Cited by 51Pluripotent Stem Cells ResearchEpigenetics and DNA MethylationGenomics and Chromatin Dynamics

TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network

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Seruggia, Davide, Oti, Martin, Tripathi, Pratibha, Canver, Matthew C., LeBlanc, Lucy, Di Giammartino, Dafne C., Bullen, Michael J., Nefzger, Christian M. +8 more·2019·Molecular Cell

Abstract

Self-renewal and pluripotency of the embryonic stem cell (ESC) state are established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. While much has been learned regarding transcription factors, the function of epigenetic regulators in these networks is less well defined. We conducted a CRISPR-Cas9-mediated loss-of-function genetic screen that identified two epigenetic regulators, TAF5L and TAF6L, components or co-activators of the GNAT-HAT complexes for the mouse ESC (mESC) state. Detailed molecular studies demonstrate that TAF5L/TAF6L transcriptionally activate c-Myc and Oct4 and their corresponding MYC and CORE regulatory networks. Besides, TAF5L/TAF6L predominantly regulate their target genes through H3K9ac deposition and c-MYC recruitment that eventually activate the MYC regulatory network for self-renewal of mESCs. Thus, our findings uncover a role of TAF5L/TAF6L in directing the MYC regulatory network that orchestrates gene expression programs to control self-renewal for the maintenance of mESC state.

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Research works printed but not linked: 64

  1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25, 25– 29. 10802651 PMC3037419
  2. Bilodeau S, Kagey MH, Frampton GM, Rahl PB, and Young RA (2009). SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 23, 2484– 2489. 19884255 PMC2779743
  3. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, (2006). Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349– 353. 16625203
  4. Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, (2017). Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nature Publishing Group 49, 625– 634. PMC5374001 28218758
  5. Cao Y, Guo WT, Tian S, He X, Wang XW, Liu X, Gu KL, Ma X, Huang D, Hu L, (2015). miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency. The EMBO Journal 34, 609– 623. 25603933 PMC4365031
  6. Carrozza MJ, Utley RT, Workman JL, and Côté J (2003). The diverse functions of histone acetyltransferase complexes. Trends in Genetics 19, 321– 329. 12801725
  7. Cartwright P (2005). LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development 132, 885– 896. 15673569
  8. Chappell J, and Dalton S (2013). Roles for MYC in the Establishment and Maintenance of Pluripotency. Cold Spring Harbor Perspectives in Medicine 3, a014381– a014381. 24296349 PMC3839598
  9. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, (2008). Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells. Cell 133, 1106– 1117. 18555785
  10. Cooper S, and Brockdorff N (2013). Genome-wide shRNA screening to identify factors mediating Gata6 repression in mouse embryonic stem cells. Development 140, 4110– 4115. 24046324 PMC3775421
  11. Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, (2015). PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. CellReports 1– 57. PMC5384103 26299972
  12. Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O’Brien K, Atsma JM, Fujiwara Y, Nguyen M, (2014). Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cell Identity. Molecular Cell 53, 32– 48. 24361252 PMC3919500
  13. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, and Lempicki RA (2003). DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4, P3. 12734009
  14. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, and Gingeras TR (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15– 21. 23104886 PMC3530905
  15. Eilers M, and Eisenman RN (2008). Myc’s broad reach. Genes Dev 22, 2755– 2766. 18923074 PMC2751281
  16. Fagnocchi L, and Zippo A (2017). Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells. Front. Cell Dev. Biol 5, 981– 19. PMC5289991 28217689
  17. Fagnocchi L, Cherubini A, Hatsuda H, Fasciani A, Mazzoleni S, Poli V, Berno V, Rossi RL, Reinbold R, Endele M, (2016). A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity. Nat Commun 7, 11903. 27301576 PMC4912626
  18. Fazzio TG, Huff JT, and Panning B (2008a). An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity. Cell 134, 162– 174. 18614019 PMC4308735
  19. Fazzio TG, Huff JT, and Panning B (2008b). An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity. Cell 134, 162– 174. 18614019 PMC4308735
  20. Gu W, Gaeta X, Sahakyan A, Chan AB, Hong CS, Kim R, Braas D, Plath K, Lowry WE, and Christofk HR (2016). Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State. Cell Stem Cell 19, 476– 490. 27618217 PMC5055460
  21. Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, (2015). Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev 29, 803– 816. 25877919 PMC4403257
  22. Hsu PD, Lander ES, and Zhang F (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 157, 1262– 1278. 24906146 PMC4343198
  23. Hu G, Kim J, Xu Q, Leng Y, Orkin SH, and Elledge SJ (2009). A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 23, 837– 848. 19339689 PMC2666338
  24. Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12, 115– 121. 25633503 PMC4509590
  25. Jackson AL, and Linsley PS (2010). Recognizing and avoiding siRNA off- target effects for target identification and therapeutic application 1– 11. 20043028
  26. Kent WJ, Zweig AS, Barber G, Hinrichs AS, and Karolchik D (2010). BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204– 2207. 20639541 PMC2922891
  27. Kim J, Cantor AB, Orkin SH, and Wang J (2009). Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells. Nat Protoc 4, 506– 517. 19325547
  28. Kim J, Chu J, Shen X, Wang J, and Orkin SH (2008). An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells. Cell 132, 1049– 1061. 18358816 PMC3837340
  29. Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, and Orkin SH (2010). A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs. Cell 143, 313– 324. 20946988 PMC3018841
  30. Langmead B, and Salzberg SL (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357– 359. 22388286 PMC3322381
  31. Lee KK, and Workman JL (2007). Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8, 284– 295. 17380162
  32. Love MI, Huber W, and Anders S (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550. 25516281 PMC4302049
  33. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, (2012). An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13, 418. 22889292 PMC3491367
  34. Mudge JM, and Harrow J (2015). Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26, 366– 378. 26187010 PMC4602055
  35. Orkin SH, and Hochedlinger K (2011). Chromatin Connections to Pluripotency and Cellular Reprogramming. Cell 145, 835– 850. 21663790 PMC4858411
  36. Papp B, and Plath K (2013). Epigenetics of Reprogramming to Induced Pluripotency. Cell 152, 1324– 1343. 23498940 PMC3602907
  37. Patro R, Duggal G, Love MI, Irizarry RA, and Kingsford C (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods 14, 417– 419. 28263959 PMC5600148
  38. Quinlan AR, and Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841– 842. 20110278 PMC2832824
  39. Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, and Young RA (2010). c-Myc Regulates Transcriptional Pause Release. Cell 141, 432– 445. 20434984 PMC2864022
  40. Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, and Manke T (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44, W160– W165. 27079975 PMC4987876
  41. Robinton DA, and Daley GQ (2012). The promise of induced pluripotent stem cells in research and therapy. Nature 481, 295– 305. 22258608 PMC3652331
  42. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, (2012). Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389– 393. 22217937 PMC3272464
  43. Sanjana NE, Shalem O, and Zhang F (2014). Improved vectors and genome-wide libraries for CRISPR screening. Nature Methods 11, 783– 784. 25075903 PMC4486245
  44. Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, (2016). Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell 164, 668– 680. 26871632 PMC4752822
  45. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84– 87. 24336571 PMC4089965
  46. Shyh-Chang N, Daley GQ, and Cantley LC (2013). Stem cell metabolism in tissue development and aging. Development 140, 2535– 2547. 23715547 PMC3666381
  47. Singh AM, and Dalton S (2009). The Cell Cycle and Myc Intersect with Mechanisms that Regulate Pluripotency and Reprogramming. Stem Cell 5, 141– 149. PMC2909475 19664987
  48. Smith KN, Singh AM, and Dalton S (2010). Myc Represses Primitive Endoderm Differentiation in Pluripotent Stem Cells. Stem Cell 7, 343– 354. PMC2954754 20804970
  49. Stadtfeld M, Maherali N, Borkent M, and Hochedlinger K (2009). A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nature Methods 7, 53– 55. 20010832 PMC3987893
  50. Sun YBY, Qu X, Howard V, Dai L, Jiang X, Ren Y, Fu P, Puelles VG, Nikolic-Paterson DJ, Caruana G, (2015). Smad3 deficiency protects mice from obesity-induced podocyte injury that precedes insulin resistance. Kidney Int 88, 286– 298. 25945408
  51. Takahashi K, and Yamanaka S (2006). Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell 126, 663– 676. 16904174
  52. Thomson JA (1998). Embryonic Stem Cell Lines Derived from Human Blastocysts. Science 282, 1145– 1147. 9804556
  53. Vander Heiden MG, Cantley LC, and Thompson CB (2009). Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. Science 324, 1029– 1033. 19460998 PMC2849637
  54. Varlakhanova NV, Cotterman RF, deVries WN, Morgan J, Donahue LR, Murray S, Knowles BB, and Knoepfler PS (2010). myc maintains embryonic stem cell pluripotency and self-renewal. Differentiation 80, 9– 19. 20537458 PMC2916696
  55. Varlakhanova N, Cotterman R, Bradnam K, Korf I, and Knoepfler PS (2011). Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics Chromatin 4, 20. 22053792 PMC3226433
  56. Wang T, Wei JJ, Sabatini DM, and Lander ES (2014). Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80– 84. 24336569 PMC3972032
  57. Whyte WA, Bilodeau S, Orlando DA, Hoke HA, Frampton GM, Foster CT, Cowley SM, and Young RA (2012). Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482, 221– 225. 22297846 PMC4144424
  58. Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, and Young RA (2013). Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes. Cell 153, 307– 319. 23582322 PMC3653129
  59. Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, and Chang HY (2008). Module Map of Stem Cell Genes Guides Creation of Epithelial Cancer Stem Cells. Cell Stem Cell 2, 333– 344. 18397753 PMC2628721
  60. Young RA (2011). Control of the Embryonic Stem Cell State. Cell 144, 940– 954. 21414485 PMC3099475
  61. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137. 18798982 PMC2592715
  62. Zhou VW, Goren A, and Bernstein BE (2010). Charting histone modifications and the functional organization of mammalian genomes. Nature Publishing Group 12, 7– 18. 21116306
  63. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, and Wei W (2014). High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487– 491. 24717434
  64. Zwaka TP, and Thomson JA (2005). Differentiation of human embryonic stem cells occurs through symmetric cell division. Stem Cells 23, 146– 149. 15671139

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Authors
Seruggia, D., Oti, M., Tripathi, P., Canver, M. C., LeBlanc, L., Di Giammartino, D. C., Bullen, M. J., Nefzger, C. M., Sun, Y. B. Y., Farouni, R., Polo, J. M., Pinello, L., Apostolou, E., Kim, J., Orkin, S. H., & Das, P. P.
Affiliations
  • Boston Children's Hospital (US)
  • Monash University (AU)
  • The University of Texas at Austin (US)
  • Australian Regenerative Medicine Institute (AU)
  • Harvard University (US)
  • Weill Cornell Medicine (US)
Corresponding author
  • Orkin, Stuart H.
  • Das, Partha Pratim
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2019-06
Volume
74
Issue
6
Pages
1148-1163.e7
ISSN
1097-2765 (ISSN-L)
OpenAlex
W2936193003
Cited by
51
References
4
Citations by year
2026: 6 · 2025: 5 · 2024: 9 · 2023: 4 · 2022: 4 · 2021: 10 · 2020: 11 · 2019: 2
FWCI
2.23
Type
journal article
Language
en
Open access
Locations
  • Molecular Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
Funders
  • NIH (HLBI U01HL100001, R01GM112722, DP2DA043813)
  • National Health and Medical Research Council (GNT1159461)
  • National Institute of Diabetes and Digestive and Kidney Diseases (F30-DK103359)
  • National Human Genome Research Institute (R00HG008399)
  • Sylvia and Charles Viertel
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
embryonic stem cell self-renewal, epigenetic regulators, c-Myc, Oct4, H3K9 acetylation, transcriptional activation, pluripotency, mouse embryonic stem cells, CRISPR-Cas9 loss-of-function screen
MeSH terms
Gene Editing, Animals, Cell Cycle, Embryo, Mammalian, Fibroblasts, Gene Expression Regulation, Histones, Humans, Signal Transduction, Proto-Oncogene Proteins c-myc, Protein Isoforms, TATA-Binding Protein Associated Factors, Epigenesis, Genetic, Cell Proliferation, Mice, Gene Regulatory Networks, Embryonic Stem Cells, Induced Pluripotent Stem Cells, HEK293 Cells, Primary Cell Culture, CRISPR-Cas Systems, Cellular Reprogramming

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