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Yong Cheng, PhD
Yong Cheng, PhD


PhD – The Pennsylvania State University
MS – Nankai University, Tianjin, China
BS – Nankai University, Tianjin, China

Research Interests

Our lab is interested in understanding the functions of the human genome, especially non-coding regulatory elements. We use high-throughput functional genomic approaches to investigate regulatory elements in normal blood development and disorders. We also interested in the application of regulatory elements in treating genetic disorders using genome editing and gene therapy.

Selected Publications

* First or co-first authors; # Corresponding or co-corresponding

Walker M, Li Y, Morales-Hernandez A, Qi Q, Parupalli C, Brown SA, Christian C, Clements WK, Cheng Y#, McKinney Freeman SL# An NFIX-mediated regulatory network governs the balance of hematopoietic stem and progenitor cells during hematopoiesis. Blood Adv Dec 7, 2022. PMID: 36478187

Shrestha D, Bag A, Wu R, Zhang Y, Tang X, Qi Q, Xing J#, Cheng Y#. Genomics and epigenetics guided identification of tissue-specific genomic safe harbors. Genome Biol Sep 21, 2022. PMID: 36131352

Feng R, Mayuranathan T, Huang P, Doerfler PA, Li Y, Yao Y, Zhang J, Palmer LE, Mayberry K, Christakopoulos GE, Xu P, Li C, Cheng Y, Blobel GA, Simon MC, Weiss MJ. Activation of γ-globin expression by hypoxia-inducible factor 1α. Nature Oct 6, 2022. PMID: 36224385

Cheng L, Li Y, Qi Q, Xu P, Feng R, Palmer L, Chen J, Wu R, Yee T, Zhang J, Yao Y, Sharma  A, Hardison RC, Weiss MJ#, Cheng Y#, Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression. Nature Genetics Jun, 2021. PMID:33958780

Qi Q, Cheng L, Tang X, He Y, Li Y, Yee T, Shrestha D, Feng R, Xu P, Zhou X, Pruett-Miller S, Hardison RC, Weiss MJ, Cheng Y#. Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis. Blood Mar 11, 2021. PMID:33512425

Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.  Nat Biotechnol Jun 15, 2020. PMID: 32541958

Cheng Y#, Tsai SQ#. Illuminating the genome-wide activity of genome editors for safe and effective therapeutics. Genome Biol Dec 22, 2019. PMID: 30577870

Cheng Y*, Ma Z*, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller AC, Giardine B, The mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio AL, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature Nov 20, 2014. PMID: 25409826

Yue F*, Cheng Y*, Breschi A*, Vierstra J*, Wu W*, Ryba T*, Sandstrom R*,Ma Z*, Davis C*,Pope BD*,Shen Y*, The mouse ENCODE Consortium. An integrated and comparative Encyclopedia of DNA elements in the mouse genome. Nature Nov 20, 2014. PMID:32728249 

Sundaram V*, Cheng Y*, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res Dec 24, 2014. PMID: 25319995

Cheng Y*, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang, Y ,Blobel GA, Weiss MJ, Hardison RC. Erythroid GATA1 function revealed by genome‐wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res Dec 19, 2009. PMID: 19887574

Cheng Y*, King DC, Dore LC, Zhang X, Zhou Y, Zhang Y, Dorman C, Abebe D, Kumar SA, Chiaromonte F, Miller W, Green RD, Weiss MJ, Hardison RC. Transcriptional enhancement by GATA1‐occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res Dec 18, 2008. PMID: 18818370

See full list of publications

Last update: October 2021