Jonathan Yuin-Han LOH

Epigenetics and Cell Fates

Profile

Jonathan Yuin-Han LOH
Lab Location: #8-01   Email: yhloh@imcb.a-star.edu.sg   Tel: 65869592

Jonathan studied Biology and graduated with B.Sc. 1st Class honours from the National University of Singapore (NUS). He then did his Ph.D. research as an A*STAR Scholar at the Stem Cell and Developmental Biology group, Genome Institute of Singapore under the mentorship of Dr Ng Huck Hui. There, he mapped the transcriptional network of Nanog and Oct4 in Embryonic Stem Cells (ESCs), and identified several novel transcription factors and histone demethylases, such as Esrrb, Rif1, Zic3, Kdm3a and Kdm4c, which play essential roles in maintaining the self-renewal and pluripotency of ESCs. During his postdoctoral fellowship at the Division of Pediatric Hematology and Oncology, Boston Children’s Hospital, Harvard Medical School, he was trained under the tutelage of Dr George Daley. There, he pioneered the use of human blood cells for reprogramming to induced pluripotent stem cells (iPSCs), and the modelling of congenital and somatic Hematologic diseases using iPSCs. Jon is now a Senior Principal Investigator at the Institute of Molecular and Cell Biology where he also serves as the Programme Coordinator for the Stem cell, Regenerative Medicine and Ageing research. Concurrently, he is an Associate Professor (Adjunct) at the NUS Yong Loo Lin School of Medicine Department of Physiology, NUS Faculty of Science Department of Biological Sciences, as well as a Faculty member of the NUS Graduate School of Integrative Sciences and Engineering. His laboratory is interested in dissecting the mechanisms regulating cell fate changes, and developing novel tools in deriving reprogrammed and differentiated cell types. His research work has earned him several prestigious national and international accolades including the Quest Technology Award, Philip Yeo Prize, Singapore Young Scientist Award, Singapore Youth Award, A*STAR Investigatorship Award, World Technology Network Fellowship, MIT TR35 Asia Pacific Award, SCSS Susan Lim’s Award and the NRF Investigatorship Award. He serves on the International Committee at the International Society for Stem Cell Research (ISSCR), the Executive Committee of the Stem Cell Society Singapore (SCSS) and the Executive Council for the Singapore Association for the Advancement of Science (SAAS).

https://jonlohstemcells.wordpress.com/

Research

Jonathan Loh's research

Pluripotency and Stemness
Pluripotent stem cells display a remarkable capacity to form differentiated cell types in laboratory cultures. The ability to derive multiple lineages from ESCs opens exciting new opportunities for its use as unlimited source of cells for the treatment of degenerative diseases such as diabetes and Parkinson’s disease. The unique properties of pluripotent cells are controlled by genetic and epigenetic factors. We had sought to identify, characterize and understand the role of transcription regulators and chromatin-modifying enzymes in regulating gene expression programs in pluripotent embryonic stem cells. We have detailed the regulatory relationships between the master regulators of ESCs, Oct4, Sox2 and Nanog (Loh et al. 2006; Chew et al. 2005). This has enhanced our understanding of the transcriptional regulatory network and how they orchestrate early cell fate decisions and establish the transcriptional landscape essential for self-renewal and pluripotency. Furthermore we have uncovered novel transcription factors such as Esrrb and Rif1 which regulate self-renewal, pluripotency and differentiation of ES cells (Figure 1) (Loh et al. 2006).

Figure 1: (A) Transcription circuitry regulating stem cell pluripotency. (B) Knockdown of Esrrb or Rif1 led to differentiation of ES cells. Cells were stained for alkaline phosphatase (pink), which is a characteristic of non-differentiated cells. (Adapted from Boyer et al 2005; Loh et al. 2006; Loh et al. 2011)

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Epigenetic and Cell Identity

We have elucidated the novel link between transcriptional circuitry and epigenetic regulation of ESCs chromatin. We showed that Oct4 controls the expression of genes which encode for histone H3 lysine 9 histone demethylases (Jmjd1a and Jmjd2c) that are important for maintaining the ESCs state through their regulation of the H3K9me status at the promoters of pluripotency genes such as Tcl1  and Nanog (Loh et al. 2007, Loh et al. 2008).

Figure 2: Transcription Network modulation. Transcription factors and epigenetic factors interact to modulate the ESC regulatory network. Several ESC-specific epigenetic factors are regulated by the core ESC transcription factors. For example, Oct4 activates the expression of histone demethylases, Jmjd1a and Jmjd2c, which in turn modify global chromatin H3K9 methylation and regulate the expression of Tcl1 and Nanog (Loh et al. 2007) (Adapted from Ng et al. 2008).

Endogenous Retroviral Elements and Stemness
ESCs repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). We have systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen (Yang et al. 2015). Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6) and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. We uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs using RNA-seq analysis. We also demonstrated direct recruitment of Chaf1a and Sumo2 to ERVs by ChIP-seq analysis. We illustrated a model where Chaf1a reinforced transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrated the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study represent the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs, and illuminates the comprehensive, interconnected and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome.

Figure 3: Work flow for systematic dissection of the cellular factors involved in retroviral repression in embryonic Stem cells by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6) and chromatin modifiers (Trim28/Eset/Atf7ip) are identified as key determinants. Sumo2 orchestrates viral silencing through sumoylation modification of Trim28. Chaf1a regulates provirus and ERVs via its interaction with Eset, Kdm1a and Hdac1/2 (Adapted from Yang et al. 2015).

Cell Fate Reversal and Reprogramming

Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients can be a good model for studying human diseases and for future therapeutic regenerative medicine. Current initiatives to establish human iPSC (hiPSC) banking face challenges in recruiting large numbers of donors with diverse diseased, genetic, and phenotypic representations. We have pioneered novel techniques in establishing iPS cells from blood cells which are more accessible and requiring lesser manipulations (Loh et al. 2009; Loh et al. 2010). More recently, we describe the efficient derivation of transgene-free hiPSCs from a single human finger-prick blood. Finger-prick sample collection can be performed on a “do-it-yourself” basis by donors and sent to the hiPSC facility for reprogramming. We show that single-drop volumes of finger-prick samples are sufficient for performing cellular reprogramming, DNA sequencing, and blood serotyping in parallel. Our novel strategy has the potential to facilitate the development of large-scale hiPSC banking worldwide (Tan et al. 2014).

 


Figure 4:
Integrative strategy for human induced pluripotent stem cells (hiPSC) banking. Illustration of the integrative strategy for hiPSC banking. Using finger-prick (FP) blood reprogramming, hiPSC facilities can recruit a diverse cohort of donors worldwide. hiPSC facility provides a kit containing sterile finger-prick and blood container to the donor. The donors will complete the informed consent form and the health questionnaire and return them back to the facility together with their FP blood. The facility is able to do a series of DNA sequencing, serological assays, as well as hiPSC derivation from a single drop of FP blood sample. Abbreviations: Ag/Ab, antigen/antibody; DIY, do-it-yourself; HLA, human leukocyte antigen; iPSC, induced pluripotent stem cell; GLP, good laboratory practice; GMP, good manufacturing practice; PCR, polymerase chain reaction; seq, sequencing; SNP, single-nucleotide polymorphism. (Adapted from Tan et al. 2014).

Deciphering the Mechanisms of Cell Fate Reprogramming
Incomplete knowledge of the mechanisms at work continues to hamper efforts to maximize reprogramming efficiency. We established a systematic genome-wide RNAi screen to determine the global regulators during the early stages of human reprogramming. Our screen identifies functional repressors and effectors that act to impede or promote the reprogramming process. Repressors and effectors form close interacting networks in pathways, including RNA processing, G protein signaling, protein ubiquitination, and chromatin modification. Combinatorial knockdown of five repressors (SMAD3, ZMYM2, SFRS11, SAE1, and ESET) synergistically resulted in 85% TRA-1-60-positive cells. Removal of the novel splicing factor SFRS11 during reprogramming is accompanied by rapid acquisition of pluripotency specific spliced forms. Mechanistically, SFRS11 regulates exon skipping and mutually exclusive splicing of transcripts in genes involved in cell differentiation, mRNA splicing, and chromatin modification. Our study provides insights into the reprogramming process, which comprises comprehensive and multi-layered transcriptional, splicing, and epigenetic machineries (Toh et al. 2016)

 


Figure 5:
Identification of genome-wide functional regulators of the early stages of human somatic cell reprogramming in a phase-specific RNAi screen. Combinatorial depletion of the top repressors allows reprogramming to proceed unhindered at a near deterministic efficiency. SFRS11, an mRNA splicer, blocks reprogramming partially through the splicing of ZNF207 isoforms. (Adapted from Toh et al. 2016).

Our current research focuses on understanding the molecular mechanisms underpinning the process of cellular reprogramming and cell fate decision. Ongoing projects include: 1) Understanding the function of DNA and Histone modifiers in cell fate changes and 2) Epigenetic Reprogramming/Transdifferentiation using defined factors expression. Ultimately we want to harness these molecular switches to derive high-quality stem cells or differentiated cell types that can potentially be used for therapeutic applications.

Staff

Department: Jonathan Yuin-Han LOH

Name: Tsz Wing SAM

Designation: SINGA Student

Email: samtw@student.imcb.a-star.edu.sg


Name: Nadia Omega CIPTA SUBRATA

Designation: SINGA Student

Email: nadiaoc@student.imcb.a-star.edu.sg


Name: Qiaorui XING

Designation: Research Fellow

Email: xingqr@imcb.a-star.edu.sg


Name: Tushar WARRIER

Designation: Research Fellow

Email: warriert@imcb.a-star.edu.sg


Name: Zihao ZHENG

Designation: Research Officer

Email: zhengzh@imcb.a-star.edu.sg


Name: Pradeep GAUTAM

Designation: SINGA Student

Email: gautamp@student.imcb.a-star.edu.sg


Name: Naresh Waran GNANASEGARAN

Designation: Research Fellow

Email: nareshwg@imcb.a-star.edu.sg


Name: Yao YI

Designation: Collaborator

Email: yaoyi@u.nus.edu


Name: Qiuye BAO

Designation: Senior Research Fellow

Email: baoqy@imcb.a-star.edu.sg


Name: Kiyofumi HAMASHIMA

Designation: Research Fellow

Email: kiyofumi@imcb.a-star.edu.sg


Name: Thanh Huong NGUYEN

Designation: Research Officer

Email: nguyenth1@imcb.a-star.edu.sg


Publications

Recent Publications

Fang HT, EL Farran CA, Xing QR, Zhang LF, Li H, Lim B, Loh YH.
Global H3.3 Dynamic Deposition Defines its Bimodal Role in Cell Fate Transition.
Nat Commun2018 April 18;9:1537.

Cheng H, Ang YKH, Li P, Fang HT, EL Farran C, Liu TM, Kong SL, Chin LZM, Lim KH, Li H, Loh YH*, Lim B.
Direct Reprogramming of Fibroblasts to Multipotent Hematopoietic Progenitors and Molecular Pathways Recruited. 
Nat Commun2016 Nov 21;7:13396.
*As Corresponding author

Khattar E, Kumar P, Liu CY, Akıncılar SC, Raju A, Lakshmanan M, Maury JJ, Qiang Y, Li S, Tan EY, Hui KM, Shi M, Loh YH, Tergaonkar V.
Telomerase reverse transcriptase promotes cancer cell proliferation by augmenting tRNA expression
 J Clin Invest. 2016 Sep 19. pii: 86042. doi: 10.1172/JCI86042. [Epub ahead of print]

Chen HY, Tan HK, Loh YH*.
Derivation of Transgene-Free Induced Pluripotent Stem Cells from a Single Drop of Blood. 
Curr Protoc Stem Cell Biol. 2016 Aug 17;38:4A.9.1-4A.9.10.
*As Corresponding author

Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, Tan DS, Robson P, Loh YH, Quake SR, Burkholder WF.
Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. 
Nat Methods. 2016 Aug 15. doi: 10.1038/nmeth.3961. [Epub ahead of print]

Sivalingam J, Lam AT, Chen HY, Yang BX, Chen AK, Reuveny S, Loh YH, Oh SK.
Superior Red Blood Cell Generation from Human Pluripotent Stem Cells Through a Novel Microcarrier-Based Embryoid Body Platform
Tissue Eng Part C Methods.
 2016 Aug;22(8):765-80. doi: 10.1089/ten.TEC.2015.0579. Epub 2016 Aug 1.

Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ.
LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. 
Cell Stem Cell. 2016 Jul 7;19(1):66-80. Epub 2016 Jun 16.

Toh CX, Chan JW, Chong ZS, Wang HF, Guo HC, Satapathy S, Ma D, Goh GY, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins JJ, Daley GQ, Wee KB, Farran CA, Li H, Lim YP, Bard FA, Loh YH*.
RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. 
Cell Rep. 2016 Jun 21;15(12):2597-607. Epub 2016 Jun 9.
*As Corresponding author

Zhang W, Ni P, Mou C, Zhang Y, Guo H, Zhao T, Loh YH*, Chen L.
Cops2 promotes pluripotency maintenance by Stabilizing Nanog Protein and Repressing Transcription. 
Sci Rep.
 2016 May 26;6:26804.
*As Corresponding author

Seah YF, El Farran CA, Warrier T, Xu J, Loh YH*.
Induced Pluripotency and Gene Editing in Disease Modelling: Perspectives and Challenges. 
Int J Mol Sci. 2015 Dec 2;16(12):28614-34.
*As Corresponding author

Yu S, Ma H, Ow JR, Goh Z, Chiang R, Yang H, Loh YH*, Wu Q.
Zfp553 Is Essential for Maintenance and Acquisition of Pluripotency. 
Stem Cells Dev. 2016 Jan 1;25(1):55-67. Epub 2015 Dec 15.
*As Corresponding author

Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH*.
Systematic identification of factors for provirus silencing in embryonic stem cells.  
Cell. 2015 Sep 24;163(1):230-45. Epub 2015 Sep 10.
*As Corresponding author

Maury JJ, El Farran CA, Ng D, Loh YH, Bi X, Bardor M, Choo AB.
RING1B O-GlcNAcylation regulates gene targeting of polycomb repressive complex 1 in human embryonic stem cells.  
Stem Cell Res. 2015 Jul;15(1):182-9. Epub 2015 Jun 17.

Ma H, Ow JR, Tan BC, Goh Z, Feng B, Loh YH, Fedele M, Li H, Wu Q. The dosage of Patz1 modulates reprogramming process. 
Sci Rep. 2014 Dec 17;4:7519.

Faucon PC, Pardee K, Kumar RM, Li H, Loh YH, Wang X.
Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions.  
PLoS One. 2014 Jul 24;9(7):e102873.

Lu Y, Loh YH*, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA.
Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells.  
Cell Stem Cell. 2014 Jul 3;15(1):92-101. Epub 2014 May 8.
*As Co-first author

Tan HK, Toh CX, Ma D, Yang B, Liu TM, Lu J, Wong CW, Tan TK, Li H, Syn C, Tan EL, Lim B, Lim YP, Cook SA, Loh YH*.
Human finger-prick induced pluripotent stem cells facilitate the development of stem cell banking. 
Stem Cells Transl Med. 2014 May;3(5):586-98. Epub 2014 Mar 19.
*As Corresponding author

Ma H, Ng HM, Teh X, Li H, Lee YH, Chong YM, Loh YH, Collins JJ, Feng B, Yang H, Wu Q.
Zfp322a Regulates mouse ES cell pluripotency and enhances reprogramming efficiency.  
PLoS Genet. 2014 Feb 13;10(2):e1004038.

Wen B, Wu H, Loh YH*, Briem E, Daley GQ, Feinberg AP.
Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions.  
BMC Genomics. 2012 Oct 26;13:566.
*As Co-first author

Bajpai VK, Mistriotis P, Loh YH, Daley GQ, Andreadis ST.
Functional vascular smooth muscle cells derived from human induced pluripotent stem cells via mesenchymal stem cell intermediates.  
Cardiovasc Res. 2012 Dec 1;96(3):391-400. Epub 2012 Aug 31.

Loh YH, Yang JC, De Los Angeles A, Guo C, Cherry A, Rossi DJ, Park IH, Daley GQ.
Excision of a viral reprogramming cassette by delivery of synthetic Cre mRNA. 
Curr Protoc Stem Cell Biol. 2012;Chapter 4:Unit4A.5.

De Los Angeles A, Loh YH, Tesar PJ, Daley GQ.
Accessing naïve human pluripotency. 
Curr Opin Genet Dev. 2012 Jun;22(3):272-82. Epub 2012 Mar 29.

Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ.
Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells.  
Nat Biotechnol. 2011 Nov 27;29(12):1117-9.

Ang WX, Toh CX, Ng HH, Loh YH*.
Reproductive medicine gets a new tool. 
J Mol Cell Biol. 2011 Dec;3(6):320-1. Epub 2011 Nov 24.
*Corresponding author

Brock A, Goh HT, Yang B, Lu Y, Li H, Loh YH.
Cellular reprogramming: a new technology frontier in pharmaceutical research. 
Pharm Res. 2012 Jan;29(1):35-52. Epub 2011 Nov 9.
*As Corresponding author

Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ.
Genomic approaches to deconstruct pluripotency. 
Annu Rev Genomics Hum Genet. 2011;12:165-85.

Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, Ruiz S, Wilbert ML, Yu J, Kirkness EF, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LS, Zhang K.
Somatic coding mutations in human induced pluripotent stem cells. 
Nature. 2011 Mar 3;471(7336):63-7.

Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL.
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. 
Nat Genet. 2010 Dec;42(12):1113-7. Epub 2010 Nov 7.

Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ.
Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. 
Cell Stem Cell. 2010 Nov 5;7(5):618-30. Epub 2010 Sep 30. *Co-second author.

Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ.
Reprogramming of T cells from human peripheral blood.  
Cell Stem Cell
. 2010 Jul 2;7(1):15-9.

Agarwal S, Loh YH, McLoughlin EM, Huang J, Park IH, Miller JD, Huo H, Okuka M, Dos Reis RM, Loewer S, Ng HH, Keefe DL, Goldman FD, Klingelhutz AJ, Liu L, Daley GQ.
Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients. 
Nature. 2010 Mar 11;464(7286):292-6. Epub 2010 Feb 17.

Yuan P, Han J, Guo G, Orlov YL, Huss M, Loh YH, Yaw LP, Robson P, Lim B, Ng HH.
Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. 
Genes Dev. 2009 Nov 1;23(21):2507-20.

Chan EM, Ratanasirintrawoot S, Park IH, Manos PD, Loh YH, Huo H, Miller JD, Hartung O, Rho J, Ince TA, Daley GQ, Schlaeger TM.
Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. 
Nat Biotechnol. 2009 Nov;27(11):1033-7. Epub 2009 Oct 11.

Loh YH, Agarwal S, Park IH, Urbach A, Huo H, Heffner GC, Kim K, Miller JD, Ng K, Daley GQ.
Generation of induced pluripotent stem cells from human blood. 
Blood. 2009 May 28;113(22):5476-9. Epub 2009 Mar 18.

Feng B, Jiang J, Kraus P, Ng JH, Heng JC, Chan YS, Yaw LP, Zhang W, Loh YH, Han J, Vega VB, Cacheux-Rataboul V, Lim B, Lufkin T, Ng HH.
Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. 
Nat Cell Biol. 2009 Feb;11(2):197-203. Epub 2009 Jan 11.

Ng JH, Heng JC, Loh YH*, Ng HH.
Transcriptional and epigenetic regulations of embryonic stem cells. 
Mutat Res. 2008 Dec 1;647(1-2):52-8. doi: 10.1016/j.mrfmmm.2008.08.009. Epub 2008 Aug 20.
*As Corresponding author

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. 
Cell. 2008 Jun 13;133(6):1106-17.

Loh YH*, Ng JH, Ng HH.
Molecular framework underlying pluripotency. 
Cell Cycle. 2008 Apr 1;7(7):885-91. Epub 2008 Jan 22.
*As Corresponding author

Jiang J, Chan YS, Loh YH*, Cai J, Tong GQ, Lim CA, Robson P, Zhong S, Ng HH.
A core Klf circuitry regulates self-renewal of embryonic stem cells. 
Nat Cell Biol. 2008 Mar;10(3):353-60. Epub 2008 Feb 10.
*As Co-second author

Loh YH, Zhang W, Chen X, George J, Ng HH.
Jmjd1a and Jmjd2c histone H3 Lys 9 demethylases regulate self-renewal in embryonic stem cells. 
Genes Dev. 2007 Oct 15;21(20):2545-57.

Lim LS, Loh YH*, Zhang W, Li Y, Chen X, Wang Y, Bakre M, Ng HH, Stanton LW.
Zic3 is required for maintenance of pluripotency in embryonic stem cells. 
Mol Biol Cell. 2007 Apr;18(4):1348-58. Epub 2007 Jan 31.
*Co-first author

Wu Q, Chen X, Zhang J, Loh YH, Low TY, Zhang W, Zhang W, Sze SK, Lim B, Ng HH.
Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. 
J Biol Chem. 2006 Aug 25;281(34):24090-4. Epub 2006 Jul 13.

Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao X.D, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH.
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. 
Nat Genet. 2006 Apr;38(4):431-40. Epub 2006 Mar 5.

Chew JL, Loh YH*, Zhang W, Chen X, Tam WL, Yeap LS, Li P, Ang YS, Lim B, Robson P, Ng HH.
Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells.
Mol Cell Biol. 2005 Jul;25(14):6031-46.* Co-first author

Rodda DJ, Chew JL, Lim LH, Loh YH, Wang B, Ng HH,
Robson P.
Transcriptional regulation of nanog by OCT4 and SOX2. 
J Biol Chem. 2005 Jul 1;280(26):24731-7. Epub 2005 Apr 27