TFIIF (RAP30/74) is a general initiation factor that also increases the rate of elongation by RNA polymerase II. A two-hybrid screen for RAP74-interacting proteins produced cDNAs encoding FCP1a, a novel, ubiquitously expressed human protein that interacts with the carboxyl-terminal evolutionarily conserved domain of RAP74. Related cDNAs encoding FCP1b lack a carboxylterminal RAP74-binding domain of FCP1a. FCP1 is an essential subunit of a RAP74-stimulated phosphatase that processively dephosphorylates the carboxyl-terminal domain of the largest RNA polymerase II subunit. FCP1 is also a stoichiometric component of a human RNA polymerase II holoenzyme complex. Initiation of transcription by RNA polymerase (RNAP)1 II involves the general transcription factors TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH (reviewed in Ref. 1). Beginning with TFIID, whose TATA box-binding protein subunit recognizes the TATA box present in many promoters, these factors can assemble in an ordered pathway in vitro onto a promoter (2, 3), resulting in the formation of a preinitiation complex containing more than 40 polypeptides. Subsequently, however, yeast and mammalian RNAP II holoenzymes that contain several or all of the general transcription factors and other polypeptides were discovered (4 -9). There is evidence that transcription by RNAP II in Saccharomyces cerevisiae generally depends on such a holoenzyme (10) and that recruitment of yeast holoenzyme to a promoter would lead to a high rate of transcription (11).During or shortly after initiation by RNAP II, the carboxylterminal domain (CTD) of its largest subunit becomes heavily phosphorylated and remains so during transcript elongation (12). The phosphorylated form of RNAP II is designated RNAP IIO, whereas the unphosphorylated form is designated RNAP IIA. One subunit of TFIIH is a protein kinase that can phosphorylate the CTD (13). Phosphorylation of the CTD by PTEFb, a different Drosophila CTD kinase, has been shown to enhance the processivity of chain elongation by RNAP II in vitro (14). Concomitant with or following the termination of transcription, the CTD must be dephosphorylated by a protein phosphatase, since RNAP IIO cannot assemble directly into a preinitiation complex on either the adenovirus-2 major late or murine dihydrofolate reductase promoter in vitro (15-17). Accordingly, CTD phosphatase may function as a global regulator of gene expression by controlling the pool of RNAP IIA available for initiation. A phosphatase whose activity is stimulated by RAP74 and dephosphorylates the CTD in a processive manner has been purified from HeLa cell extracts (18,19).Certain activator proteins increase the efficiency of RNA chain elongation downstream from the promoter. For example, RNAP II pauses with an unphosphorylated CTD about 25-40 nucleotides downstream from the initiation site of Drosophila hsp70 genes and is stimulated by heat shock and the heat shock factor to become phosphorylated and leave these pause sites (Ref. 20 and references therein). Increasing evidence suppo...

Rationale: Despite shared environmental exposures, idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease are usually studied in isolation, and the presence of shared molecular mechanisms is unknown.Objectives: We applied an integrative genomic approach to identify convergent transcriptomic pathways in emphysema and IPF.Methods: We defined the transcriptional repertoire of chronic obstructive pulmonary disease, IPF, or normal histology lungs using RNA-seq (n = 87).Measurements and Main Results: Genes increased in both emphysema and IPF relative to control were enriched for the p53/hypoxia pathway, a finding confirmed in an independent cohort using both gene expression arrays and the nCounter Analysis System (n = 193). Immunohistochemistry confirmed overexpression of HIF1A, MDM2, and NFKBIB members of this pathway in tissues from patients with emphysema or IPF. Using reads aligned across splice junctions, we determined that alternative splicing of p53/hypoxia pathway-associated molecules NUMB and PDGFA occurred more frequently in IPF or emphysema compared with control and validated these findings by quantitative polymerase chain reaction and the nCounter Analysis System on an independent sample set (n = 193). Finally, by integrating parallel microRNA and mRNA-Seq data on the same samples, we identified MIR96 as a key novel regulatory hub in the p53/hypoxia gene-expression network and confirmed that modulation of MIR96 in vitro recapitulates the disease-associated gene-expression network.Conclusions: Our results suggest convergent transcriptional regulatory hubs in diseases as varied phenotypically as chronic obstructive pulmonary disease and IPF and suggest that these hubs may represent shared key responses of the lung to environmental stresses.

Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma, but have variable outcome, and we lack tools to identify and treat PMLs at risk for progression to cancer. Here we report the identification of four molecular subtypes of PMLs with distinct differences in epithelial and immune processes based on RNA-Seq profiling of endobronchial biopsies from high-risk smokers. The Proliferative subtype is enriched with bronchial dysplasia and exhibits up-regulation of metabolic and cell cycle pathways. A Proliferative subtype-associated gene signature identifies subjects with Proliferative PMLs from normal-appearing uninvolved large airway brushings with high specificity. In progressive/persistent Proliferative lesions expression of interferon signaling and antigen processing/presentation pathways decrease and immunofluorescence indicates a depletion of innate and adaptive immune cells compared with regressive lesions. Molecular biomarkers measured in PMLs or the uninvolved airway can enhance histopathological grading and suggest immunoprevention strategies for intercepting the progression of PMLs to lung cancer.

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