PUBLISHED WORK
2019 - PRESENT
The Hainer Lab opened at the University of Pittsburgh in 2018
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
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, 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
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