A key step in retrieving the information stored in the complex genomes of eukaryotes involves the identification of transcription units and, more specifically, the recognition of promoter sequences by RNA polymerase. In eukaryotes, the task of recognizing nuclear gene promoters and then transcribing the genes is divided among three highly related enzymes, RNA polymerases I, II, and III. Each of these RNA polymerases is dedicated to the transcription of specific sets of genes, and each depends on accessory factors, the so-called transcription factors, to recognize its cognate promoter sequences.RNA polymerase I is unique among the nuclear RNA polymerases in transcribing only one set of genes, the large, tandemly repeated, ribosomal RNA genes, and thus in having to recognize a single promoter structure. RNA polymerase II transcribes the protein-coding genes (mRNA genes) as well as some small nuclear RNA (snRNA) genes. The RNA polymerase II promoters can be divided into a core region, defined as the minimal region capable of directing transcription in vitro, and a regulatory region. The regulatory regions are highly varied in structure, reflecting the highly varied synthesis patterns of cellular proteins and the need for exquisite and complex regulation of these patterns. The core promoters themselves come in different types that, in mRNA-encoding genes, can contain a TATA box, an initiator, a downstream promoter element, or various combinations thereof. The assembly of a functional RNA polymerase II transcription complex on a promoter consisting of just a TATA box has been extensively studied. All the factors involved in the process have been identified, and much is known about how these factors interact with DNA and with each other to recruit, eventually, RNA polymerase II (for reviews, see Orphanides et al. 1996;Woychik and Hampsey 2002). How RNA polymerase II transcription complexes assemble on TATA-less promoters is, however, not as well understood.RNA polymerase III is dedicated to the transcription of an eclectic collection of genes whose main common features are that they encode structural or catalytic RNAs and that they are, as a rule, shorter than 400 base pairs (bp). This length limit is consistent with the elongation properties of RNA polymerase III, which recognizes a simple run of T residues as a termination signal. The genes transcribed by RNA polymerase III encode RNA molecules involved in fundamental metabolic processes, specifically components of the protein synthesis apparatus and components of the splicing and tRNA processing apparatus, as well as RNAs of unknown function. The RNA polymerase III promoters are more varied in structure than the uniform RNA polymerase I promoters, and yet not as diverse as the RNA polymerase II promoters. They have been divided into three main types, two of which are gene-internal and generally TATA-less, and one of which is gene-external and contains a TATA box. Remarkably, we have a good, and in some cases a very detailed, understanding of how RNA polymerase III ...

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DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-, and long-range allelic coordination among the studied molecular phenotypes. We observed genetic influence on most of these phenotypes, with histone modifications exhibiting strong context-dependent behavior. Our results implicate transcription factors as primary mediators of sequence-specific regulation of gene expression programs, with histone modifications frequently reflecting the primary regulatory event.

Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain.

Genome-wide rhythms in RNA polymerase II loading and dynamic chromatin remodeling underlie periodic gene expression during diurnal cycles in the mouse liver.

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In the human small nuclear RNA (snRNA) promoters, the presence of a TATA box recognized by the TATA box-binding protein (TBP) determines the selection of RNA polymerase III over RNA polymerase II. The RNA polymerase II snRNA promoters are, therefore, good candidates for TBP-independent promoters. We show here, however, that TBP activates transcription from RNA polymerase II snRNA promoters through a non-TATA box element, the snRNA proximal sequence element (PSE), as part of a new snRNA-activating protein complex (SNAPc). In contrast to the previously identified TBP-containing complexes SL1, TFIID, and TFIIIB, which appear dedicated to transcription by a single RNA polymerase, SNAP c is also essential for RNA polymerase III transcription from the U6 snRNA promoter. The U6 initiation complex appears to contain two forms of TBP, one bound to the TATA box and one bound to the PSE as a part of SNAPc, suggesting that multiple TBP molecules can have different functions within a single promoter. In eukaryotes, transcription is carried out by three different RNA polymerases, none of which can recognize its target promoters directly. Instead, promoter elements are first recognized by specific transcription factors that then recruit the correct RNA polymerase. Because RNA polymerase I, II, and III promoters are generally very different in structure, it has long been assumed that RNA polymerase specificity is achieved through the binding of very distinct sets of transcription factors. Although it is now well established that the TATA box binding protein [TBP) participates in transcription from TATA-containing and TATA-less promoters by all three RNA polymerases, it does so as part of distinct complexes that are each dedicated to transcription by a single RNA polymerase (for review, see Hernandez 1993). Thus, SL1 (Comai et al. 1992), TFIID (for review, see Sawadogo and Sentenac 1990;Roeder 1991; Pugh and Tjian 1992;Zawel and Reinberg 1992,1993), and TFIIIB (Lobo et al. 1992;Simmen et al. 1992b;Taggart et al. 1992; White and Jackson 1992) participate in transcription by RNA polymerases I, II, and III, respectively.The promoters of human small nuclear RNA (snRNA) genes are very similar in structure even though some of them are recognized by RNA polymerase II whereas others are recognized by RNA polymerase III. They therefore serve as a model to study how RNA polymerase specificity is achieved. The human U1 and U2 snRNA promoters are recognized by RNA polymerase II and consist essentially of two elements: A proximal sequence element (PSE) located upstream of position -40, which is essential and sufficient to direct basal levels of transcription, and a distal sequence element (DSE) located upstream of position -200, which serves as a transcriptional enhancer and is characterized by the presence of an octamer motif (for review, see Dahlberg and Lund 1988;Hernandez 1992). The human U6 snRNA promoter, which is recognized by RNA polymerase III, differs from most other RNA polymerase III promoters in that it does not contain any esse...

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