PSIP1 (also known as LEDGF) conjointly binds to KMT2A (also known as MLL1 or MLL) and MEN1 (menin) (Yokoyama and Cleary 2008; Huang et al. 2012). The LEDGF-binding motif (LBM) in the N-terminus of KMT2A is missing in KMT2B (Huang et al. 2012), but the interaction of PSIP1 with MEN1-bound MLL2 complexes has been reported (van Nuland et al. 2013). Based on quantitative studies in HeLa cells, all PSIP1-containing MLL1/MLL2 complexes contain MEN1, but only about 25% of MEN1-containing MLL1/MLL2 complexes contain PSIP1 (van Nuland et al. 2013). HCFC2 has been found to be co-immunoprecipitated with PSIP1, so it is possible that a portion of MLL1 complexes with MEN1 and PSIP1 also include HCFC1 or HCFC2 (van Nuland et al. 2013).

PSIP1 (also known as LEDGF) is co-immunoprecipitated with MEN1-bound MLL2 complexes (van Nuland et al. 2013). Although the LEDGF binding motif (LBM) that is present in KMT2A is missing in KMT2B (Huang et al. 2012), PSIP1 can directly interact with MEN1 (Huang et al. 2012). Based on quantitative studies in HeLa cells, all PSIP1-containing MLL1/MLL2 complexes contain MEN1, but only about 25% of MEN1-containing MLL1/MLL2 complexes contain PSIP1 (van Nuland et al. 2013). PSIP1 appears to be more prevalent in MLL2:MEN1 complexes than in MLL1:MEN1 complexes (van Nuland et al. 2013). HCFC2 has been found to be co-immunoprecipitated with PSIP1, so it is possible that a portion of MLL2 complexes with MEN1 and PSIP1 also include HCFC1 or HCFC2 (van Nuland et al. 2013).

The DNA in the Pre-initiation complex is considerably compacted relative to its length when fully extended, probably due to binding of proteins in addition to the viral integrase. These proteins are not fully clarified, due to the difficulty of biochemical analysis of small amounts of material, but candidates include the viral NC and MA proteins, and the cellular HMGA, BAF, and PSIP1/LEDGF/p75 proteins. Purified integrase is capable of carrying out the terminal cleavage and initial strand transfer reactions.

How the PIC finds favored sites on target DNA has not been fully clarified. Active genes are favored for integration, and favored sequences at the site of integration also influence the reaction. Studies of cells depeleted in PSIP1/LEDGF/p75 suggest that this protein acts as a tethering factor binding HIV PICs near integration target DNA. Access of PICs to sites on chromosomes may be significant, since centromeric alphoid repeats are disfavored for integration, perhaps due to wrapping in compact centromeric heterochromatin. Nucleosomes bound to the integration template also affect target site selection and integration complex binding.

Concomitant with the completion of reverse transcription, the pre-integration complex is formed by shedding of some viral proteins from the viral core, and binding of cellular proteins, thereby yielding complexes capable of integration. The terminal cleavage reaction takes place in the cytoplasm, where two nucleotides are removed from each viral DNA 3' end. This serves to remove heterogeneous extra bases from the viral DNA ends occasionally added by reverse transcription, thereby yielding a homogeneous substrate for downstream steps, and also serves to stablilize the PIC. The DNA in PICs is considerably compacted relative to its length when fully extended, probably due to binding of proteins in addition to the viral integrase. These proteins are not fully clarified, due to the difficulty of biochemical analysis of small amounts of material, but candidates include the viral NC and MA proteins, and the cellular HMGA, BAF, and PSIP1/LEDGF/p75 proteins. Purified integrase is capable of carrying out the terminal cleavage and initial strand transfer reactions.

Following nuclear entry, the viral preintegration complex (PIC) must select a site for integration in a host cell chromosome, and then carry out the chemical steps of the reaction.

At the chromosomal level, HIV has been found to favor active transcription units for integration. Subsequent studies established that the cellular PSIP1/LEDGF/p75 protein is important in this reaction. PSIP1/LEDGF/p75 binds tightly to HIV integrase, and also to chromatin. Knocking down PSIP1/LEDGF/p75 in cells resulted in several perturbations of integration targeting in vivo, including reduced integration in transcription units. Thus PSIP1/LEDGF/p75 has been hypothesized to act as a tethering factor that dictates at least in part the placement of HIV integration sites.

The integration target DNA is also expected to be coated with nucleosomes. Tests of integration into mononucleosomes in vitro have shown that wrapping integration target DNA actually boosts integration activity. Kinked positions on the DNA gyre are particularly favored for integration.

Integration does not take place at a unique sequence in the integration target DNA (i.e. it is not like a restriction enzyme). However, favored and disfavored primary sequences can be detected when many integration sites are aligned. Synthesis and testing of favored HIV integration sites showed that they were favored for integration by PICs in vitro.

After a target DNA is bound, the integration reactions take place via a single-step transesterification.

Integration of both ends of the viral DNA, followed by melting of the target DNA segments between the points of joining, yields single stranded gaps at each host-virus DNA junction, and a two base overhang derived from the viral DNA. The manner by which this intermediate is subsequently repaired to yield the fully integrated provirus is unclear. For many parasitic DNA replication reactions, the parasite carries out reaction steps only up to a point that the host cannot easily reverse, forcing the host to complete the job (Bushman 2001; Craig et al. 2002). For retroviral integration, it is reasonable to infer that host DNA repair enzymes complete provirus formation. DNA gap repair enzymes are known to be involved in a variety of DNA repair pathways, so their recruitment to gaps at host-virus DNA junctions is readily envisioned. Consistent with this, known gap repair enzymes have been shown to act on model host-virus DNA junctions in vitro (Yoder and Bushman, 2000).

Transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis