A large set of proteins has been identified that binds to pre-mRNA.These proteins have been named hnRNP proteins (hnRNA is a historic name for RNA in the cell nucleus, much of which is pre-mRNA). Several different hnRNP-proteins bind to the same pre-mRNA immediately as the RNA is transcribed and an RNA-protein complex is formed.

Many of the hnRNP proteins share the same type of RNA binding domain. This concensus RNA binding domain can also be found in many other proteins that interact with mRNA, or other kinds of RNA. There are also other types of RNA binding domains found in other hnRNP proteins.

The hnRNP proteins presumably have several different functions, but these are not well known yet. It has been assumed that hnRNP proteins help package the pre-mRNA into functional complexes. For example, hnRNP proteins may be involved in presenting the pre-mRNA to the splicing machinery. It is known that hnRNP A1 protein can influence the choice of splice sites in pre-mRNA. Three hnRNP-proteins have been shown to be involved in the transport of mRNA to the cytoplasm. The hnRNP C protein contains a retention sequence that appears to prevent mRNA from being transported out of the nucleus and hnRNP A1 and hnRNP K each contain an export signal as part of their amino acid chain.

It is further possible that hnRNP proteins play a role also in the cytoplasm. The hnRNP A1 protein has been shown to accompany the mRNA into the cytoplasm and is present during translation.