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Animals are grouped into ~35 'phyla' based upon the notion of distinct body plans (1-4). Morphological and molecular analyses have revealed that a stage in the middle of development--known as [...]

First identified as histone-modifying proteins, lysine acetyltransferases (KATs) and deacetylases (KDACs) antagonize each other through modification of the side chains of lysine residues in histone proteins (1). Acetylation of many non-histone proteins involved in chromatin, metabolism or cytoskeleton regulation were further identified in eukaryotic organisms (2-6), but the corresponding enzymes and substrate-specific functions of the modifications are unclear. Moreover, mechanisms underlying functional specificity of individual KDACs (7) remain enigmatic, and the substrate spectra of each KDAC lack comprehensive definition. Here we dissect the functional specificity of 12 critical human KDACs using a genome-wide synthetic lethality screen (8-13) in cultured human cells. The genetic interaction profiles revealed enzyme-substrate relationships between individual KDACs and many important substrates governing a wide array of biological processes including metabolism, development and cell cycle progression. We further confirmed that acetylation and deacetylation of the catalytic subunit of the adenosine monophosphate-activated protein kinase (AMPK), a critical cellular energy-sensing protein kinase complex, is controlled by the opposing catalytic activities of HDAC1 and p300. Deacetylation of AMPK enhances physical interaction with the upstream kinase LKB1, leading to AMPK phosphorylation and activation, and resulting in lipid breakdown in human liver cells. These findings provide new insights into previously underappreciated metabolic regulatory roles of HDAC1 in coordinating nutrient availability and cellular responses upstream of AMPK, and demonstrate the importance of high-throughput genetic interaction profiling to elucidate functional specificity and critical substrates of individual human KDACs potentially valuable for therapeutic applications., To study the functional specificity of individual KDACs, we developed a genome-wide genetic interaction profiling technology in cultured human cells by RNA interference (RNAi) using a pooled human short hairpin [...]

A correction to the article "Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK" published in the 2012 issue is presented.

Isolation of high-quality and nondegraded RNA is a prerequisite for many modern molecular biology applications. A variety of RNA extraction products and protocols are available for the standard model organisms, yet species-specific peculiarities of less well studied organisms often require specific protocol adaptations. Here we describe a robust RNA extraction protocol for planarians that is widely used in the community. The protocol combines tissue homogenization in TRIzol with phenol-chloroform extraction and subsequent purification over commercial columns. The purified RNA can be used for many downstream applications, such as cDNA synthesis and next-generation sequencing (NGS, RNA-seq).

Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background and Purpose: Gastrointestinal stromal tumors (GISTs) involving the small intestine are less common than those involving the stomach, and data on small intestinal stromal tumors (SISTs) are more limited. This study investigated the clinicopathological characteristics and prognostic factors of SISTs and compared them with those of gastric stromal tumors (GSTs)., Methods: A total of 82 surgically resected and pathologically diagnosed smooth muscle tumors of small bowel in patients treated from January 1986 to December 2000 were included. Immunohistochemical studies were performed on these tumors with antibodies of CD117, CD34, smooth muscle actin (SMA), desmin and S-100. The results were analyzed and compared with 74 cases of GSTs diagnosed and treated from January 1986 to December 1997., Results: Among the 82 small intestine tumors, 71 were CD117-positive (86.6%) and were classified as SISTs. Of the 71 SISTs, 70.4% were immunoreactive to CD34, 88.7% to SMA, 46.5% to S-100, but none to desmin. Survival analysis demonstrated that tumor size < 5 cm (p = 0.021), mitosis number < 5/50 high-power field (p < 0.001), SMA-positive (p = 0.027), non-epithelioid cell type (p = 0.005) and tumor with skeinoid fibers (p = 0.010) predicted longer disease-free survival after operation. Multivariate analysis revealed that mitotic number (p = 0.001), cell morphology (p = 0.031) and tumor size (p = 0.004) were independent prognostic factors. In comparison to GSTs, SISTs exhibited significantly lower rates of CD34, but significantly higher rates of SMA and S-100 immunoreactivity., Conclusions: SISTs exhibited a different immunophenotype from GSTs. SMA reactivity is a predictor of benign clinical behavior in SISTs. Tumor mitotic numbers, tumor size, and cell type were independent prognostic factors for patients with SISTs after operation.

Background and Purpose: Gastrointestinal stromal tumors (GISTs), identified by the presence of CD117 (KIT), were previously classified as gastric and intestinal smooth muscle tumors prior to the availability of immunohistochemical methods. This study evaluated the percentage of GISTs previously diagnosed as gastric smooth muscle tumors in our hospital during an 11-year period., Methods: A total of 81 surgically resected gastric smooth muscle tumor specimens from 81 patients were collected from January 1986 to December 1997. Immunohistochemical studies were performed on these tumors with antibodies of CD34, CD117, smooth muscle actin (SMA), S-100, and desmin., Results: Among the 81 tumors, 74 (91.4%) were CD117-positive and were classified as GISTs. Among the 74 GISTs, CD34 was positive in 72 tumors (97.3%), SMA was positive in 12 tumors (16.2%), desmin was positive in 5 tumors (6.7%), and S-100 was positive in 4 tumors (5.4%). The 7 tumors classified as non-GISTs had the following immunohistochemical characteristics: 1 was a CD117-negative CD34-positive stromal tumor (GINST) [1/81, 1.2%]; 3 were schwannomas with strong S-100-positive characteristics (3/81, 3.7%); and 3 were smooth muscle tumors with both SMA- and desmin-positive status (3/81, 3.7%). No clear relationship between CD117 or CD34 expression and prognosis was found for these tumors., Conclusions: The majority (91.4%) of gastric tumors originally diagnosed as gastric smooth muscle tumors were GISTs, except for small groups of smooth muscle tumors and schwannomas.