Cofactor Gene Symbol Functions in ESCs Reference Coactivators FACT complex SPT16 Oct4-associated protein [11,17] Recruitment of TBP and TFIIB of transcription pre-initiation complex [50]   SSRP1 Oct4-associated protein, and also c-Myc binding partner [11,17,56] Yes-YAP-Tead pathway YAP Maintains ES identity,as OE inhibited ESC differentiation [39] Activates pluripotency genes [41] DNA repair proteins MSH2/MSH6 Oct4-associated proteins [11,12,17] Acts as a "sliding clamp" that disassembles histone [45] XPC-RAD23B-CETN2 Located at Oct4 and Nanog promoters [47] Required for ESC identity and somatic cell reprogramming [47] Regulates of histone modification to mediate transcription [48] Mediators Med6 Required for Oct4 maintenance [109] Med7 Med10 Med14 Med17 Med24 Med27 Med28 Med30 Med12 Required for Oct4 maintenance [109] Nanog-associated protein, regulates Nanog and Nanog target genes [114] Med15 Required for Oct4 and Nanog expression in hESCs [109,116] Med21 Required for Oct4 maintenance [109] Required for ESC survival [113] CDK8 Regulates Myc and Myc target genes [123] MECO Regulates transcription of ncRNA genes [125] Cohesin and associated proteins Smc1a Oct4-associated protein, [12] Required to maintain ESC identity and viability [133,137] Smc3 Required to maintain ESC identity [133] Stag2 Nanog-associated protein [133] Rad21 Required to maintain ESC identity [133]   Regulates Nanog and Nanog target genes [16] Nibpl Required for Oct4 maintenance [109] Wapl Nanog-associated protein [16,133] Condensin Smc2 Required for ESC survival [34] Smc4 Involved in interphase high-order chromatin organization [137] Histone acetyltrans-ferases (HATs) P300/CBP complex Component of ESC transcription factor network and modulates Nanog expression [9,21] Cooperates with CHD7 [29] Involved in ES cell differentiation [22,28] Tip60-p400 Oct4-associated protein [12]     Cooperates with Nanog or H3K4me3 [34] Corepressors CCR4-NOT complex Cnot1 Prevents ESC differentiation, repression of trophectodermal genes  [84] Cnot2 Cnot3 Essential for ESC pluripotency for inducing c-Myc and Zfx, independently of Oct4/Nanog/Sox2 [83,84] Repression of trophectodermal genes [84] KRAB-ZFP-Trim28  Trim28 Interacts with Nanog and Oct4, essential for ES pluripotency [16,34,83,92] Chromatin de-condensation by recruitment of chromatin remodelling complexes [92] Co-repressor to ZFP57 for maintenance of genomic imprinting, possibly by recruiting DNA methyltransferases and HP1 family [97-99] Co-repressor to ZFP809, and other un-identified transcription factors, for repressing retrovirus expression [102-106] Histone deacetyla-ses (HDACs) Sin3a Essential for proliferation, viability and genomic integrity of ESCs [34,68] Interact with Sox2 and Nanog, and positively regulates Nanog [15,69] NuRD complex Essential for derivation of ESCs [73] Represses lineage genes to maintain the full pluripotency of ES cells [15,73,75] Forms a repressive ESC-specific NODE complex together with Oct4 and Nanog [15] Interacts with other chromatin modifiers to mediate gene regulation [76-78] Implicated in Sall4-mediated transcription repression [81]

Table 1: Known functions of cofactors in ES cells.