HMGN1, an abundant nucleosomal binding protein, can affect both the chromatin higher order structure and the modification of nucleosomal histones, but it alters the expression of only a subset of genes. We investigated specific gene targeting by HMGN1 in the context of estrogen induction of gene expression. Knockdown and overexpression experiments indicated that HMGN1 limits the induction of several estrogenregulated genes, including TFF1 and FOS, which are induced by estrogen through entirely distinct mechanisms. HMGN1 specifically interacts with estrogen receptor ␣ (ER␣), both in vitro and in vivo. At the TFF1 promoter, estrogen increases HMGN1 association through recruitment by the ER␣. HMGN1 S20E/S24E, although deficient in binding nucleosomal DNA, still interacts with ER␣ and, strikingly, still represses estrogen-driven activation of the TFF1 gene. On the FOS promoter, which lacks the ER␣ binding sites, constitutively bound serum response factor (SRF) mediates estrogen stimulation. HMGN1 also interacts specifically with SRF, but HMGN1 S20E/S24E does not. Consistent with the protein interactions, only wildtype HMGN1 significantly inhibits the estrogen-driven activation of the FOS gene. Mechanistically, the inhibition of estrogen induction of several ER␣-associated genes, including TFF1, by HMGN1 correlates with decreased levels of acetylation of Lys9 on histone H3. Together, these findings indicate that HMGN1 regulates the expression of particular genes via specific protein-protein interactions with transcription factors at target gene regulatory regions.The HMGN family of proteins modulates the chromatin structure in vertebrates. These small, highly charged, abundant proteins bind with higher affinity to nucleosomes than to double-stranded DNA. Nucleosomal binding is due to both direct interactions with nucleosomal DNA and interactions of HMGN proteins with histones (10,18,24,46,66,71,75). The binding of HMGN to chromatin relaxes the higher order chromatin structure. In particular, HMGN1 counteracts the ability of histone H1 to compact chromatin through competition for H1 binding sites on the chromatin. Such structural mechanisms result in the general transcription stimulation by HMGN proteins on chromatin templates in vitro (20,74). The binding of HMGN proteins to nucleosomes also alters the posttranslational modification of nucleosomal histones at several distinct sites, which can result in either transcriptional stimulation or inhibition (42,43,77).Despite the seemingly indiscriminate effects of HMGN on chromatin compactness and histone modifications, the overexpression or knockout of HMGN proteins modulates the expression of only a small subset of genes, some of which are activated and others are inhibited by HMGNs (42,63,79). These results raised the question as to why HMGN proteins would affect transcription only at specific promoters. HMGN proteins exhibit no nucleosome binding preference based on the underlying DNA sequences in the nucleosomes (72). Thus, it is unlikely that the targeting of HMGNs t...