Genomic imprinting results in preferential expression of the paternal or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and ...adult brain. This approach uncovered parent-of-origin allelic effects of more than 1300 loci. We identified parental bias in the expression of individual genes and of specific transcript isoforms, with differences between brain regions. Many imprinted genes are expressed in neural systems associated with feeding and motivated behaviors, and parental biases preferentially target genetic pathways governing metabolism and cell adhesion. We observed a preferential maternal contribution to gene expression in the developing brain and a major paternal contribution in the adult brain. Thus, parental expression bias emerges as a major mode of epigenetic regulation in the brain.
Summary
Comprehensive analysis of gene function requires the detailed examination of mutant alleles. In Arabidopsis thaliana, large collections of sequence‐indexed insertion and chemical mutants ...provide potential loss‐of‐function alleles for most annotated genes. However, limitations for phenotypic analysis include gametophytic or early sporophytic lethality, and the ability to recombine mutant alleles in closely linked genes, especially those present as tandem duplications. Transgene‐mediated gene silencing can overcome some of these shortcomings through tissue‐specific, inducible and partial gene inactivation, or simultaneous targeting of several, sequence‐related genes. In addition, gene silencing is a convenient approach in species or varieties for which exhaustive mutant collections are not yet available. Typically, gene function is reduced post‐transcriptionally, effected by small RNAs that act in a sequence‐specific manner by base pairing to complementary mRNA molecules. A recently introduced approach is the use of artificial microRNAs (amiRNAs). Here, we review various strategies for small RNA‐based gene silencing, and describe in detail the design and application of amiRNAs in many plant species.
Phosphatidic acid (PA) is an essential phospholipid involved in membrane biosynthesis and signal transduction in all eukaryotes. This review focuses on its role as lipid second messenger during plant ...stress, metabolism, and development. The contribution of different individual isoforms of enzymes that generate and break down PA will be discussed and the downstream responses highlighted, with particular focus on proteins that bind PA. Through characterization of several of these PA targets, a molecular and genetic basis for PA's role in plant stress and development is emerging.
Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignancy with very poor prognosis. Genome-wide, high-throughput technologies have made major advances in understanding the molecular basis of ...this disease, although important mechanisms are still unclear. Recent data have revealed specific genetic mutations (for example, KRAS, IDH1 and IDH2), epigenetic silencing, aberrant signaling pathway activation (for example, interleukin (IL)-6/signal transducer and activator of transcription 3 (STAT3), tyrosine kinase receptor-related pathways) and molecular subclasses with unique alterations (for example, proliferation and inflammation subclasses). In addition, some ICCs share common genomic traits with hepatocellular carcinoma. All this information provides the basis to explore novel targeted therapies. Currently, surgery at early stage is the only effective therapy. At more advanced stages, chemotherapy regimens are emerging (that is, cisplatin plus gemcitabine), along with molecular targeted agents tested in several ongoing clinical trials. Nonetheless, a first-line conclusive treatment remains an unmet need. Similarly, there are no studies assessing tumor response related with genetic alterations. This review explores the recent advancements in the knowledge of the molecular alterations underlying ICC and the future prospects in terms of therapeutic strategies leading towards a more personalized treatment of this neoplasm.
Thyroid cancer is the most common type of endocrine-related malignancy, whose incidence rates have increased dramatically in the last few decades. Neoplasms of follicular origin generally have ...excellent prognosis, with the exception of less differentiated tumors. Follicular-derived thyroid cancer can manifest as a variety of morphologically distinct entities, characterized by various degrees of differentiation and invasiveness. Histological evaluation is thus crucial for the definition of patients' prognosis. However, within each histological subtype, tumor behavior can be highly variable, and, in this respect, molecular characterization can provide insightful information to refine the risk stratification of tumors. In addition to the importance of its prognostic role, molecular testing can be used to support the differential diagnosis of thyroid nodules in the absence of marked cyto-morphological aberrations. Finally, with the advent of targeted drugs, the presence of molecular alterations will guide the therapeutic strategies for patients with advanced tumors who do not respond to standard treatment. This review aims to describe the genetic landscape of follicular-derived thyroid tumors also highlighting differences across histological subtypes.
This commentary remarks on the study conducted by Lu et al, which contributes to the existing knowledge on translocation renal cell carcinoma (tRCC) by examining how race may influence susceptibility ...to tRCC and how distinct transcriptomic profiles among different races may explain variations in tRCC prognosis.
The lengths of human telomeres, which protect chromosome ends from degradation and end fusions, are crucial determinants of cell lifespan. During embryogenesis and in cancer, the telomerase enzyme ...counteracts telomeric DNA shortening. As shown in cancer cells, human telomerase binds the shelterin component TPP1 at telomeres during the S phase of the cell cycle, and adds ~60 nucleotides in a single round of extension, after which telomerase is turned off by unknown mechanisms. Here we show that the human CST (CTC1, STN1 and TEN1) complex, previously implicated in telomere protection and DNA metabolism, inhibits telomerase activity through primer sequestration and physical interaction with the protection of telomeres 1 (POT1)–TPP1 telomerase processivity factor. CST competes with POT1–TPP1 for telomeric DNA, and CST–telomeric-DNA binding increases during late S/G2 phase only on telomerase action, coinciding with telomerase shut-off. Depletion of CST allows excessive telomerase activity, promoting telomere elongation. We propose that through binding of the telomerase-extended telomere, CST limits telomerase action at individual telomeres to approximately one binding and extension event per cell cycle. Our findings define the sequence of events that occur to first enable and then terminate telomerase-mediated telomere elongation.
The retained N-terminal methionine (Met) residue of a nascent protein is often N-terminally acetylated (Nt-acetylated). Removal of N-terminal Met by Met-aminopeptidases frequently leads to ...Nt-acetylation of the resulting N-terminal alanine (Ala), valine (Val), serine (Ser), threonine (Thr), and cysteine (Cys) residues. Although a majority of eukaryotic proteins (for example, more than 80% of human proteins) are cotranslationally Nt-acetylated, the function of this extensively studied modification is largely unknown. Using the yeast Saccharomyces cerevisiae, we found that the Nt-acetylated Met residue could act as a degradation signal (degron), targeted by the Doa10 ubiquitin ligase. Moreover, Doa10 also recognized the Nt-acetylated Ala, Val, Ser, Thr, and Cys residues. Several examined proteins of diverse functions contained these N-terminal degrons, termed AcN-degrons, which are a prevalent class of degradation signals in cellular proteins.
An ultrasensitive photoelectrochemical immunoassay of cancer biomarker α-fetoprotein (AFP) is proposed that uses titanium dioxide (TiO2) coupled with AFP–CdTe–GOx bioconjugate, which featured AFP ...antigen and glucose oxidase (GOx) labels linked to CdTe quantum dots (QDs) for signal amplification. The synthesized CdTe QDs yielded a homogeneous and narrow size distribution, which allowed the binding of AFP and GOx on CdTe QDs. Greatly enhanced sensitivity for AFP came from a dual signal amplification strategy. First, an effective matching of energy levels between the conduction bands of CdTe QDs and TiO2 allowed for fast electron injection from excited CdTe QDs to TiO2 upon irradiation, which reduced the recombination process of electron–hole pairs and prompted photoelectrochemical performance. Second, GOx enzyme could catalyze glucose to produce H2O2, which acted as a sacrificial electron donor to scavenge the photogenerated holes in the valence band of CdTe QDs, further causing an enhanced photocurrent. Thus, on the basis of the dual signal amplification strategy, the competitive immunosensor based on the specific binding of anti-AFP antibodies to AFP and AFP–CdTe–GOx bioconjugates was achieved. This proposed biosensor for AFP possessed largely increased linear detection range from 0.5 pg/mL to 10 μg/mL with a detection limit of 0.13 pg/mL. The proposed amplification strategy shows high sensitivity, stability, and reproducibility and can become a promising platform for other protein detection.
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