Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

BACKGROUND

CUT&RUN is an efficient epigenome profiling method that identifies sites of DNA binding protein enrichment genome-wide with high signal to noise and low sequencing requirements. Currently, the analysis of CUT&RUN data is complicated by its exceptionally low background, which renders programs designed for analysis of ChIP-seq data vulnerable to oversensitivity in identifying sites of protein binding.

RESULTS

Here we introduce Sparse Enrichment Analysis for CUT&RUN (SEACR), an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling. SEACR discriminates between true and false-positive peaks with near-perfect specificity from "gold standard" CUT&RUN datasets and efficiently identifies enriched regions for several different protein targets. We also introduce a web server ( http://seacr.fredhutch.org ) for plug-and-play analysis with SEACR that facilitates maximum accessibility across users of all skill levels.

CONCLUSIONS

SEACR is a highly selective peak caller that definitively validates the accuracy of CUT&RUN for datasets with known true negatives. Its ease of use and performance in comparison with existing peak calling strategies make it an ideal choice for analyzing CUT&RUN data.

Parallel evolution of transcriptome architecture during genome reorganization

Assembly of genes into operons is generally viewed as an important process during the continual adaptation of microbes to changing environmental challenges. However, the genome reorganization events that drive this process are also the roots of instability for existing operons. We have determined that there exists a statistically significant trend that correlates the proportion of genes encoded in operons in archaea to their phylogenetic lineage. We have further characterized how microbes deal with operon instability by mapping and comparing transcriptome architectures of four phylogenetically diverse extremophiles that span the range of operon stabilities observed across archaeal lineages: a photoheterotrophic halophile (Halobacterium salinarum NRC-1), a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and an anaerobic hyperthermophile (Pyrococcus furiosus DSM 3638). We demonstrate how the evolution of transcriptional elements (promoters and terminators) generates new operons, restores the coordinated regulation of translocated, inverted, and newly acquired genes, and introduces completely novel regulation for even some of the most conserved operonic genes such as those encoding subunits of the ribosome. The inverse correlation (r=-0.92) between the proportion of operons with such internally located transcriptional elements and the fraction of conserved operons in each of the four archaea reveals an unprecedented view into varying stages of operon evolution. Importantly, our integrated analysis has revealed that organisms adapted to higher growth temperatures have lower tolerance for genome reorganization events that disrupt operon structures.

GTC: A web server for integrating systems biology data with web tools and desktop applications

Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using many popular web-based and desktop applications.

Integration and visualization of systems biology data in context of the genome

Background

High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment.

Results

The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data.

A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome.

Conclusions

Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Prevalence of group A rotavirus, human calicivirus, astrovirus, and adenovirus type 40 and 41 infections among children with acute gastroenteritis in Dijon, France

Group A rotaviruses, human caliciviruses, astroviruses, and adenovirus types 40 and 41 were detected by enzyme immunoassay or reverse transcription-PCR in 61, 14, 6, and 3% of stool specimens from 414 children consulting for gastroenteritis between 1995 and 1998. These data highlight the importance of caliciviruses in infantile gastroenteritis. Among these, Norwalk-like viruses belonging to genogroup II were predominant.

[Neurophysiological study of peripheral nerves in newborn infants with congenital hypothyroidism. Value in the surveillance of replacement therapy]

The authors studied prospectively with electrophysiological means, peripheral nerve maturation of 18 neonates with congenital hypothyroidism compared to 18 controls. Before replacement therapy, a large reduction of sural nerve action potential amplitude and of Hoffmann's reflex was observed. It was accompanied by a moderate reduction in nerve conduction velocity. These results imply a myelinic and even more an axonal pathology. It is related to the anatomical type of hypothyroidism and to serum T4 deficiency. It is transient and disappears after 6 months of hormonal replacement therapy. In conclusion, this study gives new informations on the consequences of congenital hypothyroidism on peripheral nerves.

Alterations of serum high-density lipoproteins and hepatic lipase activity in congenital hypothyroidism

Fourteen term newborns and infants with congenital hypothyroidism were studied before (T0) and after (T1) 1 month of replacement therapy. From T0 to T1 serum total cholesterol and high-density-lipoprotein cholesterol remained constant and at normal levels whereas low-density-lipoprotein apolipoprotein B and triacyglycerol concentrations increased slightly. The proportion of large-size high-density-lipoprotein subfraction was high at T0 and decreased very significantly at T1. Conversely, postheparin serum hepatic lipase activity was low before treatment and increased after thyroxine therapy. Lipoprotein lipase activity remained low throughout the study. These results suggest that, in contrast to adult hypothyroidism, low-density-lipoprotein catabolism is not altered in congenital hypothyroidism. However, as in adults, a defect of lipolytic enzyme activities is present and can induce an impairment of the elimination of cholesterol via the high-density-lipoprotein route and, potentially, of the catabolism of triglyceride-rich lipoproteins. Beyond the scope of congenital hypothyroidism, one should keep in mind these results when attending infants with transient low thyroid hormone levels and lipid intolerance.

[Treatment of citrullinemia. Apropos of a case followed from birth. Importance of alpha-ketonic acids]

From day 1 to day 3, the protein intake of this neonate was restricted to 1 g/kg/d. It included a) essential amino acids (i.e. histidine, lysine, threonine, tryptophan), b) arginine (1,000 mg/d), c) alphaketoisovaleric 500 mg/d, alpha-ketoisocaproic (500 mg/d), alphaketobetamethylvaleric (500 mg/d), alphaketogammamethylthiobutyric (200 mg/d), betaphenylpyruvic (400 mg/d) acids. 250 mg/kg/d of sodium benzoate were given. Caloric and water intakes were 120 cal/kg/d and 120 ml/kg/d respectively. Afterwards, this procedure was modified according to clinical and biological data including serum ammonia and amino acid levels. Alpha-ketonic acid absorption and metabolism were studied on day 29. Both were fast. The detection of alloisoleucine, which is not metabolized was the consequence of the use of alphaketobetamethylvaleric acid. Until the age of 21 months, clinical and metabolic status was satisfactory. At this time, repeated seizures without metabolic failure were accompanied by psychomotor damages.

Hepatic response to insulin in control of glucose kinetics in the neonatal lamb

Imprecise control of neonatal glucose homeostasis may be partially due to decreased hepatic response to insulin. In prior kinetic studies the effect of that response could not be determined because the hormonal effects of insulin could not be separated from those of glucagon. Somatostatin (SRIF) suppresses secretion of both and has been used to differentiate the hormonal effects. Eighteen term lambs (age 4.2 +/- 0.3 days and birth weight 4.0 +/- 0.2 kg (M +/- SEM] were infused with 0.9% NaCl at 0.06 mL.kg-1 min-1 plus 100 microCi/kg D[6-3H] glucose by prime plus constant infusion. Ra (production) and Rd (utilization) were measured during infusion of SRIF or SRIF plus replacement insulin (0.2 mU.kg-1 min-1). There was a rise in pl. glucose (98 +/- 10 to 119 +/- 10 mg/dL (P less than .0001)); a fall (46.2%) in pl insulin [13 +/- 2 to 7 +/- 1 microU/mL (P less than .0004); a rise in Ra (7.8 +/- 1.5 to 13.2 +/- 4.1 mg.kg-1 min-1 P less than .047); and a rise in Rd (7.7 +/- 1.4 to 11.3 +/- 3.0 mg.kg-1 min-1 (P less than .047)) in SRIF treated animals compared to nontreated controls. There was no change in plasma glucagon (454 +/- 182 to 255 +/- 141 pg/mL) in SRIF treated animals compared to nontreated controls. All perturbations were eliminated when SRIF plus replacement insulin produced control insulin levels. Insulin suppression in the neonatal period resulted in glucagon being unopposed which produced an elevated rate of glucose production and elevated plasma glucose concentration.

[An XX male newborn infant. A genetic and endocrinologic study]

The second child of a non consanguineous couple had a male phenotype with two intrascrotal testes of normal size however a scrotum bifidum was noted. The karyotype of the child was 46 XX and the parents one's was normal. No Y specific sequence was detected by using four Y specific probes (47 B, 12 F3, 52 D and 118). During the first semester of life, hormonal investigations showed a normal testicular function.

[Second prenatal diagnosis in a familial form of male pseudohermaphroditism caused by 17 keto-reductase deficiency: prediction confirmed by a normal third male infant]

In the first child of this family, the diagnosis of male pseudo-hermaphroditism due to 17 keto-reductase deficiency was established at two months of age after HCG test. During the second pregnancy, amniocentesis was performed for fetal karyotype and steroid determination in the amniotic fluid: an affected male fetus was suspected and this prediction was confirmed at birth. For the third pregnancy, a prenatal diagnosis was requested again and made, according to the same procedure: a normal male fetus was predicted and this diagnosis was confirmed at birth; this study demonstrates the feasibility and reliability of a prenatal diagnosis for 17 keto-reductase deficiency.

[Treatment of neonatal hypothyroidism. Comparative effects of levothyroxine and thyroid extracts]

The authors compare the effects of treatment with thyroid extracts and levothyroxine on T3, T4 and TSH levels in 2 groups of 8 hypothyroid infants. Serum TSH levels were lower in infants receiving thyroid extracts on and after the 15th day. The interest of a treatment associating T4 and T3 and of adapted doses of LT4 is discussed.

[Post-crisis elevation of adrenocorticotropic hormone and prolactin in epileptic children]

In six children, aged from 8 to 12 years, presenting with primary generalized epilepsy a significant rise in plasma ACTH and prolactin levels (as compared with levels measured 5 days later) was observed either during a generalized seizure demonstrated by EEG (3 cases) or within 1 hour of a generalized seizure (3 cases). The neurophysiological basis for these post-epileptic endocrine disturbances is a sudden depression of dopaminergic and GABA-ergic pathways. As a result, these endocrine changes, already well documented in adults, may be regarded as a good biological marker of the epileptic origin of a paroxysmal attack.

Comparison of morphologic features and mitotic rate to cytometrically determined DNA content of poorly differentiated lymphocytic lymphomas

A direct correlation between the percentage of cells in S phase of the cell cycle and the clinical behavior of lymphocytic lymphomas of low, intermediate, and high grade malignancy has been described. The histopathologist has used the mitotic rate and other morphologic criteria such as size of cells and nuclear characteristics as predictors/indicators of the aggressiveness of a tumor. We compared the S phase values of 22 cases of poorly differentiated lymphocytic lymphoma (PDL) of the B cell type, using flow cytometric measurement of DNA content, to morphologic features and mitotic rate (MR). The 22 cases were divided into 3 histologic groups: nodular PDL composed of small, cleaved lymphocytes (11 cases); follicular mantle zone lymphoma and those of intermediate differentiation (6 cases); and "blastic" PDL (5 cases). In Group 1 there was excellent correlation of MR, percentage of cells in S phase, and proportion of large cells (transformed lymphocytes) per high power field (HPF). In Group 2, this correlation was not found between MR and percentage of cells in S phase in five of the six cases. The high S phase in this group did correlate with the large proportion of large cells found primarily in pseudofollicular proliferation centers and in remnants of true follicular centers. These cells may have a prolonged S phase and thus fewer mitoses were seen. In Group 3, although both MR and S phases were high, a direct correlation between them as noted in the Group 1 cases was not seen, but an excellent correlation of the high S phase and the number of blasts was present. The fact that three of the five patients in this group died rapidly (within less than 2 years of presentation) and the two survivors were experiencing rapid progression of disease, supports the concept that this group represents a clearly different, more aggressive subclass of PDL.

[Gestational bone age of newborn infants]

A method for bone age calculation for neonates is reported. Criteria for maturation and growth are separately analysed. The chosen X ray charts were thorax including mandibula and profile of the right leg. 126 neonates 28 to 41 weeks of gestational age were studied. A linear regression is given. An area of confidence for growth and maturation for each gestational age has been designed. When gestational age is known, it gives the opportunity to appreciate the impact of a given pathology on these 2 data.

Mechanisms of beta sympathomimetic action on neonatal glucose homeostasis in the lamb

Beta sympathomimetic drugs are used clinically to inhibit premature labor. Significant alterations in glucose homeostasis have been documented in both mother and offspring. To determine the mechanism(s) of beta sympathomimetic drugs on neonatal glucose homeostasis, ritodrine hydrochloride was infused in a newborn term lamb model of glucose kinetics by a crossover design. There was a progressive rise in plasma glucose concentration and plasma insulin concentration during ritodrine hydrochloride infusion compared with the control (saline) infusion. The rise in plasma glucose concentration was associated with a progressive rise in Ra (rate of appearance, production) and Rd (rate of disappearance, utilization). The ritodrine hydrochloride-infused animals had a progressive rise in [insulin/glucose] compared with our prior studies in the newborn lamb, suggesting direct stimulation of pancreatic beta cell secretion. In the neonatal lamb, beta sympathomimetic drugs directly stimulate both hepatic glucose production and pancreatic beta cell secretion. These effects explain, in part, why infants of mothers infused with ritodrine hydrochloride may evidence alterations in neonatal glucose homeostasis.

[Prenatal diagnosis in a familial form of male pseudohermaphroditism due to 17-keto reductase deficiency]

In an infant considered at birth as a female but with easily palpable gonads in the labia major, the XY karyotype and the endocrine studies (determination of plasma levels of steroid hormones under basal conditions and during hCG stimulation) were consistent with the diagnosis of male pseudohermaphroditism due to 17-keto reductase deficiency. During the second pregnancy an amniocentesis revealed a 46 XY karyotype. Endocrine studies performed on the amniotic fluid at midgestation suggested that the fetus was affected by the same enzyme defect. After birth, the diagnosis was demonstrated with anatomical an endocrine studies.

[Posthemorrhage porencephalic cysts in the neonatal period. Diagnosis. Etiology. Development. Value of transfontanellar echography]

Cerebral echotomography interest in showing neonatal cerebral hemorrhage and their follow up toward porencephaly is pointed out in 4 neonates. The authors recall the electroencephalographic features which can lead to the diagnosis. Then, they insist upon a new concept which is the long delay between onset of the cyst and onset of hemiplegia. The rationnal for this concept is the gradual maturation of the pyramidal tracts in infancy.

[Transfontanellar echography in the early detection of traumatic subdural hematoma in the infant. Apropos of a case]

About one case of skull injury in a infant, brain ultrasonography potency is underlined. This technic allowed to diagnose a subdural hematoma which was inapparent clinically and by complementary investigations.

[Enlarging fractures of skull bones. Apropos of 2 cases]

The authors report two cases of children, who had a severe head injury with large skull fracture. If neurological evolution was good, on the other hand, skull fracture went on to develop, to give a bone defect with a leptomeningeal cyst of arachnoidal origin, as it is pointed out by the classical authors. The authors insist upon the specificity of this entity in childhood, and upon the necessity to observe by repeated clinical and radiological examinations any young child who have a large skull fracture.

Natural killer and suppressor T-cell chronic lymphocytic leukemia

A patient with low-grade lymphocytosis, splenomegaly, and neutropenia, but adequate myeloid leukogenesis, was found to have chronic lymphocytic leukemia, which represented a clonal proliferation of a distinct T-lymphocyte subset. The lymphocytes did not form E rosettes but had an OKT3+, OKT4+, OKT6+, OKT8+, OKT11+, HNK-1+, HNK-36+, OKIa1+, OKM1+ phenotype and functionally had suppressor and natural killer activity. Morphologically, they were large granular lymphocytes, which were strongly acid phosphatase positive and nonspecific esterase negative. They did not respond to mitogens, or to allogeneic cells. Initially, the spleen appeared to be the most involved organ and, judging from the high proportion of leukemic splenic lymphocytes in the S and G2/M phases of the cell cycle, was also the organ of origin of the leukemic cells. Only a few leukemic cells in the blood and bone marrow were in S and G2/M phases. After splenectomy, the lymphocyte count rose considerably and the bone marrow became progressively more infiltrated by tumor nodules. One year after diagnosis, the patient was started on chemotherapy because of progressive anemia. He responded to the chemotherapy by normalization of the hemoglobin and neutrophil count and had a moderate decrease in the bone marrow involvement and peripheral lymphocytosis.

[Intra-uterine gestational age. The value of calcification of dental crowns (author's transl)]

Calcification in the first decidual molar tooth first appears at the 33-34th week of gestation; and the second at the 36-37th week. It is therefore a stable and precise index of gestational age. It can be estimated in over two-thirds of films of the intra-uterine contents chosen at random. The search for this sign can complement or take the place of looking for epiphyseal centres in the knee. It gives information about gestational age in pathological conditions where bony maturation is abnormal.