Jay Hesselberth, PhD

Professor, Biochemistry & Molecular Genetics

FacultyPhoto
Graduate School
  • PhD, University of Texas - Austin (2003)
Undergraduate School
  • BS, University of Iowa (IA) (1998)
Department
Biochemistry & Molecular Genetics

Professional Titles

  • Associate Professor

Publications

  • Schutz, K., Hesselberth, J.R., Fields, S. Capture and sequence analysis of RNAs with terminal 2',3'-cyclic phosphates. (2010) RNA 16:621-31
  • Chen, X., Hoffman, M.M., Bilmes, J., Hesselberth, J.R., Noble, W.S. A dynamic Bayesian network apprach for identifying protein-binding footprints from single molecule-based sequence data. (2010) Bioinformatics. Accepted.
  • High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S. Genome Res. 2010 Sep;20(9):1288-96
  • Jay R. Hesselberth, “Lives that introns lead after splicing”, WIREs RNA Reviews, In Revision.
  • Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res. 2014 Feb 5. [Epub ahead of print] PubMed PMID: 24500209
  • Balakrishnan I, Yang X, Brown J, Ramakrishnan A, Torok-Storb B, Kabos P, Hesselberth JR, Pillai MM. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells. 2014 Mar;32(3):662-73. PubMed PMID: 24038734
  • Hesselberth JR. Lives that introns lead after splicing. Wiley Interdiscip Rev RNA. 2013 Nov-Dec;4(6):677-91. PubMed PMID: 23881603
  • Li X, Zhang W, Xu T, Ramsey J, Zhang L, Hill R, Hansen KC, Hesselberth JR, Zhao R. Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly. Nucleic Acids Res. 2013 Apr 1;41(6):3805-18. PubMed PMID: 23393194
  • Ilango Balakrishnan, Xiaodong Yang, Joseph Brown, Aravind Ramakrishnan, Beverly Torok-Storb, Pe-ter Kabos, Jay R Hesselberth and Manoj M Pillai, Genome-wide analysis of miR-mRNA interactions in the marrow microenvironment. In Revision.
  • Xueni Li, Wenzheng Zhang, Tao Xu, Jolene Ramsey, Lingdi Zhang, Jay R. Hesselberth, Rui Zhao, Genome-wide in vivo RNA binding sites of the spliceosomal protein Prp8. (2013) Nucleic Acids Res, In press.
  • Mosher J, Zhang W, Blumhagen RZ, D'Alessandro A, Nemkov T, Hansen KC, Hesselberth JR, Reis T. Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat. Dev Biol. 2015 Sep 15;405(2):280-90. PubMed PMID: 26209258
  • Peach SE, York K, Hesselberth JR. Global analysis of RNA cleavage by 5'-hydroxyl RNA sequencing. Nucleic Acids Res. 2015 Sep 30;43(17):e108. PubMed PMID: 26001965
  • Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. Elife. 2015 Jan 27;4. PubMed PMID: 25626169
  • Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. Elife. 2015 Jan 27;4. PubMed PMID: 25626169
  • Koh KD, Balachander S, Hesselberth JR, Storici F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods. 2015 Mar;12(3):251-7, 3 p following 257. PubMed PMID: 25622106
  • Chatfield KC, Coughlin CR 2nd, Friederich MW, Gallagher RC, Hesselberth JR, Lovell MA, Ofman R, Swanson MA, Thomas JA, Wanders RJ, Wartchow EP, Van Hove JL. Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing. Mitochondrion. 2015 Mar;21:1-10. PubMed PMID: 25575635
  • Koh KD, Balachander S, Hesselberth JR, Storici F. Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods. 2015 Mar;12(3):251-7. PubMed PMID: 25622106
  • Cooper DA, Banerjee S, Chakrabarti A, García-Sastre A, Hesselberth JR, Silverman RH, Barton DJ. RNase L targets distinct sites in influenza A virus RNAs. J Virol. 2015 Mar;89(5):2764-76. PubMed PMID: 25540362
  • Chatfield KC, Coughlin CR 2nd, Friederich MW, Gallagher RC, Hesselberth JR, Lovell MA, Ofman R, Swanson MA, Thomas JA, Wanders RJ, Wartchow EP, Van Hove JL. Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing. Mitochondrion. 2015 Jan 6;21C:1-10. [Epub ahead of print] PubMed PMID: 25575635
  • Cooper DA, Banerjee S, Chakrabarti A, García-Sastre A, Hesselberth JR, Silverman RH, Barton DJ. RNase L Targets Distinct Sites in Influenza A Virus RNAs. J Virol. 2015 Mar 1;89(5):2764-76. PubMed PMID: 25540362
  • Kosmaczewski SG, Edwards TJ, Han SM, Eckwahl MJ, Meyer BI, Peach S, Hesselberth JR, Wolin SL, Hammarlund M. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. EMBO Rep. 2014 Dec;15(12):1278-85. PubMed PMID: 25366321
  • Hansen EC, Ransom M, Hesselberth JR, Hosmane NN, Capoferri AA, Bruner KM, Pollack RA, Zhang H, Drummond MB, Siliciano JM, Siliciano R, Stivers JT. Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. Elife. 2016 Sep 20;5. PubMed PMID: 27644592
  • Gillen AE, Yamamoto TM, Kline E, Hesselberth JR, Kabos P. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics. 2016 May 5;17:338. PubMed PMID: 27150721
  • Bryan DS, Ransom M, Adane B, York K, Hesselberth JR. High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res. 2014 Sep;24(9):1534-42. PubMed PMID: 25015380
  • Garrey SM, Katolik A, Prekeris M, Li X, York K, Bernards S, Fields S, Zhao R, Damha MJ, Hesselberth JR. A homolog of lariat-debranching enzyme modulates turnover of branched RNA. RNA. 2014 Aug;20(8):1337-48. PubMed PMID: 24919400
  • Pillai MM, Gillen AE, Yamamoto TM, Kline E, Brown J, Flory K, Hesselberth JR, Kabos P. HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer. Breast Cancer Res Treat. 2014 Jul;146(1):85-97. PubMed PMID: 24906430
  • Cherry PD, White LK, York K, Hesselberth JR. Genetic bypass of essential RNA repair enzymes in budding yeast. RNA. 2017 Dec 6. [Epub ahead of print] PubMed PMID: 29212664
  • Sclafani RA, Hesselberth JR. O Cdc7 kinase where art thou?. Curr Genet. 2017 Nov 13. [Epub ahead of print] PubMed PMID: 29134273
  • Cooper DA, Jha BK, Silverman RH, Hesselberth JR, Barton DJ. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res. 2014 Apr;42(8):5202-16. PubMed PMID: 24500209
  • Ransom M, Bryan DS, Hesselberth JR. High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes. Methods Mol Biol. 2018;1672:63-76. PubMed PMID: 29043617
  • Rossbach D, Bryan DS, Hesselberth JR, Sclafani R. Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae . G3 (Bethesda). 2017 Nov 6;7(11):3757-3774. PubMed PMID: 28924058
  • Balakrishnan I, Yang X, Brown J, Ramakrishnan A, Torok-Storb B, Kabos P, Hesselberth JR, Pillai MM. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells. 2014 Mar;32(3):662-73. PubMed PMID: 24038734
  • Gillen AE, Brechbuhl HM, Yamamoto TM, Kline E, Pillai MM, Hesselberth JR, Kabos P. Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes. Mol Cancer Res. 2017 Dec;15(12):1741-1751. PubMed PMID: 28912168
  • Riemondy KA, Sheridan RM, Gillen A, Yu Y, Bennett CG, Hesselberth JR. valr: Reproducible genome interval analysis in R. F1000Res. 2017;6:1025. PubMed PMID: 28751969
  • Riemondy KA, Ransom M, Alderman C, Gillen AE, Fu R, Finlay-Schultz J, Kirkpatrick GD, Di Paola J, Kabos P, Sartorius CA, Hesselberth JR. Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. Nucleic Acids Res. 2018 Nov 29. [Epub ahead of print] PubMed PMID: 30496484
  • Pollyea DA, Stevens BM, Jones CL, Winters A, Pei S, Minhajuddin M, D'Alessandro A, Culp-Hill R, Riemondy KA, Gillen AE, Hesselberth JR, Abbott D, Schatz D, Gutman JA, Purev E, Smith C, Jordan CT. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia. Nat Med. 2018 Nov 12. [Epub ahead of print] PubMed PMID: 30420752
  • Riemondy KA, Gillen AE, White EA, Bogren LK, Hesselberth JR, Martin SL. Dynamic temperature-sensitive A-to-I RNA editing in the brain of a heterothermic mammal during hibernation. RNA. 2018 Nov;24(11):1481-1495. PubMed PMID: 30065024
  • Tuttle KD, Krovi SH, Zhang J, Bedel R, Harmacek L, Peterson LK, Dragone LL, Lefferts A, Halluszczak C, Riemondy K, Hesselberth JR, Rao A, O'Connor BP, Marrack P, Scott-Browne J, Gapin L. TCR signal strength controls thymic differentiation of iNKT cell subsets. Nat Commun. 2018 Jul 9;9(1):2650. PubMed PMID: 29985393
  • Cherry PD, White LK, York K, Hesselberth JR. Genetic bypass of essential RNA repair enzymes in budding yeast. RNA. 2018 Mar;24(3):313-323. PubMed PMID: 29212664
  • Sclafani RA, Hesselberth JR. O Cdc7 kinase where art thou?. Curr Genet. 2018 Jun;64(3):677-680. PubMed PMID: 29134273
  • Ransom M, Bryan DS, Hesselberth JR. High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes. Methods Mol Biol. 2018;1672:63-76. PubMed PMID: 29043617
  • Rossbach D, Bryan DS, Hesselberth JR, Sclafani R. Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae . G3 (Bethesda). 2017 Nov 6;7(11):3757-3774. PubMed PMID: 28924058
  • Gillen AE, Brechbuhl HM, Yamamoto TM, Kline E, Pillai MM, Hesselberth JR, Kabos P. Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes. Mol Cancer Res. 2017 Dec;15(12):1741-1751. PubMed PMID: 28912168
  • Riemondy KA, Sheridan RM, Gillen A, Yu Y, Bennett CG, Hesselberth JR. valr: Reproducible genome interval analysis in R. F1000Res. 2017;6:1025. PubMed PMID: 28751969
  • Allawzi A, McDermott I, Delaney C, Nguyen K, Banimostafa L, Trumpie A, Hernandez-Lagunas L, Riemondy K, Gillen A, Hesselberth J, El Kasmi K, Sucharov CC, Janssen WJ, Stenmark K, Bowler R, Nozik-Grayck E. Redistribution of EC-SOD resolves bleomycin-induced inflammation via increased apoptosis of recruited alveolar macrophages. FASEB J. 2019 Dec;33(12):13465-13475. PubMed PMID: 31560857
  • Koh KD, Balachander S, Hesselberth JR, Storici F. Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Nat Methods. 2019 Aug;16(8):787-788. PubMed PMID: 31324896
  • Tamburini BAJ, Finlon JM, Gillen AE, Kriss MS, Riemondy KA, Fu R, Schuyler RP, Hesselberth JR, Rosen HR, Burchill MA. Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells. Front Immunol. 2019;10:1036. PubMed PMID: 31156626
  • Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL. Single cell RNA sequencing identifies TGFß as a key regenerative cue following LPS-induced lung injury. JCI Insight. 2019 Mar 26;5. PubMed PMID: 30913038
  • Cherry PD, Peach SE, Hesselberth JR. Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response. Elife. 2019 Mar 15;8. PubMed PMID: 30874502
  • Riemondy KA, Ransom M, Alderman C, Gillen AE, Fu R, Finlay-Schultz J, Kirkpatrick GD, Di Paola J, Kabos P, Sartorius CA, Hesselberth JR. Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. Nucleic Acids Res. 2019 Feb 28;47(4):e20. PubMed PMID: 30496484
  • Yang W, Trahan GD, Howell ED, Speck NA, Jones KL, Gillen AE, Riemondy K, Hesselberth J, Bryder D, Ernst P. Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis. Stem Cell Reports. 2020 Jan 16. [Epub ahead of print] PubMed PMID: 31951812
  • Ancar R, Li Y, Kindler E, Cooper DA, Ransom M, Thiel V, Weiss SR, Hesselberth JR, Barton DJ. Physiologic RNA targets and refined sequence specificity of coronavirus EndoU. RNA. 2020 Dec;26(12):1976-1999. PubMed PMID: 32989044
  • Gillen AE, Riemondy KA, Amani V, Griesinger AM, Gilani A, Venkataraman S, Madhavan K, Prince E, Sanford B, Hankinson TC, Handler MH, Vibhakar R, Jones KL, Mitra S, Hesselberth JR, Foreman NK, Donson AM. Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology. Cell Rep. 2020 Aug 11;32(6):108023. PubMed PMID: 32783945
  • Fu R, Gillen AE, Sheridan RM, Tian C, Daya M, Hao Y, Hesselberth JR, Riemondy KA. clustifyr: an R package for automated single-cell RNA sequencing cluster classification. F1000Res. 2020;9:223. PubMed PMID: 32765839
  • Richer AL, Riemondy KA, Hardie L, Hesselberth JR. Simultaneous measurement of biochemical phenotypes and gene expression in single cells. Nucleic Acids Res. 2020 Jun 4;48(10):e59. PubMed PMID: 32286626
  • Yang W, Trahan GD, Howell ED, Speck NA, Jones KL, Gillen AE, Riemondy K, Hesselberth J, Bryder D, Ernst P. Enhancing Hematopoiesis from Murine Embryonic Stem Cells through MLL1-Induced Activation of a Rac/Rho/Integrin Signaling Axis. Stem Cell Reports. 2020 Feb 11;14(2):285-299. PubMed PMID: 31951812
  • Carvill GL, Matheny T, Hesselberth J, Demarest S. Haploinsufficiency, Dominant Negative, and Gain-of-Function Mechanisms in Epilepsy: Matching Therapeutic Approach to the Pathophysiology. Neurotherapeutics. 2021 Jul;18(3):1500-1514. PubMed PMID: 34648141
  • Riemondy KA, Venkataraman S, Willard N, Nellan A, Sanford B, Griesinger AM, Amani V, Mitra S, Hankinson TC, Handler MH, Sill M, Ocasio J, Weir SJ, Malawsky DS, Gershon TR, Garancher A, Wechsler-Reya RJ, Hesselberth JR, Foreman NK, Donson AM, Vibhakar R. Neoplastic and immune single cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma. Neuro Oncol. 2021 Jun 2. [Epub ahead of print] PubMed PMID: 34077540
  • Carpentier KS, Sheridan RM, Lucas CJ, Davenport BJ, Li FS, Lucas ED, McCarthy MK, Reynoso GV, May NA, Tamburini BAJ, Hesselberth JR, Hickman HD, Morrison TE. MARCO( ) lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination. EMBO J. 2021 Nov 15;40(22):e108966. PubMed PMID: 34618370
  • Puntambekar S, Hesselberth JR, Riemondy KA, Fu R. Cell-level metadata are indispensable for documenting single-cell sequencing datasets. PLoS Biol. 2021 May;19(5):e3001077. PubMed PMID: 33945522
  • Walsh SM, Sheridan RM, Lucas ED, Doan TA, Ware BC, Schafer J, Fu R, Burchill MA, Hesselberth JR, Tamburini BAJ. Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node. Elife. 2021 Apr 12;10. PubMed PMID: 33843587
  • Fu R, Gillen AE, Grabek KR, Riemondy KA, Epperson LE, Bustamante CD, Hesselberth JR, Martin SL. Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal. Front Physiol. 2020;11:624677. PubMed PMID: 33536943
  • White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet. 2022;13:1037134. PubMed PMID: 36386798
  • Riemondy KA, Venkataraman S, Willard N, Nellan A, Sanford B, Griesinger AM, Amani V, Mitra S, Hankinson TC, Handler MH, Sill M, Ocasio J, Weir SJ, Malawsky DS, Gershon TR, Garancher A, Wechsler-Reya RJ, Hesselberth JR, Foreman NK, Donson AM, Vibhakar R. Neoplastic and immune single-cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma. Neuro Oncol. 2022 Feb 1;24(2):273-286. PubMed PMID: 34077540
  • Direct detection of RNA repair by nanopore sequencing Laura K. White, Saylor M. Strugar, Andrea MacFadden, Jay R. Hesselberth bioRxiv 2022.05.29.493267; doi: https://doi.org/10.1101/2022.05.29.493267
  • Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Jagannathan S. Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay. bioRxiv. 2024 Jan 11. PubMed PMID: 38260612
  • Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin AL, Hesselberth JR, Hickman HD, Tamburini BA, Morrison TE. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. JCI Insight. 2024 Jan 9. [Epub ahead of print] PubMed PMID: 38194268
  • Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin A, Hesselberth JR, Hickman HD, Tamburini BAJ, Morrison TE. Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. bioRxiv. 2023 Oct 13. PubMed PMID: 37873393
  • Tamburini B, Doan T, Forward T, Lucas E, Fleming I, Uecker-Martin A, Hesselberth J, Morrison T. Vaccine-induced antigen archiving enhances local memory CD8 T cell responses following an unrelated viral infection. Res Sq. 2023 Sep 25. PubMed PMID: 37841845
  • Ivanova DL, Thompson SB, Klarquist J, Harbell MG, Kilgore AM, Lasda EL, Hesselberth JR, Hunter CA, Kedl RM. Vaccine adjuvant-elicited CD8( ) T cell immunity is co-dependent on T-bet and FOXO1. Cell Rep. 2023 Aug 29;42(8):112911. PubMed PMID: 37516968
  • White LK, Strugar SM, MacFadden A, Hesselberth JR. Nanopore sequencing of internal 2'-PO(4) modifications installed by RNA repair. RNA. 2023 Jun;29(6):847-861. PubMed PMID: 36854608


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