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1.  Chromatin Organization and Transcriptional Regulation 
Cell type specific transcriptional regulation must be adhered to in order to maintain cell identity throughout the lifetime of an organism, yet flexible enough to allow for responses to endogenous and exogenous stimuli. This regulation is mediated not only by molecular factors (e.g. cell type specific transcription factors, histone and DNA modifications), but also on the level of chromatin and genome organization. In this review we focus on recent findings that have contributed to our understanding of higher order chromatin structure and genome organization within the nucleus. We highlight new findings on the dynamic positioning of genes relative to each other, as well as to their chromosome territory and the nuclear lamina, and how the position of genes correlates with their transcriptional activity.
doi:10.1016/j.gde.2012.11.006
PMCID: PMC3612554  PMID: 23270812
2.  Nuclear Location and the Control of Developmental Progression 
It is now well established that the mammalian genome is highly organized. Chromosomes are structured as territories that only sporadically intermingle. Chromosome territories themselves are segregated into distinct environments, i.e. the transcriptionally inert/repressive (heterochromatic) and permissive (euchromatic) compartments. The transcriptionally permissive compartment is organized into domains (~0.5–3Mb) that consist of bundles of loops, are gene-rich and closely associated by activating epigenetic marks. During ontogeny and developmental progression chromatin states are highly dynamic. Recent studies have shown that loci and domains readily switch compartments. Switching nuclear neighborhoods is closely associated with changes in transcriptional activity and extensive chromatin reorganization. Here we discuss the implications of a dynamic genome and how it relates to the control of developmental progression.
doi:10.1016/j.gde.2012.11.010
PMCID: PMC3613431  PMID: 23266214
3.  The role of chromatin insulators in nuclear architecture and genome function 
Eukaryotic genomes are intricately arranged into highly organized yet dynamic structures that underlie patterns of gene expression and cellular identity. The recent adaptation of novel genomic strategies for assaying nuclear architecture has significantly extended and accelerated our ability to query the nature of genome organization and the players involved. In particular, recent explorations of physical arrangements and chromatin landscapes in higher eukaryotes have demonstrated that chromatin insulators, which mediate functional interactions between regulatory elements, appear to play an important role in these processes. Here we reflect on current findings and our rapidly expanding understanding of insulators and their role in nuclear architecture and genome function.
doi:10.1016/j.gde.2012.11.003
PMCID: PMC3632654  PMID: 23298659
Chromatin; Epigenetics; CTCF; TFIIIC; Nuclear Organization
4.  Mechanisms by which transcription factors gain access to target sequence elements in chromatin 
Transcription factors (TF) bind DNA sequence motifs, but the presence of a consensus DNA element is not sufficient to direct TF binding to chromatin. Recent genomic data have revealed that accessibility, as measured by DNase sensitivity and the presence of active histone marks, is necessary for TF binding. DNA sequence provides the initial specification of the accessibility of DNA elements within chromatin that permits TF binding. In yeast, it is known that poly(dA-dT) tracts directly encode low-nucleosome occupancy at promoters. Recent evidence suggests that CpG islands in mammals are inherently refractory to higher-order chromatin structure and remain accessible, despite favoring nucleosome formation in vitro. Taken together, these studies support a model for how accessibility originates and then propagates throughout regulatory cascades and development.
doi:10.1016/j.gde.2012.11.008
PMCID: PMC3651763  PMID: 23266217
5.  Chromatin dynamics at the replication fork: there’s more to life than histones 
Before each division, eukaryotic cells face the daunting task of completely and accurately replicating a heterogeneous, chromatinized genome and repackaging both resulting daughters. Because replication requires strand separation, interactions between the DNA and its many associated proteins – including histones – must be transiently broken to allow the passage of the replication fork. Here, we will discuss the disruption and re-establishment of chromatin structure during replication, and the consequences of these processes for epigenetic inheritance.
doi:10.1016/j.gde.2012.12.007
PMCID: PMC3657310  PMID: 23347596
6.  miRNA profiling of cancer 
A steadily growing number of studies have shown that microRNAs have key roles in the regulation of cellular processes and that their dysregulation is essential to keep the malignant phenotype of cancer cells. The distorted and unique expression profile of microRNAs in different types and subsets of tumor coupled with their presence in biological fluids make of microRNAs an attractive source of sensitive biomarkers. Here, we will discuss how microRNA profiles are altered in cancer, highlighting their potential as sensitive biomarkers for cancer risk stratification, outcome prediction and classification of histological subtypes. We will also evaluate the current knowledge on the use of microRNAs as circulating biomarkers, hoping that further studies will lead to the application of microRNA signature in prognostic and predictive markers that can improve patient health.
doi:10.1016/j.gde.2013.01.004
PMCID: PMC3632255  PMID: 23465882
7.  MicroRNAs in the Ionizing Radiation Response and in Radiotherapy 
Radiotherapy is a form of cancer treatment that utilizes the ability of ionizing radiation to induce cell inactivation and cell death, generally via inflicting DNA double-strand breaks. However, different tumors and their normal surrounding tissues are not equally sensitive to radiation, posing a major challenge in the field: to seek out factors that influence radiosensitivity. In this review, we summarize the evidence for microRNA (miRNA) involvement in the radioresponse and discuss their potential as radiosensitizers. MicroRNAs are endogenous small, noncoding RNAs that regulate gene expression post-transcriptionally, influencing many processes including, as highlighted here, cellular sensitivity to radiation. Profiling studies demonstrate that miRNA expression levels change in response to radiation, while certain miRNAs, when overexpressed or knocked down, alter radiosensitivity. Finally, we discuss specific miRNA-target pairs that affect response to radiation and DNA damage as good potential targets for modulating radioresponsitivity.
doi:10.1016/j.gde.2013.01.002
PMCID: PMC3617065  PMID: 23453900
8.  Impact of induced pluripotent stem cells on the study of central nervous system disease 
The derivation of pluripotent stem cells from somatic tissues has provided researchers with a source of patient-specific stem cells. The potential applications of this technology are truly momentous, and include cellular modeling of disease processes, drug discovery, and cell-based therapy. Here, we review the use of induced pluripotent stem cells (iPSCs) to study CNS disease. Since the iPSC field is still in its infancy, we also discuss some of the challenges that will need to be overcome before the potential of this technology to study and to treat neurological and psychiatric disorders can be fully harnessed.
doi:10.1016/j.gde.2011.01.008
PMCID: PMC3932563  PMID: 21277194
9.  Mechanisms Coordinating ELAV/Hu mRNA Regulons 
The 5’ and 3’ untranslated regions (UTRs) of messenger RNAs (mRNAs) function as platforms that can determine the fate of each mRNA individually and in aggregate. Multiple mRNAs that encode proteins that are functionally related often interact with RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) that coordinate their expression in time and space as RNA regulons within the ribonucleoprotein (RNP) infrastructure we term the ribonome. Recent ribonomic methods have emerged that can determine which mRNAs are bound and regulated by RBPs and ncRNAs, some of which act in combination to determine global outcomes. ELAV/Hu proteins bind to AU-rich elements (ARE) in mRNAs and regulate their stability from splicing to translation, and the ubiquitous HuR protein has been implicated in cancerous cell growth. Recent work is focused on mechanistic models of how ELAV/Hu proteins increase mRNA stability and translation by repressing microRNAs (miRs) and the RNA induced silencing complex (RISC) via ARE-based ribonucleosomes that may affect global functions of mRNA regulons.
doi:10.1016/j.gde.2012.12.006
PMCID: PMC3617084  PMID: 23312841
10.  Regulation and dysregulation of 3′UTR-mediated translational control 
Summary
Translational control provides numerous advantages in regulation of gene expression including rapid responsiveness, intracellular localization, non-destruction of template mRNA, and coordinated regulation of transcript ensembles. Transcript-selective, translational control is driven by the specific interaction of factor(s) with the 5′ or 3′ untranslated region (UTR), thereby influencing initiation, elongation, or termination of mRNA translation. The mean length of human 3′UTRs is greater than that of 5′UTR, indicating the expanded potential for motifs, structural elements, and binding sites for trans-acting factors that exert transcript-selective translation control. New and unexpected mechanisms of 3′UTR-mediated translational control and their contributions to disease have received increasing attention during the last decade. Here, we briefly review a few recent and representative discoveries of 3′UTR-mediated translational control, emphasizing the novel aspects of these regulatory mechanisms and their potential pathophysiological significance.
doi:10.1016/j.gde.2012.12.004
PMCID: PMC3644486  PMID: 23312843
11.  Chromatin: a molecular interface between cancer and aging 
To prevent cancer, mammals have evolved potent tumor suppression mechanisms, including senescence and apoptosis. These processes depend on regulation of chromatin. Chromatin-dependent tumor suppressor pathways are activated in pre-malignant cells and tissues harboring cancer-causing genetic alterations, and also in normal aged tissue, the latter likely due to accumulation of genetic and cellular damage. Paradoxically, however, disruption of chromatin structure may also promote cancer. Apparent defects in chromatin structure accumulate with age, the biggest single risk factor for cancer. Evidence suggests that these age-associated perturbations in chromatin structure contribute to the age-associated increase in incidence of cancer. Thus, alterations in chromatin structure can both suppress and promote the onset of cancer, and both activities are inextricably linked to aging.
doi:10.1016/j.gde.2010.10.007
PMCID: PMC3895593  PMID: 21087854
12.  Oscillatory signaling processes: the how, the why and the where 
Oscillatory processes in biological signal transduction have come under progressively increasing scrutiny in terms of their functional significance and mechanisms of emergence and regulation. Since oscillatory processes can be a by-product of rapid adaptation and can also easily emerge if the feedbacks underlying adaptive processes are inadvertently artificially enhanced, one needs to exercise caution in both claiming the existence of in vivo oscillations and in seeking to assign to them a specific functional significance. Nevertheless, oscillations can be a powerful means of encoding and transferring information both in time and in space, thus possessing important potential advantages for evolutionary selection and stabilization. Thus periodicity in the cell responses to diverse persistent external stimuli might become a more recognized and even expected feature of signaling processes.
doi:10.1016/j.gde.2010.08.007
PMCID: PMC3895451  PMID: 20971631
13.  Genome Sequencing and Cancer 
New technologies for DNA sequencing, coupled with advanced analytical approaches, are now providing unprecedented speed and precision in decoding human genomes. This combination of technology and analysis, when applied to the study of cancer genomes, is revealing specific and novel information about the fundamental genetic mechanisms that underlie cancer’s development and progression. This review outlines the history of the past several years of development in this realm, and discusses the current and future applications that will further elucidate cancer’s genomic causes.
doi:10.1016/j.gde.2012.03.005
PMCID: PMC3890425  PMID: 22534183
14.  Dynamics and precision in retinoic acid morphogen gradients 
Summary
Retinoic acid (RA) regulates many cellular behaviors during embryonic development and adult homeostasis. Like other morphogens, RA forms gradients through the use of localized sources and sinks, feedback, and interactions with other signals; this has been particularly well studied in the context of hindbrain segmentation in vertebrate embryos. Yet, as a small lipophilic molecule derived from a dietary source—vitamin A—RA differs markedly from better-studied polypeptide morphogens in its mechanisms of transport, signaling, and removal. Computational models suggest that the distinctive features of RA gradients make them particularly robust to large perturbations. Such features include combined positive and negative feedback effects via intracellular fatty acid binding proteins and RA-degrading enzymes. Here, we discuss how these features, together with feedback interactions among RA target genes, help enable RA to specify multiple, accurate pattern elements in the developing hindbrain, despite operating in an environment of high cellular and biochemical uncertainty and noise.
doi:10.1016/j.gde.2012.11.012
PMCID: PMC3790664  PMID: 23266215
15.  Phenotypic Models of Evolution and Development: Geometry as Destiny 
Quantitative models of development that consider all relevant genes typically are difficult to fit to embryonic data alone and have many redundant parameters. Computational evolution supplies models of phenotype with relatively few variables and parameters that allows the patterning dynamics to be reduced to a geometrical picture for how the state of a cell moves. The clock and wavefront model, that defines the phenotype of somitogenesis, can be represented as a sequence of two discrete dynamical transitions (bifurcations). The expression-time to space map for Hox genes and the posterior dominance rule are phenotypes that naturally follow from computational evolution without considering the genetics of Hox regulation.
doi:10.1016/j.gde.2012.09.001
PMCID: PMC3609406  PMID: 23026724
16.  The importance of geometry in mathematical models of developing systems 
Understanding the interaction between the spatial variation of extracellular signals and the interpretation of such signals in embryonic development is difficult without a mathematical model, but the inherent limitations of a model can have a profound impact on its utility. A central issue is the level of abstraction needed, and here we focus on the role of geometry in models and how the choice of the spatial dimension can influence the conclusions reached. A widely-studied system in which the proper choice of geometry is critical is embryonic development of Drosophila melanogaster, and we discuss recent work in which 3D embryo-scale modeling is used to identify key modes of transport, analyze gap gene expression, and test BMP-mediated positive feedback mechanisms.
doi:10.1016/j.gde.2012.09.007
PMCID: PMC3765006  PMID: 23107453
17.  Visualizing cancer and immune cell function with metabolic positron emission tomography 
Cancer cells and immune cells modulate their metabolism according to specific needs during cancer progression and immune responses. The ability to measure cellular metabolic function in vivo would enable the evaluation of tumors and their response to therapy and also the effectiveness of cellular immune responses to cancer. Positron emission tomography (PET) is a highly sensitive clinical imaging modality that enables whole-body, quantitative measurements of tissue biochemical function. Here, we review work using PET probes for specific metabolic pathways to measure cell function in cancer and immunity. We focus on the use of probes for glycolysis and nucleoside salvage and then discuss the development of new metabolic probes that visualize distinct parameters of cell function during disease.
doi:10.1016/j.gde.2009.10.008
PMCID: PMC3799818  PMID: 19931447
18.  Does transcription factor induced pluripotency accurately mimic embryo derived pluripotency? 
When Takahashi and Yamanaka first demonstrated that just four transcription factors could reprogram a fibroblast to a pluripotent stem cell, the first wave of data to emerge focused on how similar these induced pluripotent stem cells (iPSCs) were to embryo-derived pluripotent stem cells (ESCs) [1]. The next wave of data focused on determining the degree of difference between iPSCs and ESCs [2]. Now the focus is on tweaking the process to generate iPSCs that are more similar to ESCs [3, 4]. Because transcription factor based reprogramming allows for nearly any type of cell to be created from any donor cell, there is obviously enormous interest in this technique as a tool for both basic developmental biology and for clinical applications. In this review, I will attempt to summarize the data that serve to distinguish these types of pluripotent stem cells and speculate on any ramifications of the differences.
doi:10.1016/j.gde.2012.07.003
PMCID: PMC3753773  PMID: 23079387
19.  Epigenetic Obstacles Encountered By Transcription Factors: Reprogramming Against All Odds 
Reprogramming of a somatic nucleus to an induced pluripotent state can be achieved in vitro through ectopic expression of Oct4 (Pou5f1), Sox2, Klf4 and c-Myc. While the ability of these factors to regulate transcription in a pluripotent context has been studied extensively, their ability to interact with and remodel a somatic genome remains underexplored. Several recent studies have begun to provide mechanistic insights that will eventually lead to a more rational design and improved understanding of nuclear reprogramming.
doi:10.1016/j.gde.2012.08.002
PMCID: PMC3490009  PMID: 22922161
20.  The role of pluripotency gene regulatory network components in mediating transitions between pluripotent cell states☆ 
Pluripotency is a property that early embryonic cells possess over a considerable developmental time span. Accordingly, pluripotent cell lines can be established from the pre-implantation or post-implantation mouse embryo as embryonic stem (ES) or epiblast stem (EpiSC) cell lines, respectively. Maintenance of the pluripotent phenotype depends on the function of specific transcription factors (TFs) operating within a pluripotency gene regulatory network (PGRN). As cells move from an ES cell to an EpiSC state, the PGRN changes with expression of some TFs reduced (e.g. Nanog) or eliminated (e.g. Esrrb). Re-expressing such TFs can move cells back to an earlier developmental identity and is being applied to attempt establishment of human cell lines with the properties of mouse ES cells.
doi:10.1016/j.gde.2013.06.003
PMCID: PMC3790975  PMID: 23932125
21.  Long non-coding RNAs and enhancers 
Long non-coding RNAs (ncRNAs) are emerging as important regulatory factors in mammalian genomics. A number of reports within the last 2 years have identified thousands of actively expressed long ncRNA transcripts with distinct properties. The long ncRNAs show differential expression patterns and regulation in a w ide variety of cells and tissues, adding significant complexity to the understanding of their biological role. Furthermore, genome-wide studies of transcriptional enhancers based on chromatin modifications and enhancer binding proteins have led to the identification of putative enhancers and provided insight into their tissue-specific regulation of gene expression. In an exciting turn of events, new evidence is indicating that long ncRNAs are associated with enhancer regions and that such non-coding transcription correlate with the increased activity of the neighboring genes. Moreover, additional experiments suggest that enhancer-function can be mediated through a transcribed long ncRNA and that this might be a common function for long ncRNAs. Here, we review recent advances made both in the genome-wide characterization of enhancers and in the identification of new classes of long ncRNAs, and discuss the functional overlap of these two classes of regulatory elements.
doi:10.1016/j.gde.2011.01.020
PMCID: PMC3779066  PMID: 21330130
22.  Multi-Disciplinary Methods to Define RNA-Protein Interactions and Their Regulatory Networks 
The advent of high-throughput technologies including deep-sequencing and protein mass spectrometry is facilitating the acquisition of large and precise data sets towards the definition of post-transcriptional regulatory networks. While early studies that investigated specific RNA-protein interactions in isolation laid the foundation for our understanding of the existence of molecular machines to assemble and process RNAs, there is a more recent appreciation of the importance of individual RNA-protein interactions that contribute to post-transcriptional gene regulation. The multitude of RNA-binding proteins (RBPs) and their many RNA targets has only been captured experimentally in recent times. In this review, we will examine current multidisciplinary approaches towards elucidating RNA-protein networks and their regulation.
doi:10.1016/j.gde.2013.01.003
PMCID: PMC3624891  PMID: 23453689
23.  Small temporal RNAs in animal development 
The lin-4/miR-125 and let-7 microRNAs are at the heart of the heterochronic pathway, which controls temporal cell fate determination during Caenorhabditis elegans development. These small temporal RNAs are clustered along with a third microRNA, miR-100, in the genomes of most animals. Their conserved temporal and neural expression profile suggests a general role in cell fate determination during nervous system differentiation. By triggering consecutive differentiation programs, these microRNAs likely help to determine birth-order dependent temporal identity and thereby contribute to neural stem cell multipotency.
doi:10.1016/j.gde.2012.04.001
PMCID: PMC3419770  PMID: 22578317
24.  Small RNAs in development – insights from plants 
microRNAs (miRNAs) and small interfering RNAs (siRNAs), which constitute two major classes of endogenous small RNAs in plants, impact a multitude of developmental and physiological processes by imparting sequence specificity to gene and genome regulation. Although lacking the third major class of small RNAs found in animals, Piwi-interacting RNAs (piRNAs), plants have expanded their repertoire of endogenous siRNAs, some of which fulfill similar molecular and developmental functions as piRNAs in animals. Research on plant miRNAs and siRNAs has contributed invaluable insights into small RNA biology, thanks to the highly conserved molecular logic behind the biogenesis and actions of small RNAs. Here, I review progress in the plant small RNA field in the past two years, with an emphasis on recent findings related to plant development. I do not recount the numerous developmental processes regulated by small RNAs; instead, I focus on major principles that have been derived from recent studies and draw parallels, when applicable, between plants and animals.
doi:10.1016/j.gde.2012.04.004
PMCID: PMC3419802  PMID: 22578318
argonaute; miRNA; siRNAs; piRNAs; cell-to-cell movement; germ line
25.  Intestinal stem cell function in Drosophila and Mice 
Epithelial cells of the digestive tracts of most animals are short-lived, and are constantly replenished by the progeny of long-lived, resident intestinal stem cells. Proper regulation of intestinal stem cell maintenance, proliferation and differentiation is critical for maintaining gut homeostasis. Here we review recent genetic studies of stem cell-mediated homeostatic growth in the Drosophila midgut and the mouse small intestine, highlighting similarities and differences in the mechanisms that control stem cell proliferation and differentiation.
doi:10.1016/j.gde.2012.04.002
PMCID: PMC3426656  PMID: 22608824

Results 1-25 (216)