We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

One of the main engines that drives cellular transformation is the loss of proper control of the mammalian cell cycle. The cyclin-dependent kinase inhibitor p21 (also known as p21 WAF1/Cip1 ) promotes cell cycle arrest in response to many stimuli. It is well positioned to function as both a sensor and an effector of multiple anti-proliferative signals. This Review focuses on recent advances in our understanding of the regulation of p21 and its biological functions with emphasis on its p53-independent tumour suppressor activities and paradoxical tumour-promoting activities, and their implications in cancer.Higher eukaryotes have evolved multiple checkpoint mechanisms to monitor and respond to cellular perturbations, halting cellular progression until errors are fixed or the environment becomes permissible to the faithful transmission of genetic material 1 . Perturbations in checkpoint mechanisms are detrimental to the integrity of the genome, promote cancer development 2 and significantly affect the efficacy of anticancer treatment 3 . The tumour suppressor protein p53 mediates the DNA damage-induced checkpoint through the transactivation of various growth inhibitory or apoptotic genes. Among these, the small 165 amino acid protein p21 (also known as p21 WAF1/Cip1 ) mediates p53-dependent G1 growth arrest 4,5 . Earlier studies supported the view that p21 suppresses tumours by promoting cell cycle arrest in response to various stimuli. Additionally, substantial evidence from biochemical and genetic studies indicates that p21 acts as a master effector of multiple tumour suppressor pathways for promoting anti-proliferative activities that are independent of the classical p53 tumour suppressor pathway (FIG. 1). Despite its profound role in halting cellular proliferation and its ability to promote differentiation and cellular senescence, recent studies suggest that, under certain conditions, p21 can promote cellular proliferation and oncogenicity 6 . Consequently, p21 is often misregulated in human cancers, but its expression, depending on the cellular context and circumstances, suggests that it can act as a tumour suppressor or as an oncogene (TABLE 1). p21 mediates its various biological activities primarily by binding to and inhibiting the kinase activity of the cyclin-dependent kinases (CDKs) CDK2 and CDK1 (also known as CDC2) leading to growth arrest at specific stages in the cell cycle (FIG. 2). In addition, by binding to proliferating cell nuclear antigen (PCNA), p21 interferes with PCNA-dependent DNA NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript polymerase activity, thereby inhibiting DNA replication and modulating various PCNAdependent DNA repair processes. In this Review we discuss recent advances concerning the complex role of p21 in the development of cancer. We describe the various effector functions of p21 that allow it to exert its biological activities. We further describe our current understanding of the various mechanisms that control p21 expression, both transcri...

The maintenance of the eukaryotic genome requires precisely coordinated replication of the entire genome each time a cell divides. To achieve this coordination, eukaryotic cells use an ordered series of steps to form several key protein assemblies at origins of replication. Recent studies have identified many of the protein components of these complexes and the time during the cell cycle they assemble at the origin. Interestingly, despite distinct differences in origin structure, the identity and order of assembly of eukaryotic replication factors is highly conserved across all species. This review describes our current understanding of these events and how they are coordinated with cell cycle progression. We focus on bringing together the results from different organisms to provide a coherent model of the events of initiation. We emphasize recent progress in determining the function of the different replication factors once they have been assembled at the origin.

New types of small RNAs distinct from microRNAs (miRNAs) are progressively being discovered in various organisms. In order to discover such novel small RNAs, a library of 17-to 26-base-long RNAs was created from prostate cancer cell lines and sequenced by ultra-high-throughput sequencing. A significant number of the sequences are derived from precise processing at the 59 or 39 end of mature or precursor tRNAs to form three series of tRFs (tRNA-derived RNA fragments): the tRF-5, tRF-3, and tRF-1 series. These sequences constitute a class of short RNAs that are second most abundant to miRNAs. Northern hybridization, quantitative RT-PCR, and splinted ligation assays independently measured the levels of at least 17 tRFs. To demonstrate the biological importance of tRFs, we further investigated tRF-1001, derived from the 39 end of a Ser-TGA tRNA precursor transcript that is not retained in the mature tRNA. tRF-1001 is expressed highly in a wide range of cancer cell lines but much less in tissues, and its expression in cell lines was tightly correlated with cell proliferation. siRNAmediated knockdown of tRF-1001 impaired cell proliferation with the specific accumulation of cells in G2, phenotypes that were reversed specifically by cointroducing a synthetic 29-O-methyl tRF-1001 oligoribonucleotide resistant to the siRNA. tRF-1001 is generated in the cytoplasm by tRNA 39-endonuclease ELAC2, a prostate cancer susceptibility gene. Our data suggest that tRFs are not random by-products of tRNA degradation or biogenesis, but an abundant and novel class of short RNAs with precise sequence structure that have specific expression patterns and specific biological roles.[Keywords: Small RNA; tRNA; deep sequencing; cancer cell proliferation] Supplemental material is available at http://www.genesdev.org.

During the last few years, studies on microRNA (miRNA) and cancer have burst onto the scene. Profiling of the miRNome (global miRNA expression levels) has become prevalent and abundant miRNome data are currently available from various cancers. The pattern of miRNA expression can be correlated with cancer type, stage, and other clinical variables, so that miRNA profiling can be used as a tool for cancer diagnosis and prognosis. miRNA expression analyses also suggested oncogenic (or tumor suppressive) roles of miRNAs. miRNAs play roles in almost all aspects of cancer biology such as proliferation, apoptosis, invasion/metastasis, and angiogenesis. Given that many miRNAs are deregulated in cancers but have not yet been further studied, it is expected that more miRNAs will emerge as players in the etiology and progression of cancer. miRNAs will be also discussed as a tool for cancer therapy. SYNOPSIS During the last decade, a major discovery in biology was the discovery of small RNAs, including miRNA (microRNA) and siRNA (small interfering RNA), as highlighted by the 2002 December issue of Science magazine (1). Since RNA interference (RNAi) phenomenon was discovered in nematodes (2), siRNA has provided a technical breakthrough for short term genetics in mammalian systems. The big impact of small RNAs was well celebrated by the 2006 Nobel prize awarded to the two scientists who discovered RNAi. On the other side, miRNAs shed new insight on the post-transcriptional regulation of gene expression. miRNAs were also first discovered in worms (3, 4), and later in a number of animals, plants, and viruses. During the last couple of years, the miRNA field has been expanding with many recent publications implicating miRNAs in diverse cellular processes. Cancer is a major cause of death in the United States (“Cancer Facts & Figures 2007” from American Cancer Society; http://www.cancer.org/docroot/stt/stt_0.asp). Cancer is a complex genetic disease caused by the accumulation of mutations that lead to deregulation of gene expression and uncontrolled cell proliferation. Given the wide impact of miRNAs on gene expression, it is not surprising that a number of miRNAs have been implicated in cancer. In this review, the links between miRNA and cancer will be comprehensively described and discussed.