Newly spliced mRNAs in mammalian cells are characterized by a complex of proteins at exon–exon junctions. This complex recruits Upf3 and Upf2, which function in nonsense‐mediated mRNA decay (NMD). Both Upf proteins are detected on mRNA bound by the major nuclear cap‐binding proteins CBP80/CBP20 but not mRNA bound by the major cytoplasmic cap‐binding protein eIF4E. These and other data indicate that NMD targets CBP80‐bound mRNA during a ‘pioneer’ round of translation, but whether nuclear eIF4E also binds nascent but dead‐end transcripts is unclear. Here we provide evidence that nuclear CBP80 but not nuclear eIF4E is readily detected in association with intron‐containing RNA and the C‐terminal domain of RNA polymerase II. Consistent with this evidence, we demonstrate that RNPS1, Y14, SRm160, REF/Aly, TAP, Upf3X and Upf2 are detected in the nuclear fraction on CBP80‐bound but not eIF4E‐bound mRNA. Each of these proteins is also detected on CBP80‐bound mRNA in the cytoplasmic fraction, indicating a presence on mRNA after export. The dynamics of mRNP composition before and after mRNA export are discussed.

Initiation of transcription of protein‐encoding genes by RNA polymerase II (Pol II) was thought to require transcription factor TFIID, a complex comprised of the TATA box‐binding protein (TBP) and TBP‐associated factors (TAF_IIs). In the presence of TBP‐free TAF_II complex (TFTC), initiation of Pol II transcription can occur in the absence of TFIID. TFTC containing the GCN5 acetyltransferase acetylates histone H3 in a nucleosomal context. We have identified a 130 kDa subunit of TFTC (SAP130) that shares homology with the large subunit of UV‐damaged DNA‐binding factor. TFTC preferentially binds UV‐irradiated DNA, UV‐damaged DNA inhibits TFTC‐mediated Pol II transcription and TFTC is recruited in parallel with the nucleotide excision repair protein XP‐A to UV‐damaged DNA. TFTC preferentially acetylates histone H3 in nucleosomes assembled on UV‐damaged DNA. In agreement with this, strong histone H3 acetylation occurs in intact cells after UV irradiation. These results suggest that the access of DNA repair machinery to lesions within chromatin may be facilitated by TFTC via covalent modification of chromatin. Thus, our experiments reveal a molecular link between DNA damage recognition and chromatin modification.