top of page


2019 - PRESENT

The Hainer Lab opened at the University of Pittsburgh in 2018

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

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

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

BJ Patty and SJ Hainer. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. Biology 2020 August 6; 9(8): 213 PDF

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, 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 copperFASEB J. 2019 Dec; 33(12):14556-14574 PDF

*indicates co-first authors

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


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

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

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


bottom of page