PUBLISHED WORK
2019 - PRESENT
The Hainer Lab opened at the University of Pittsburgh in 2018
SA Tripplehorn, MK Shirra, SM Lardo, HG Marvil, SJ Hainer*, KA Arndt*. A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes. In revision; bioRxiv. https://doi.org/10.1101/2024.12.06.627179 2024 *denotes co-corresponding authors PDF
BJ Patty, C Jordan, SM Lardo, K Troy, SJ Hainer. H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells. Epigenetics & Chromatin. 2024 Nov 1;17(1):32. PDF
ML Lynskey, EE Brown, R Bhargava, AR Wondisford, JB Ouriou, O Freund, RW Bowman, SM Lardo, S Schmaus-Hayes, SJ Hainer, RJ O’Sullivan. HIRA protects telomeres against R-loop-induced instability in ALT cancer cells. Cell Reports. 2024 Nov 26;43(11):114964 PDF
An oligodendrocyte silencer element provides a framework to assess the pathogenic impact of lamin B1 structural variants
B Nmezi, G Rodriguez Bey, T DeFrancesco Oranburg, K Dudnyk, SM Lardo, N Herdman, A Jacko, S Rubio, EL Alcocer, J Kofler, D Kim, J Rankin, E Kivuva, N Gutowski, K Schon, J van den Ameele, PF Chinnery, SB Sousa, F Palavra, C Toro, FP e Vairo, J Saute, L Pan, M Alturkustani, R Hammond, F Gros-Louis, M Gold, Y Park, G Bernard, R Raininko, J Zhou, SJ Hainer, Q Padiath. An oligodendrocyte silencer element provides a framework to assess the pathogenic impact of lamin B1 structural variants. Nature Communications 2024. PDF
O Verdejo-Torres, DC Klein, L Novoa-Aponte, J Carrazco-Carrillo, D Bonilla-Pinto, A Rivera, F Fitisemanu, ML Jiménez-González, L Flinn, AT Pezacki, A Lanzirotti, CJ Chang, LA Ortiz-Frade, JG. Navea, C Blaby-Haas, SJ Hainer, T Padilla-Benavides. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. PLoS Genet. 2024 Dec 5;20(12):e1011495 PDF
BJ Patty and SJ Hainer. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. In revision; bioRxiv. https://doi.org/10.1101/2024.04.12.589208 2024. PDF
C Viner, CA Ishak, J Johnson, NJ Walker, H Shi, MK Sjoberg-Herrera, SY Shen, SM Lardo, DJ Adams, AC Ferguson-Smith, DD de Carvolho, SJ Hainer, TL Bailey, MM Hoffman. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biology. 2024; 25(1):11. PDF
DC Klein, SM Lardo, and SJ Hainer. The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9. Cancer Research Communications. 2023; 3(12) PDF
DC Klein, SM Lardo, KN McCannell, and SJ Hainer. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biology. 2023; 21,167 PDF
DC Klein, K Troy, SA Tripplehorn, and SJ Hainer. The esBAF and ISW1 nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. BMC Genomics. 2023; 24,201 PDF
H Zou, B Poore, EE Brown, J Qian, B Xie, V Razskazovskiy, D Ayrapetian, E Asimakidou, V Sharma, S Xia, F Liu, A Chen, Y Guan, Z Li, S Wanggou, X Wu, O Saulnier, M Ly, W Fellows-Mayle, G Xi, T Tomita, AC Resnick, SC Mack, EH Raabe, CG Eberhart, D Sun, BE Stronach, S Agnihotri, G Kohanbash, S Lu, K Herrup, JN Rich, GK Gittes, A Broniscer, Z Hu, X Li, IF Pollack, RM Friedlander, SJ Hainer*, MD Taylor*, B Hu*. A neurodevelopmental epigenetic programme mediated by SMARCD3-DAB1-Reelin signalling is hijacked to promote medullablastoma metastasis. Nature Cell Biology. 2023 Mar;25(3):493-507 PDF
*denotes co-corresponding authors
C McCann, M Quinteros, I Adelugba, M Morgada, AR Castelblanco, EJ Davis, A Lanzirotti, SJ Hainer, A Vila, P Cobine, JG Navea, T Padilla-Benavides. The mitochondrial Cu+ transporter PiC2 (Slc25a3) is a target of MTF1 required for development of skeletal muscle in vitro by contributing to cytochrome c oxidase metallation. Frontiers in Molecular Biosciences. 2022; (9). PDF
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SM Lardo and SJ Hainer. Single cell factor localization on chromatin using ultra-low input cleavage under targets and release using nuclease. J. Vis. Exp. 2022; (180), e63536. PDF
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BJ Patty and SJ Hainer. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nature Protocols 16, 2633–2666 (2021). PDF
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BJ Patty and SJ Hainer. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. Biology 2020 August 6; 9(8): 213 PDF
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K Troy, Y Liu*, SJ Hainer*. PathSTORM: a road to early cancer detection. Molecular & Cellular Oncology 2020 PDF
*denotes co-corresponding authors
SJ Hainer* and CD Kaplan*. Specialized RSC: substrate specificities for a conserved chromatin remodeler. BioEssays. 2020 July; 42(7):e2000002 PDF
J Xu, H Ma, H Ma, W Jiang, M Duan, S Zhao, C Gao, E-R Hahm, SM Lardo, K Troy, M Sun, R Pai, DB Stolz, S Singh, RE Brand, DJ Hartman, J Hu, SJ Hainer*, Y Liu*. Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis. Nature Communications, 2020 April 20; 11(1): 1899 PDF
*indicates co-corresponding authors
NA Fraunhoffer, N Agarwal, K Takeishi, A Ostrowska, AC l’Hortet, J Guzman-Lepe, K Morita, K Troy, WM Mars, S Paranjpe, GK Michalopoulos, A Bell, SJ Hainer, IJ Fox, and A Soto-Gutierrez. Cellular location of HNF4a is linked with terminal liver failure in humans. Hepatology Communications, 2020 April 21; PDF
DC Klein and SJ Hainer. Chromatin Regulation and Dynamics in Stem Cells. Current Topics in Developmental Biology, 2020;138:1-71 PDF
DC Klein and SJ Hainer. Genomic Methods in Profiling DNA Accessibility and Factor Localization. Chromosome Research, 2020 Mar; 28 (1): 69-85 PDF
SJ Hainer*, A Boskovic, KN McCannell, OJ Rando, and TG Fazzio*. Profiling of Pluripotency Factors in Single Cells and Early Embryos. Cell. 2019 April 2 pii: S0092-8674(19)30276-4. PDF
*indicates co-corresponding authors
C Tavera-Montañez*, SJ Hainer*, D Cangussu, Y Xiao, P Reyes-Gutierrez, Y Yoon, J Rivera- Pérez, AN Imbalzano, JG Navea, TG Fazzio and T Padilla-Benavides. MTF1, a classic metal sensing transcription factor, promotes myogenesis in response to copper. FASEB J. 2019 Dec; 33(12):14556-14574 PDF
*indicates co-first authors
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SJ Hainer* and TG Fazzio*. High-Resolution Chromatin Profiling Using CUT&RUN. Current Protocols in Molecular Biology. 2019 Jan 28:e85. PDF
*indicates co-corresponding authors
PRE-2018
Postdoctoral work with Thomas Fazzio 2012-2017
Graduate work with Joseph Martens 2007-2012
D Acharya, SJ Hainer, Y Yoon, F Wang, I Bach, JA Rivera-Perez, TG Fazzio. KAT-independent gene regulation by Tip60 promotes ESC self-renewal but not pluripotency. Cell Reports. 2017 19: 671-679. PDF
SJ Hainer, KN McCannell, J Yu, L Ee, LJ Zhu, OJ Rando, TG Fazzio. DNA methylation directs genomic localization of Mbd2 and Mbd3 in ES cells. eLIFE. 2016 Nov 16;5. PDF
SJ Hainer and JA Martens. Regulation of chaperone binding and nucleosome dynamics by key residues within the globular domain of histone H3. Epigenetics & Chromatin. 2016 Apr 30;9:17. PDF
SJ Hainer and TG Fazzio. Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Reports. 2015 Oct 6;13(1):61-9. PDF
SJ Hainer, W Gu, BR Carone, BL Landry, OJ Rando, CC Mello, TG Fazzio. Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes & Development. 2015 Feb 15;29(4): 362-378. PDF
PB Chen, LJ Zhu, SJ Hainer, KN McCannell, TG Fazzio. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics. 2014 15:1104. PDF
BR Carone, JH Hung, SJ Hainer, MT Chou, DM Carone, Z Weng, TG Fazzio, OJ Rando. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Developmental Cell. 2014 Jul 14:11-22. PDF
SJ Hainer, BA Charsar, SB Cohen, JA Martens. Identification of mutant versions of the Spt16 histone chaperone that are defective for transcription-coupled nucleosome occupancy in Saccharomyces cerevisiae. G3 (Bethesda). 2012 May 2:555-567. PDF
The PAF1 Complex Represses SER3 Transcription In Saccharomyces
Cerevisiae By Facilitating Intergenic Transcription-Dependent Nucleosome Occupancy Of The SER3 Promoter
JA Pruneski, SJ Hainer, KO Petrov, JA Martens. The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter. Eukaryotic Cell. 2011 Oct;10(10):1283-94. PDF
Identification Of Histone Mutations That Are Required For Transcription-Coupled Nucleosome Occupancy
SJ Hainer and JA Martens. Identification of histone mutations that are required for transcription-coupled nucleosome occupancy. Molecular and Cellular Biology. 2011 Sep;31(17):3557-68. PDF
SJ Hainer and JA Martens. Transcription of ncDNA across regulatory sequences: many roads lead to local gene regulation. Transcription. 2011 May/June 2(3):120-123. PDF
SJ Hainer, JA Pruneski, RD Mitchell, R Monteverde, JA Martens. Intergenic transcription causes repression by directing nucleosome assembly. Genes & Development. 2011 Jan 1;25(1):29-40. PDF