Cofactor Gene Symbol Functions in ESCs Reference
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]
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]
CCR4-NOT complex Cnot1 Prevents ESC differentiation, repression of trophectodermal genes  [84]
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.