proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms

The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition

Epigenetics plays an important role in the priming the dynamic response of airway epithelial cells to infectious and environmental stressors. Here, we examine the epigenetic role of the SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) in the epithelial response to RSV infection. Depletion of SMARCA4 destabilized the abundance of the SMARCE1/ARID1A SWI/SNF subunits, disrupting the innate response and triggering a hybrid epithelial/mesenchymal (E/M) state. Assaying SMARCA4 complex-regulated open chromatin domains by transposase cleavage -next generation sequencing (ATAC-Seq), we observed that the majority of cleavage sites in uninfected cells have reduced chromatin accessibility. Paradoxically, SMARCA4 complex-depleted cells showed enhanced RSV-inducible chromatin opening and gene expression in the EMT pathway genes, MMP9, SNAI1/2, VIM, and CDH2. Focusing on the key MMP9, we observed that SMARCA4 complex depletion reduced basal BRD4 and RNA Polymerase II binding, but enhanced BRD4/Pol II binding in response to RSV infection. In addition, we observed that MMP9 secretion in SMARCA4 complex deficient cells contributes to mesenchymal transition, cellular fusion (syncytia) and subepithelial myofibroblast transition. We conclude the SMARCA4 complex is a transcriptional repressor of epithelial plasticity, whose depletion triggers a hybrid E/M state that affects the dynamic response of the small airway epithelial cell in mucosal remodeling via paracrine MMP9 activity.

Further evidence supporting the Diff-Quik stain for sperm chromatin integrity testing

OBJECTIVE

To correlate intracytoplasmic sperm injection (ICSI) fertilization with chromatin status assessed by the Diff-Quik procedure modified with a one-minute soak step, and to determine the association of chromatin status with in vitro fertilization (IVF) pregnancy.

STUDY DESIGN

This was a retrospective study of 81 IVF patients. Gradient-centrifuge washed sperm remaining after ICSI were fixed, stained by Diff-Quik, immersed in water for 1 minute, and analyzed under oil immersion light microscopy. Sperm nuclear coloration (types A-D), strict morphology, fertilization, and pregnancy status were determined.

RESULTS

Sperm with light purple staining (type A) were correlated (R = 0.48, p < 0.05) with ICSI fertilization. The intraassay and interassay coefficients of variation were 5.9% and 4.1%, respectively. Sperm strict normal morphology was correlated neither with ICSI fertilization (R = 0.24, p > 0.05) nor with type A sperm (R = 0.35, p > 0.05). Sperm incubated in Fenton reagent that damaged DNA showed a time-dependent decrease in percent type A sperm. However, there was no correlation with IVF pregnancy status.

CONCLUSION

This retrospective study showed that the inclusion of a one-minute soak step post-Diff-Quik staining enhanced the detection of sperm chromatin abnormalities related to ICSI fertilization. Fenton reagent-treated sperm suggested that the staining patterns correlated with DNA damage. A large prospective trial should be undertaken to confirm these findings.

Identifying different types of chromatin using Giemsa staining

Mixtures of polychrome methylene blue-eosin Y (i.e., Giemsa stain) are widely used in biological staining. They induce a striking purple coloration of chromatin DNA (the Romanowsky-Giemsa effect), which contrasts with the blue-stained RNA-containing cytoplasm and nucleoli. After specific prestaining treatments that induce chromatin disorganization (giving banded or harlequin chromosomes), Giemsa staining produces a differential coloration, with C- and G-bands appearing in purple whereas remaining chromosome regions are blue. Unsubstituted (TT) and bromo-substituted (BT) DNAs also appear purple and blue, respectively. The same occurs in the case of BT and BB chromatids.In addition to discussing the use of Giemsa stain as a suitable method to reveal specific features of chromosome structure, some molecular processes and models are also described to explain Giemsa staining mechanisms of chromatin.

A decision support system to detect morphologic changes of chromatin arrangement in normal-appearing cells

Several studies have described malignancy-associated changes (MACs) of chromatin arrangement in the nuclei of apparently normal cells adjacent to and distant from an invasive cancer area. MAC assessment is a hard task, since it requires a deep knowledge of morphologic features of chromatin arrangement. The aim of this work is to verify the reproducibility of the subjective evaluation of the expert on the basis of a decision support system (DSS) that automatically and objectively reproduces MAC diagnosis. A set of 61 patients with suspected clinical diagnosis for lung cancer has been taken into account. The scientist who first described MAC defined each patient as MAC positive or negative on the basis of the MAC diagnosis performed on all cells of the related cytologic sample. A DSS based on an artificial neural network has been set up to learn the relation between 14 morphometric and texture parameters, computed on each nucleus by image processing techniques, with the MAC diagnosis of the expert on each cell. The results show that an objective automatic assessment on MAC by the DSS can effectively support the MAC diagnosis. The method adopted in this approach may be also appropriate for other problems, where an automatic classification of visually inspected patterns of biological micro- and submicrostructure is needed.

Chromatin acetylation, memory, and LTP are impaired in CBP+/- mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration

We studied a mouse model of the haploinsufficiency form of Rubinstein-Taybi syndrome (RTS), an inheritable disorder caused by mutations in the gene encoding the CREB binding protein (CBP) and characterized by mental retardation and skeletal abnormalities. In these mice, chromatin acetylation, some forms of long-term memory, and the late phase of hippocampal long-term potentiation (L-LTP) were impaired. We ameliorated the L-LTP deficit in two ways: (1) by enhancing the expression of CREB-dependent genes, and (2) by inhibiting histone deacetyltransferase activity (HDAC), the molecular counterpart of the histone acetylation function of CBP. Inhibition of HDAC also reversed the memory defect observed in fear conditioning. These findings suggest that some of the cognitive and physiological deficits observed on RTS are not simply due to the reduction of CBP during development but may also result from the continued requirement throughout life for both the CREB co-activation and the histone acetylation function of CBP.

Chromatin remodeling in plants

In the past two years, a variety of forward genetic screens have revealed predicted plant chromatin remodeling components that are involved in either differential histone acetylation or ATP-dependent SWI2/SNF2-related complexes. Combined with the results of recent reverse genetic studies, these findings have begun to provide the groundwork for determining the function of chromatin-based control in plants.

Higher-order structure of chromatin and chromosomes

The linear array of nucleosomes that comprises the primary structure of chromatin is folded and condensed to varying degrees in nuclei and chromosomes forming 'higher order structures'. We discuss the recent findings from novel experimental approaches that have yielded significant new information on the different hierarchical levels of chromatin folding and their functional significance.

Image analysis of mesothelioma. I. differentiation of mesothelioma from adenocarcinoma of the lung

OBJECTIVE

To explore the usefulness of nuclear micromorphometric analysis for the differentiation between epithelial mesothelioma and metastatic adenocarcinoma in the chest wall.

STUDY DESIGN

High-resolution images of 2,100 nuclei from 27 cases of epithelial mesothelioma and 15 cases of adenocarcinoma of the lung were recorded. Stepwise discriminant analysis and a nonparametric classifier were applied to derive estimates for a case diagnosis correct classification rate.

RESULTS

Nuclei from epithelial mesothelioma and adenocarcinoma of the lung showed statistically significantly different properties, but there was a region of overlap in feature space such that approximately 15-20% of cases could not be correctly classified. The lesion signatures derived from the mesothelioma cases with discriminant function scores that might result in case misclassification and the cases of adenocarcinoma of the lung spanned a similar range of degree of nuclear abnormality. However, the distribution of nuclear abnormality values for the mesothelioma cases has a mode at 0.87 SD from normal, whereas the distribution seen in lung adenocarcinoma cases had a mode at about 3.7 SD.

CONCLUSION

Cases of epithelial mesothelioma and adenocarcinoma of the lung have nuclei with a wide range of deviation from normal in the spatial and statistical distribution of their nuclear chromatin. For approximately 80% of cases, correct case classification can be provided by nuclear micromorphometric analysis. Cases of epithelial mesothelioma with highly abnormal nuclei overlap in feature space with nuclei from adenocarcinoma of the lung. However, it is possible that characterization by a lesion signature may allow correct assignment for those cases.

The use of fractal features from the periphery of cell nuclei as a classification tool

A polygonization-based method is used to estimate the fractal dimension and several new scalar lacunarity features from digitized transmission electron micrographs (TEM) of mouse liver cell nuclei. The fractal features have been estimated in different segments of 1D curves obtained by scanning the 2D cell nuclei in a spiral-like fashion called "peel-off scanning". This is a venue to separate estimates of fractal features in the center and periphery of a cell nucleus. Our aim was to see if a small set of fractal features could discriminate between samples from normal liver, hyperplastic nodules and hepatocellular carcinomas. The Bhattacharyya distance was used to evaluate the features. Bayesian classification with pooled co-variance matrix and equal prior probabilities was used as the rule for classification. Several single fractal features estimated from the periphery of the cell nuclei discriminated samples from the hyperplastic nodules and hepatocellular carcinomas from normal ones. The outer 25-30% of the cell nuclei contained important texture information about the differences between the classes. The polygonization-based method was also used as an analysis tool to relate the differences between the classes to differences in the chromatin structure.

Two types of telomeric chromatin in Tetrahymena thermophila

The telomeric d(GGGGTT).d(AACCCC) repeat tracts (G4T2 repeats) in Tetrahymena thermophila macronuclei were shown previously to be packaged in a non-nucleosomal DNA-protein complex. Here, we demonstrate that these telomeric repeats, together with a short region of the immediately adjacent non-telomeric sequence, exist in two distinct types of chromatin. The non-nucleosomal complex (type I complex) comprises approximately 90 to 97% of telomeric DNA, has no apparent underlying periodic nucleosomal substructure, and includes the whole telomeric tract as well as the immediately adjacent sequence. Type II chromatin, comprising the remaining approximately 3 to 10% of the total telomeric DNA, consists of tightly packed nucleosomes clustered at the inner border of the telomeric tracts, with a periodicity of 154(+/-3) bp. This packing is similar to that of telomeric nucleosomes in vertebrates. However, in contrast to the unstability of vertebrate telomeric mononucleosomes, the T. thermophila mononucleosomes were stable to micrococcal nuclease digestion. During the natural lengthening of the T. thermophila telomeric DNA tracts that occurs in vegetatively dividing cells, the overall ratio of type I and type II chromatin did not change. However, type I complex expanded with the length of the telomeric DNA repeat tract, and the number of telomeric nucleosomes increased from an average of one, up to three to four, per telomeric tract. This finding of telomeric nucleosomes in T. thermophila suggests that the difference between vertebrates and lower eukaryotes in telomeric chromatin structure is quantitative rather than qualitative. We propose that deposition of nucleosomes competes with non-nucleosomal complex formation on telomeric DNA, resulting in a sub-population of chimeric telomeres containing inner nucleosomes abutting a distal, variable length of type I complex.

[Classification of condensed structures of chromatin in interphase nuclei]

A new classification of condensed structures is suggested based on the analysis of modern data and ideas of the structure and functional transformations of chromosomes in cells of eucaryotes for the cellular cycle under conditions of individual and historical development.

Isopycnic centrifugation of sheared L-cell chromatin in metrizamide gradients

Isopycnic gradient centrifugation of L-929 cell chromatin in a 38% (W/V) metrizamide solution yields two distinct fractions. The fraction banding at a density of 1.24 gm/cm(2) (H chromatin) contains about 10% of the DNA present in the fraction banding at a density of 1.18 gm/cm(2) (L chromatin). Both fractions contain the same proportions of satellite to main band DNA's. Some differences can be seen in the DNA: protein ratios and types of proteins present in the H and L chromatin fractions.