1. Yao D*, Tycko J*,#, Oh JW*, Bounds LR*, Gosai SJ*, Lataniotis L*, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JE, Bassik MC, Reilly SK#. Multicenter integrated analysis of noncoding CRISPRi screens. Nature Methods. 2024 Mar 19. doi: 10.1038/s41592-024-02216-7. (*These authors contributed equally. # Co-corresponding authors.)

  2. Chung C-I, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. Phase separation of YAP-MAML2 differentially regulates the transcriptome. PNAS. 2024 Feb 13;121(7):e2310430121. doi: 10.1073/pnas.2310430121. Epub 2024 Feb 5. PMID: 38315854.

  3. Ren X*, Yang H*, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High throughput PRIME editing screens identify functional DNA variants in the human genome. Molecular Cell. 2023 Dec 21;83(24):4633-4645.e9. doi: 10.1016/j.molcel.2023.11.021. PMID: 38134886; PMCID: PMC10766087. (*These authors contributed equally.)

    		 On the cover: In this issue of Molecular Cell, Ren et al. develop PRIME, a prime-editing-mediated high-throughput genetic screen method for single-base resolution analysis of genomic sequences. Using PRIME, the authors identify essential nucleotides for enhancer activity and disease-associated functional genetic variants. The plum blossoms in a snowy winter indicate the positive hits (functional variants) identified by PRIME, while bare trees indicate genomic regions without any sequences that are considered as positive hits. The multiple plum blossoms in different positions align with PRIME's ability to simultaneously identify functional sequences across the genome.

  4. Yang X*, Jones IR*, Chen PB*, Yang H*, Ren X*, Zheng L, Li B, Li YE, Sun Q, Wen J, Beaman C, Cui X, Li Y, Wang W, Hu M, Ren B#, Shen Y#. Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons. bioRxiv. 2023 Aug 30. doi: 10.1101/2023.08.30.555359. (*These authors contributed equally. # Co-corresponding authors.)

  5. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y#, Shen Y#. Functional characterization of Alzheimer’s disease genetic variants in microglia. Nature Genetics. 2023 Oct;55(10):1735-1744. doi: 10.1038/s41588-023-01506-8. Epub 2023 Sep 21. PMID: 37735198. (# Co-corresponding authors.)

  6. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. PMID: 37419111.

  7. Ren X, Takagi MA, Shen Y. Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR. STAR Protoc. 2023 Feb 1;4(1):102084. doi: 10.1016/j.xpro.2023.102084. Epub ahead of print. PMID: 36853689; PMCID: PMC9918420.

  8. Sun W*, Wang N*, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L. Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem. 2023 Jan;15(1):21-32. doi: 10.1038/s41557-022-01038-4. Epub 2022 Oct 6. PMID: 36202986; PMCID: PMC9840682. (*These authors contributed equally.)

  9. Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom. 2022 Nov 9;2(11):100177. doi: 10.1016/j.xgen.2022.100177. Epub 2022 Sep 14. PMID: 36381608; PMCID: PMC9648144.

  10. Jones IR, Ren X, Shen Y. High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Human Molecular Genetics. 2022, Aug 16; 31(1):47-53. doi: 10.1093/hmg/ddac193 PMID: 35972825 PMCID: PMC9585669 

  11. Ravichandran M, Hu J, Cai C, Ward NP, Venida A, Foakes C, Kuljanin M, Yang A, Hennessey CJ, Yang Y, Desousa BR, Rademaker G, Staes AAL, Cakir Z, Jain IH, Aguirre AJ, Mancias JD, Shen Y, DeNicola GM, Perera RM. Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer. Cancer Discov. 2022, Jun 30. 12(9):2198-2219 doi: 10.1158/2159-8290.CD-22-0044 PMID: 35771494.

  12. Yang H, Ting X, Geng YH, Xie Y, Nierenberg JL, Huo YF, Zhou YT, Huang Y, Yu YQ, Yu XY, Li ZF, Ziv E, Zhang H,Fang WG, Shen Y, Tian XX. The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression. Sci Adv 2022, June 10. 8(23):eabn3509. doi: 10.1126/sciadv.abn3509 PMID: 35687692 PMCID: PMC9187238

  13. Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. PNAS, 2021 Dec 21;118(51):e2024795118. doi: 10.1073/pnas.2024795118. PMID: 34921112 PMCID: PMC8713794

  14. Li YE*, Preissl S*, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. An atlas of gene regulatory elements in adult mouse cerebrum. Nature, 2021 Oct;598(7879):129-136. doi: 10.1038/s41586-021-03604-1. Epub 2021 Oct 6. PMID: 34616068 PMCID: PMC8494637 (*These authors contributed equally.)

  15. Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W, Shen Y. Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Sci Adv, 2021 Sep 17;7(38):eabi4360. doi: 10.1126/sciadv.abi4360. Epub 2021 Sep 15. PMID: 34524848 PMCID: PMC8443183 

  16. Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA; University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL, Petit F, Ahituv N. Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nat Commun, 2021 Apr 16;12(1):2282. doi: 10.1038/s41467-021-22470-z. PMID: 33863876 PMCID: PMC805232 

  17. Wang X*, Jiang W*, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK. The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex. Mol Brain, 2021 Mar 16;14(1):54. doi: 10.1186/s13041-021-00767-w. PMID: 33726789 PMCID: PMC7962252 (*These authors contributed equally.)

  18. Song M*, Pebworth MP*, Yang X*, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Bingkun L, Maliskova L, Liu W, Pollen AA, Li Y, Wang T, Hu M*,#, Kriegstein AR#, Shen Y#. Cell-type-specific 3D epigenomes in the developing human cortex. Nature, 2020 Nov;587(7835):644-649. doi: 10.1038/s41586-020-2825-4. Epub 2020 Oct 14. PMID: 33057195 PMCID: PMC7704572 (*These authors contributed equally. # Co-corresponding authors.)

  19. ENCODE Project Consortium*; Moore JE, Purcaro MJ*, Pratt HE*, Epstein CB*, Shoresh N*, Adrian J*, Kawli T*, Davis CA*, Dobin A*, Kaul R*, Halow J*, Van Nostrand EL*, Freese P*, Gorkin DU*, Shen Y*, He Y*, Mackiewicz M*, Pauli-Behn F*, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. PMID: 32728249 PMCID: PMC9095460 (*These authors contributed equally.)

  20. Gorkin D*, Barozzi I*, Zhao Y*, Zhang Y*, Huang H*, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzerv-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 Jul;583(7818):744-751. doi: 10.1038/s41586-020-2093-3. Epub 2020 Jul 29. PMID: 32728240 PMCID: PMC7398618 (*These authors contributed equally.)

  21. Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y. SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. PLoS One. 2020 Apr 29;15(4):e0228760. doi: 10.1371/journal.pone.0228760. eCollection 2020. PMID: 32348304 PMCID: PMC7190163 

  22. Huh R, Yang Y, Jiang Y, Shen Y, Li Y.  SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Research, 2020 Jan 10;48(1):86-95. doi: 10.1093/nar/gkz959. PMID: 31777938 PMCID: PMC6943136 

  23. Song M, Yang X, Ren X, Maliskova L, Li B, Jones I, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon J, Judge LM, Conklin BR, Song H, Gan L, Shen Y. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nature Genetics, 2019 Aug;51(8):1252-1262. doi: 10.1038/s41588-019-0472-1. Epub 2019 Jul 31. PMID: 31367015 PMCID: PMC6677164

  24. Alexander J, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD.  Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLIFE, 2019 May 24:8:e41769. doi: 10.7554/eLife.41769. PMID: 31124784 PMCID: PMC6534382

  25. Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho S, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L. Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. PLos Biol, 2019 Feb 8;17(2):e3000134. doi: 10.1371/journal.pbio.3000134. eCollection 2019 Feb. PMID: 30735499 PMCID: PMC6383943

  26. Li Y, Hu M, Shen Y.  Gene regulation in the 3D genome. Human Molecular Genetics, 2018 Aug 1;27(R2):R228-R233. doi: 10.1093/hmg/ddy164. PMID: 29767704; PMCID: PMC6061806.

  27. Emmerson E, May A, Nathan S, Pacheco NC, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM. SOX2 regulates acinar cell development in the salivary gland. eLIFE, 2017 Jun 17:6:e26620. doi: 10.7554/eLife.26620. PMID: 28623666 PMCID: PMC5498133

  28. Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan K, Ren B.  A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Method, 2017 Jun;14(6):629-635. doi: 10.1038/nmeth.4264. Epub 2017 Apr 17. PMID: 28417999; PMCID: PMC5490986.

  29. He Y, Gorkin D, Dickel D, Nery J, Castanon R, Lee AY, Shen Y, Visel A, Pennacchio L, Ren B, Ecker J.  Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PNAS, 2017 Feb 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114. Epub 2017 Feb 13. PMID: 28193886 PMCID: PMC5338528

  30. Diao Y*, Li B, Young I, Lee AY, Meng Z, Maliskova L, Guan K, Shen Y*,#, Ren B#. A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening. Genome Research, 2016 Mar;26(3):397-405. doi: 10.1101/gr.197152.115. Epub 2016 Jan 26. PMID: 26813977; PMCID: PMC4772021. (*These authors contributed equally. # Co-corresponding authors.)

  31. Dixon JR*, Jung I*, Selvaraj S*, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19;518(7539):331-6. doi: 10.1038/nature14222. PMID: 25693564; PMCID: PMC4515363.

  32. Yue F*, Cheng Y*, Breschi A*, Vierstra J*, Wu W*, Ryba T*, Sandstrom R*, Ma Z*, Davis C*, Pope BD*, Shen Y*, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA#, Snyder MP#, Guigo R#, Gingeras TR#, Gilbert DM#, Hardison RC#, Beer MA*,#, Ren B#; Mouse ENCODE Consortium. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. PMID: 25409824; PMCID: PMC4266106. (*These authors contributed equally. # Co-corresponding authors.)

  33. Huang K*, Shen Y*, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G.  A panel of CpG methylation patterns distinguishes human embryonic stem cells and induced pluripotent stem cells. Stem Cell Reports. 2013 Dec 26;2(1):36-43. doi: 10.1016/j.stemcr.2013.11.003. PMID: 24511466; PMCID: PMC3916755. (*These authors contributed equally.)

  34. Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics. 2013 Oct;45(10):1198-206. doi: 10.1038/ng.2746. Epub 2013 Sep 1. PMID: 23995138; PMCID: PMC4095776.

  35. Mouse ENCODE Consortium; Stamatoyannopoulos JA#, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418. PMID: 22889292; PMCID: PMC3491367. (# The corresponding author.)

  36. Shen Y*, Yue F*, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B.  A map of cis-regulatory sequences in the mouse genome. Nature. 2012 Aug 2;488(7409):116-20. doi: 10.1038/nature11243. PMID: 22763441; PMCID: PMC4041622. (*These authors contributed equally.)

  37. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.  Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082. PMID: 22495300; PMCID: PMC3356448.

  38. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012 Jun 8;149(6):1368-80. doi: 10.1016/j.cell.2012.04.027. Epub 2012 May 17. PMID: 22608086; PMCID: PMC3589129.. 

  39. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS#, Reiter JF#.  Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012;8(3):e1002576. doi: 10.1371/journal.pgen.1002576. Epub 2012 Mar 15. PMID: 22438827; PMCID: PMC3305387. (# Co-corresponding authors.)

  40. Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. Functional Modules Distinguish Human Induced Pluripotent Stem Cells from Embryonic Stem Cells. Stem Cells Dev. 2011 Nov;20(11):1937-50. doi: 10.1089/scd.2010.0574. Epub 2011 Jun 20. PMID: 21542696; PMCID: PMC3202894.

  41. Shen Y, Fouse SD, and Fan G. Genome-wide DNA methylation profiling: the mDIP- Chip technology. Methods Mol Biol. 2009;568:203-16. doi: 10.1007/978-1-59745-280-9_13. PMID: 19582429.

  42. Shen Y, Matsuno Y, Fouse S, Rao N, Root S, Xu RH, Pellegrini M, Riggs A, and Fan G. X-inactivation in female human embryonic stem cells is in a non-random pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4709-14. doi: 10.1073/pnas.0712018105. Epub 2008 Mar 13. PMID: 18339804; PMCID: PMC2290804.

  43. Fouse S, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, and Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, Polycomb binding and histone H3 lys4/lys27 trimethylation. Cell Stem Cell. 2008 Feb 7;2(2):160-9. doi: 10.1016/j.stem.2007.12.011. PMID: 18371437; PMCID: PMC3070208.

  44. Shen Y, Chow J, Wang Z, Fan G. Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells. Human Molecular Genetics. 2006 Sep 1;15(17):2623-35. doi: 10.1093/hmg/ddl188. Epub 2006 Jul 26. PMID: 16870691.

  45. Fan G#, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve J, Shuai K, Sun YE#. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development. 2005 Aug;132(15):3345-56. doi: 10.1242/dev.01912. PMID: 16014513. (# Co-corresponding authors.)