Zhang H, Yan W, Fu L & Shi YB. (2023). Comparative Analysis of Transcriptome Profiles Reveals Distinct and Organ-Dependent Genomic and Nongenomic Actions of Thyroid Hormone in Xenopus tropicalis Tadpoles. Thyroid 33(4). PMID:36503276; doi: 10.1089/thy.2022.0469
• Tanizaki Y, Zhang H, Shibata Y & Shi YB. (2023). Organ-specific effects on target binding due to knockout of thyroid hormone receptor α during Xenopus metamorphosis. Dev Growth Differ 65(1). PMID:36397722; doi: 10.1111/dgd.12825
• Dang Do AN, Sleat DE, Campbell K*, Johnson N*, Zheng H, Wassif CA, Dale R & Porter FD. (2023). Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res 22(7). PMID:37338096; doi: 10.1021/acs.jproteome.3c00199
• Bao L, Fu L, Su Y, Chen Z, Peng Z, Sun L, Gonzalez FJ, Wu C, Zhang H, Shi B & Shi YB. (2023). Amino acid transporter SLC7A5 regulates Paneth cell function to affect the intestinal inflammatory response. bioRxiv. PMID:36789439

2022

• Tanizaki Y, Zhang H, Shibata Y & Shi YB. (2022). Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway. Commun Biol 5(1). PMID:35132135; doi: 10.1038/s42003-022-03061-0
• Walling LR, Kouse AB, Shabalina SA, Zhang H & Storz G. (2022). A 3’ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria. Nucleic Acids Res 50(17). PMID:36062564; doi: 10.1093/nar/gkac748
• Li F, Lee M, Esnault C, Wendover K, Guo Y, Atkins P, Zaratiegui M & Levin HL. (2022). Identification of an integrase-independent pathway of retrotransposition. Sci Adv 8(26). PMID:35767609; doi: 10.1126/sciadv.abm9390
• Baxter LL, Watkins-Chow DE, Johnson N*, Farhat NY, Platt FM, Dale R, Porter FD, Pavan WJ & Rodriguez-Gil JL. (2022). Correlation of age of onset and clinical severity in Niemann-Pick disease type C1 with lysosomal abnormalities and gene expression. Sci Rep 12(1). PMID:35140266; doi: 10.1038/s41598-022-06112-y
• El-Gazzar A, Kang H, Fratzl-Zelman N, Webb E, Barnes AM, Jovanovic M, Mehta SG, Datta V, Saraff V, Dale R, Rauch F, Marini JC & Högler W. (2022). SMAD3 mutation in LDS3 causes bone fragility by impairing the TGF-β pathway and enhancing osteoclastogenesis. Bone Rep 17. PMID:35874167; doi: 10.1016/j.bonr.2022.101603
• Lee DR, Rhodes C, Mitra A, Zhang Y, Maric D, Dale R & Petros TJ. (2022). Transcriptional heterogeneity of ventricular zone cells in the ganglionic eminences of the mouse forebrain. Elife 11. PMID:35175194; doi: 10.7554/eLife.71864
• Thompson JJ, Lee DJ, Mitra A, Frail S, Dale R & Rocha PP. (2022). Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat Commun 13(1). PMID:35871075; doi: 10.1038/s41467-022-31938-5
• Tanizaki Y, Shibata Y, Zhang H & Shi YB. (2022). Thyroid Hormone Receptor α Controls the Hind Limb Metamorphosis by Regulating Cell Proliferation and Wnt Signaling Pathways in Xenopus tropicalis. Int J Mol Sci 23(3). PMID:35163147; doi: 10.3390/ijms23031223
• Rhodes CT, Thompson JJ, Mitra A, Asokumar D, Lee DR, Lee DJ, Zhang Y, Jason E*, Dale R, Rocha PP & Petros TJ. (2022). An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nat Commun 13(1). PMID:35858915; doi: 10.1038/s41467-022-31793-4
• Kean CM, Tracy CJ, Mitra A, Rahat B, Van Winkle MT, Gebert CM, Noeker JA, Calof AL, Lander AD, Kassis JA & Pfeifer K. (2022). Decreasing Wapl dosage partially corrects embryonic growth and brain transcriptome phenotypes in Nipbl(+/-) embryos. Sci Adv 8(48). PMID:36449618; doi: 10.1126/sciadv.add4136

2021

• Beck DB, Basar MA, Asmar AJ, Thompson JJ, Oda H, Uehara DT, Saida K, Pajusalu S, Talvik I, D’Souza P, Bodurtha J, Mu W, Barañano KW, Miyake N, Wang R, Kempers M, Tamada T, Nishimura Y, Okada S, Kosho T, Dale R, Mitra A, Macnamara E, Undiagnosed Diseases Network, Matsumoto N, Inazawa J, Walkiewicz M, Õunap K, Tifft CJ, Aksentijevich I, Kastner DL, Rocha PP & Werner A. (2021). Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. Sci Adv 7(4). PMID:33523931; doi: 10.1126/sciadv.abe2116
• Tanizaki Y, Shibata Y, Zhang H & Shi YB. (2021). Analysis of Thyroid Hormone Receptor α-Knockout Tadpoles Reveals That the Activation of Cell Cycle Program Is Involved in Thyroid Hormone-Induced Larval Epithelial Cell Death and Adult Intestinal Stem Cell Development During Xenopus tropicalis Metamorphosis. Thyroid 31(1). PMID:32515287; doi: 10.1089/thy.2020.0022
• Stamos DB, Clubb LM, Mitra A, Chopp LB, Nie J, Ding Y, Das A, Venkataganesh H, Lee J, El-Khoury D, Li L, Bhandoola A, Bosselut R & Love PE. (2021). The histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development. J Exp Med 218(12). PMID:34726730; doi: 10.1084/jem.20202012
• Tseng WC, Johnson Escauriza AJ, Tsai-Morris CH, Feldman B, Dale R, Wassif CA & Porter FD. (2021). The role of Niemann-Pick type C2 in zebrafish embryonic development. Development 148(7). PMID:33722902; doi: 10.1242/dev.194258
• Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale R, Storz G & Wade JT. (2021). Regulatory roles of Escherichia coli 5’ UTR and ORF-internal RNAs detected by 3’ end mapping. Elife 10. PMID:33460557; doi: 10.7554/eLife.62438
• Gaikwad S, Ghobakhlou F, Young DJ, Visweswaraiah J, Zhang H & Hinnebusch AG. (2021). Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs. Elife 10. PMID:33764298; doi: 10.7554/eLife.64283
• Mahadevan V, Mitra A, Zhang Y, Yuan X, Peltekian A, Chittajallu R, Esnault C, Maric D, Rhodes C, Pelkey KA, Dale R, Petros TJ & McBain CJ. (2021). NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile Brain. Front Mol Neurosci 14. PMID:34630033; doi: 10.3389/fnmol.2021.712609
• Rodriguez-Gil JL, Baxter LL, Watkins-Chow DE, Johnson N*, Davidson CD, Carlson SR, Incao AA, NISC Comparative Sequencing Program, Wallom KL, Farhat NY, Platt FM, Dale R, Porter FD & Pavan WJ. (2021). Transcriptome of HPβCD-treated Niemann-Pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics. Hum Mol Genet 30(24). PMID:34296265; doi: 10.1093/hmg/ddab194
• Sen ND, Zhang H & Hinnebusch AG. (2021). Down-Regulation of Yeast Helicase Ded1 by Glucose Starvation or Heat-Shock Differentially Impairs Translation of Ded1-Dependent mRNAs. Microorganisms 9(12). PMID:34946015; doi: 10.3390/microorganisms9122413
• Shibata Y, Tanizaki Y, Zhang H, Lee H, Dasso M & Shi YB. (2021). Thyroid Hormone Receptor Is Essential for Larval Epithelial Apoptosis and Adult Epithelial Stem Cell Development but Not Adult Intestinal Morphogenesis during Xenopus tropicalis Metamorphosis. Cells 10(3). PMID:33802526; doi: 10.3390/cells10030536
• Park KS, Rahat B, Lee HC, Yu ZX, Noeker J, Mitra A, Kean CM, Knutsen RH, Springer D, Gebert CM, Kozel BA & Pfeifer K. (2021). Cardiac pathologies in mouse loss of imprinting models are due to misexpression of H19 long noncoding RNA. Elife 10. PMID:34402430; doi: 10.7554/eLife.67250

2020

• Chang E*, Fu C, Coon SL, Alon S, Bozinoski M, Breymaier M, Bustos DM, Clokie SJ, Gothilf Y, Esnault C, Michael Iuvone P, Mason CE, Ochocinska MJ, Tovin A, Wang C, Xu P, Zhu J, Dale R & Klein DC. (2020). Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. J Pineal Res 69(3). PMID:32533862; doi: 10.1111/jpi.12673
• Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H & Levin HL. (2020). Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Rep 30(8). PMID:32101745; doi: 10.1016/j.celrep.2020.01.094
• Zhou F, Zhang H, Kulkarni SD, Lorsch JR & Hinnebusch AG. (2020). eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA 26(4). PMID:31915290; doi: 10.1261/rna.073536.119
• Matson CA, Choi S, Livak F, Zhao B, Mitra A, Love PE & Singh NJ. (2020). CD5 dynamically calibrates basal NF-κB signaling in T cells during thymic development and peripheral activation. Proc Natl Acad Sci U S A 117(25). PMID:32513716; doi: 10.1073/pnas.1922525117
• Li L, Mitra A, Cui K, Zhao B, Choi S, Lee JY, Stamos DB, El-Khoury D, Warzecha C, Pfeifer K, Hardwick J, Zhao K, Venters B, Davé UP & Love PE. (2020). Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood 135(25). PMID:32181817; doi: 10.1182/blood.2019000794
• Kang H, Jha S, Ivovic A, Fratzl-Zelman N, Deng Z, Mitra A, Cabral WA, Hanson EP, Lange E, Cowen EW, Katz J, Roschger P, Klaushofer K, Dale R, Siegel RM, Bhattacharyya T & Marini JC. (2020). Somatic SMAD3-activating mutations cause melorheostosis by up-regulating the TGF-β/SMAD pathway. J Exp Med 217(5). PMID:32232430; doi: 10.1084/jem.20191499
• Guo X, Plank-Bazinet J, Krivega I, Dale R & Dean A. (2020). Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Res 48(18). PMID:32960220; doi: 10.1093/nar/gkaa736
• Nakajima K, Tanizaki Y, Luu N, Zhang H & Shi YB. (2020). Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption. Gen Comp Endocrinol 287. PMID:31794731; doi: 10.1016/j.ygcen.2019.113349
• Aksenova V, Smith A, Lee H, Bhat P, Esnault C, Chen S, Iben J, Kaufhold R, Yau KC, Echeverria C, Fontoura B, Arnaoutov A & Dasso M. (2020). Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway. Nat Commun 11(1). PMID:32917881; doi: 10.1038/s41467-020-18266-2

2019

• Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG & Lorsch JR. (2019). Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 17(1). PMID:31810458; doi: 10.1186/s12915-019-0718-5
• Martin KB, Williams IM, Cluzeau CV, Cougnoux A, Dale R, Iben JR, Cawley NX, Wassif CA & Porter FD. (2019). Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1. Int J Mol Sci 21(1). PMID:31906248; doi: 10.3390/ijms21010292