Combinatorial Code Research Articles

Generic binding sites, generic DNA‐binding domains: where does specific promoter recognition come from?

A transcription reaction relies on the specific recognition of cis-regulatory regions containing short DNA motifs. Such sequences are bound by transcription factors (TFs) involved in the recruitment, direct or not, of the transcriptional machinery. A eukaryotic genome can contain tens of genes encoding TFs that recognize very similar consensus DNA target sequences. In this review, we explore in a simple way how TFs coexpressed in the same cells and recognizing generic consensus sites with generic DNA-binding domains can achieve a specific modulation of target gene expression. We dissect the strategy followed by eukaryotes, which involves the formation of complex nucleoprotein structures involving many TFs and their cognate binding sites. This multiplicity of actors increases the effective length of the target DNA recognized by the TFs and might help paralogous TFs establish specific interactions. From this perspective, eukaryotic gene regulation implies the cooperation of several TFs, which is also the basis of information integration. Such cooperative TFs are likely to form a combinatorial partner code whose ultimate molecular hallmark is the assembly of enhanceosome-like structures ensuring the formation of an activation surface that is complementary to other coactivators and to the transcriptional machinery itself.

Embryonic Development and Skeletogenesis of the Pharyngeal Jaw Apparatus in the Cichlid Nile Tilapia (Oreochromis niloticus)

The evolution of a specialized pharyngeal jaw apparatus (PJA) has been argued to be the key evolutionary innovation that allowed the explosive adaptive radiation of cichlid fishes in East African lakes. Subsequent studies together with recent molecular phylogenies have shown that similar innovations evolved independently several times within the teleosts, which poses the questions: (1) how similar are the developmental mechanisms responsible for these changes in divergent taxa and (2) how did such complex features arise independently in evolution? A detailed knowledge of PJA development in cichlids and other teleosts is needed to address these questions. Here, we provide a detailed account of the development of the PJA in one species of cichlid, the Nile tilapia (Oreochromis niloticus), from the early segmentation and patterning of its embryonic precursors - pharyngeal arches 3 to 7 - to its ossification. We find that pharyngeal segmentation occurs sequentially from anterior to posterior during early segmentation stages through the mid-pharyngula period. We show a clear combinatorial code of Hox gene expression such that each posterior arch is defined by a distinctive Hox signature. Posterior arch chondrogenesis in tilapia is essentially complete by the end of the hatching period, and most elements become ossified over the next two days. Our results reveal that both the fusion of lower jaw bones and articulation between the neurocranium and upper jaws occur during post-embryonic development.

Nonredundant Requirement for Multiple Histone Modifications for the Early Anaphase Release of the Mitotic Exit Regulator Cdc14 from Nucleolar Chromatin

In Saccharomyces cerevisiae, the conserved phosphatase Cdc14 is required for the exit from mitosis. It is anchored on nucleolar chromatin by the Cfi1/Net1 protein until early anaphase, at which time it is released into the nucleoplasm. Two poorly understood, redundant pathways promote Cdc14 release, the FEAR (Cdc fourteen early release) network and the MEN (mitotic exit network). Through the analysis of genetic interactions, we report here a novel requirement for the ubiquitination of histone H2B by the Bre1 ubiquitin ligase in the cell cycle–dependent release of Cdc14 from nucleolar chromatin when the MEN is inactivated. This function for H2B ubiquitination is mediated by its activation of histone H3 methylation on lysines 4 and 79 (meH3K4 and meH3K79) but, surprisingly, is not dependent on the histone deacetylase (HDAC) Sir2, which associates with Cdc14 on nucleolar chromatin as part of the RENT complex. We also observed a defect in Cdc14 release in cells lacking H3 lysine 36 methylation (meH3K36) and in cells lacking an HDAC recruited by this modification. These histone modifications represent previously unappreciated factors required for the accessibility to and/or action on nucleolar chromatin of FEAR network components. The nonredundant role for these modifications in this context contrasts with the notion of a highly combinatorial code by which histone marks act to control biological processes.

Selected commensal‐related bacteria and Toll‐like receptor 3 agonist combinatorial codes synergistically induce interleukin‐12 production by dendritic cells to trigger a T helper type 1 polarizing programme

Enteric infections remain a major health problem causing millions of deaths in developing countries. The interplay among the host intestinal epithelium, the mucosa-associated immune system and microbiota performs an essential role in gut homeostasis and protection against infectious diseases. Dendritic cells (DCs) play a key role in orchestrating protective immunity and tolerance in the gut. The mechanisms by which DCs adapt their responses and discriminate between virulent microbes and trillions of innocuous bacteria remain ill-defined. Here we investigated the effect of cross-talk between commensal-related bacteria (CB) and Toll-like receptor (TLR) agonists on DC activation and the outcome of the in vitro T helper response. Human monocyte-derived DCs were exposed to eight different Gram-positive or Gram-negative CB strains prior to activation with five different TLR agonists. The key polarizing cytokines interleukin (IL)-12p70, IL-10, IL-1beta and IL-6 were quantified and the fate of naïve T-cell differentiation was evaluated. We identified a unique combination of Lactobacillus casei and TLR3 signals that acted in synergy to selectively increase IL-12p70 secretion. Exposure to poly(I:C) converted L. casei-treated DCs into potent promoters of T helper type 1 (Th1) responses. We propose that DCs can integrate harmless and dangerous non-self signals delivered by viral products, to mount robust Th1 responses. Thus, in vivo DC targeting with selective probiotics may improve strategies for the management of enteric diseases.

Antagonistic SR proteins regulate alternative splicing of tumor-related Rac1b downstream of the PI3-kinase and Wnt pathways

The small GTPase Rac1 regulates signaling pathways controlling actin-dependent cell motility as well as gene transcription. An alternative splicing variant Rac1b is overexpressed in a subset of colorectal tumors and is required to sustain tumor cell viability. Thus, it is of therapeutic interest to understand the molecular mechanism behind the overexpression of Rac1b through alternative splicing. Here we describe that ASF/SF2 and SRp20 are two antagonistic splicing factors regulating Rac1b expression in colorectal tumor cells. Using an Rac1 minigene, we identified that SRp20 increased skipping of alternative exon 3b in HT29 colorectal cells, whereas ASF/SF2 increased its inclusion. The depletion of the endogenous expression of these splicing factors by specific small interfering RNA confirmed that ASF/SF2 acts as an enhancer of endogenous Rac1b splicing, whereas SRp20 acts as a silencer. Point mutations in exon 3b defined two adjacent regulatory regions required for skipping or inclusion of exon 3b, which are recognized in vitro by SRp20 and ASF/SF2, respectively. Both splicing factors were found to be regulated by upstream signaling pathways: the inhibition of the phosphatidylinositol 3-kinase pathway increased protein levels of ASF/SF2 and promoted Rac1b, whereas activation of beta-catenin/TCF4 increased expression of SRp20 and inhibited that of Rac1b. Together, these data reveal that signaling pathways act in concert to target independent splicing factors and achieve the correct combinatorial code to regulate alternative splicing of the small GTPase Rac1.

EIF4E: New Family Members, New Binding Partners, New Roles

Eukaryotic initiation factor 4E (eIF4E) has long been known as the cap-binding protein that participates in recruitment of mRNA to the ribosome. A number of recent advances have not only increased our understanding of how eIF4E acts in translation but also uncovered non-translational roles. New structures have been determined for eIF4E in complex with various ligands and for other cap-binding proteins. We have also learned that most eukaryotic organisms express multiple eIF4E family members, some involved in general translation but others having specialized functions, including repression of translation. A number of new eIF4E-binding proteins have been reported, some of which tether it to specific mRNAs.

Bmi-1 regulates the Ink4a/Arf locus to control pancreatic β-cell proliferation

The molecular mechanisms that regulate the age-induced increase of p16(INK4a) expression associated with decreased beta-cell proliferation and regeneration are not well understood. We report that in aged islets, derepression of the Ink4a/Arf locus is associated with decreased Bmi-1 binding, loss of H2A ubiquitylation, increased MLL1 recruitment, and a concomitant increase in H3K4 trimethylation. During beta-cell regeneration these histone modifications are reversed resulting in reduced p16(INK4a) expression and increased proliferation. We suggest that PcG and TrxG proteins impart a combinatorial code of histone modifications on the Ink4a/Arf locus to control beta-cell proliferation during aging and regeneration.

More restrictive Gray codes for some classes of pattern avoiding permutations

In a recent article [W.M.B. Dukes, M.F. Flanagan, T. Mansour, V. Vajnovszki, Combinatorial Gray codes for classes of pattern avoiding permutations, Theoret. Comput. Sci. 396 (2008) 35–49], Dukes, Flanagan, Mansour and Vajnovszki present Gray codes for several families of pattern avoiding permutations. In their Gray codes two consecutive objects differ in at most four or five positions, which is not optimal. In this paper, we present a unified construction in order to refine their results (or to find other Gray codes). In particular, we obtain more restrictive Gray codes for the two Wilf classes of Catalan permutations of length n; two consecutive objects differ in at most two or three positions which is optimal for n odd. Other refinements have been found for permutation sets enumerated by the numbers of Schröder, Pell, even index Fibonacci numbers and the central binomial coefficients. A general efficient generating algorithm is also given.

MicroRNA Gene Networks in Oncogenesis

MicroRNAs are small non-coding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. They are involved in cellular development, differentiation, proliferation and apoptosis and play a significant role in cancer. Examination of tumor-specific microRNA expression profiles has revealed widespread deregulation of these molecules in diverse cancers. Several studies have shown that microRNAs function either as tumor suppressor genes or oncogenes, whose loss or overexpression respectively has diagnostic and prognostic significance. It seems that microRNAs act as major regulators of gene expression. In this review, we discuss microRNAs’ role in cancer and how microRNAs exert their functions through regulation of their gene targets. Bioinformatic analysis of putative miRNA binding sites has indicated several novel potential gene targets involved in apoptosis, angiogenesis and metastatic mechanisms. Matching computational prediction analysis together with microarray data seems the best method for microRNA gene target identification. MicroRNAs together with transcription factors generate a complex combinatorial code regulating gene expression. Thus, manipulation of microRNA-transcription factor gene networks may be provides a novel approach for developing cancer therapies.

Heterogeneous Sensory Innervation and Extensive Intrabulbar Connections of Olfactory Necklace Glomeruli

The mammalian nose employs several olfactory subsystems to recognize and transduce diverse chemosensory stimuli. These subsystems differ in their anatomical position within the nasal cavity, their targets in the olfactory forebrain, and the transduction mechanisms they employ. Here we report that they can also differ in the strategies they use for stimulus coding. Necklace glomeruli are the sole main olfactory bulb (MOB) targets of an olfactory sensory neuron (OSN) subpopulation distinguished by its expression of the receptor guanylyl cyclase GC-D and the phosphodiesterase PDE2, and by its chemosensitivity to the natriuretic peptides uroguanylin and guanylin and the gas CO2. In stark contrast to the homogeneous sensory innervation of canonical MOB glomeruli from OSNs expressing the same odorant receptor (OR), we find that each necklace glomerulus of the mouse receives heterogeneous innervation from at least two distinct sensory neuron populations: one expressing GC-D and PDE2, the other expressing olfactory marker protein. In the main olfactory system it is thought that odor identity is encoded by a combinatorial strategy and represented in the MOB by a pattern of glomerular activation. This combinatorial coding scheme requires functionally homogeneous sensory inputs to individual glomeruli by OSNs expressing the same OR and displaying uniform stimulus selectivity; thus, activity in each glomerulus reflects the stimulation of a single OSN type. The heterogeneous sensory innervation of individual necklace glomeruli by multiple, functionally distinct, OSN subtypes precludes a similar combinatorial coding strategy in this olfactory subsystem.

On combinatorial Gray codes with distance 3

We suggest a construction of the cyclic binary combinatorial Gray codes with distance 3 and dimension n = 2k – 1, where k = 3, 4, . . . We give a method of construction of Hamiltonian cycles in the graphs of minimum distances of binary Hamming codes. For all admissible lengths n ≥ 15, we give nonlinear perfect binary codes whose graphs of minimum distances contain a Hamiltonian cycle.

Mapping of Class I and Class II Odorant Receptors to Glomerular Domains by Two Distinct Types of Olfactory Sensory Neurons in the Mouse

The repertoire of approximately 1200 odorant receptors (ORs) is mapped onto the array of approximately 1800 glomeruli in the mouse olfactory bulb (OB). The spatial organization of this array is influenced by the ORs. Here we show that glomerular mapping to broad domains in the dorsal OB is determined by two types of olfactory sensory neurons (OSNs), which reside in the dorsal olfactory epithelium. The OSN types express either class I or class II OR genes. Axons from the two OSN types segregate already within the olfactory nerve and form distinct domains of glomeruli in the OB. These class-specific anatomical domains correlate with known functional odorant response domains. However, axonal segregation and domain formation are not determined by the class of the expressed OR protein. Thus, the two OSN types are determinants of axonal wiring, operate at a higher level than ORs, and contribute to the functional organization of the glomerular array.

Effects of the Vector Combinatorial Codeconnection Parameters on the Performance of an OCDMA System for High-Speed Networks

In this paper, we study the performance of optical code-division multiple access (OCDMA) systems using vector combinatorial (VC) code under various link parameters. The impact of the fiber dispersion effects on the multi-user interference (MUI) is reported using a commercial optical systems simulator, Virtual Instrument Photonic (VPITM). The VC code is compared mathematically with other codes which use similar techniques. We analyzed and optimized the data rate, fiber length, and channel spacing in order to reduce the BER without the need to deploy dispersion compensating devices. The performance and optimization of VC code in OCDMA system is reported. We have demonstrated that, for a high data rate (higher than 2.5 Gb/s), even if dispersion compensated devices are not deployed, the BER can be significantly improved when the VC code desired parameters are selected. We have shown that when compensation dispersion devices are not deployed in the system, there is a tradeoff between the limited dispersion effects and the MUI.

Combinatorial batch codes

In this paper, we study batch codes, which wereintroduced by Ishai, Kushilevitz, Ostrovsky and Sahai in [4].A batch code specifies a method to distribute adatabase of $n$ items among $m$ devices (servers)in such a way that any $k$ itemscan be retrieved by reading at most $t$ items from each of the servers. It is of interest to devise batch codes thatminimize the total storage, denoted by $N$, over all $m$ servers.We restrict out attention to batch codesin which every server stores a subset ofthe items. This is purely a combinatorial problem, sowe call this kind of batch code a ''combinatorial batch code''.We only study the special case $t=1$, where,for various parameter situations, we are able to presentbatch codes that are optimal with respect to the storagerequirement, $N$. We also study uniform codes, where every item isstored in precisely $c$ of the $m$ servers (such a codeis said to have rate $1/c$). Interesting new resultsare presented in the cases $c = 2, k-2$ and $k-1$. In addition,we obtain improved existence results for arbitraryfixed $c$ using the probabilistic method.

Spectral Amplitude Coding OCDMA: Performance Analysis on Detection Schemes using Vectors Combinatorial Code Families

Article Spectral Amplitude Coding OCDMA: Performance Analysis on Detection Schemes using Vectors Combinatorial Code Families was published on December 1, 2009 in the journal Journal of Optical Communications (volume 30, issue 4).

The Neural Basis for Combinatorial Coding in a Cortical Population Response

We have used a combination of theory and experiment to assess how information is represented in a realistic cortical population response, examining how motion direction and timing is encoded in groups of neurons in cortical area MT. Combining data from several single-unit experiments, we constructed model population responses in small time windows and represented the response in each window as a binary vector of 1s or 0s signifying spikes or no spikes from each cell. We found that patterns of spikes and silence across a population of nominally redundant neurons can carry up to twice as much information about visual motion than does population spike count, even when the neurons respond independently to their sensory inputs. This extra information arises by virtue of the broad diversity of firing rate dynamics found in even very similarly tuned groups of MT neurons. Additionally, specific patterns of spiking and silence can carry more information than the sum of their parts (synergy), opening up the possibility for combinatorial coding in cortex. These results also held for populations in which we imposed levels of nonindependence (correlation) comparable to those found in cortical recordings. Our findings suggest that combinatorial codes are advantageous for representing stimulus information on short time scales, even when neurons have no complicated, stimulus-dependent correlation structure.

Matching Categorical Object Representations in Inferior Temporal Cortex of Man and Monkey

Inferior temporal (IT) object representations have been intensively studied in monkeys and humans, but representations of the same particular objects have never been compared between the species. Moreover, IT's role in categorization is not well understood. Here, we presented monkeys and humans with the same images of real-world objects and measured the IT response pattern elicited by each image. In order to relate the representations between the species and to computational models, we compare response-pattern dissimilarity matrices. IT response patterns form category clusters, which match between man and monkey. The clusters correspond to animate and inanimate objects; within the animate objects, faces and bodies form subclusters. Within each category, IT distinguishes individual exemplars, and the within-category exemplar similarities also match between the species. Our findings suggest that primate IT across species may host a common code, which combines a categorical and a continuous representation of objects.

SNP-Based Genome-Wide Identification of Hematopoiesis-Restricted Minor Histocompatibility Antigens

T-cell recognition of minor histocompatibility antigens (mHag) plays an important role in the graft-versus-tumor (GVT) effect of allogeneic stem cell transplantation (allo-SCT). However, mHag recognition is also associated with graft-versus-host disease (GVHD). It is assumed that the selective infusion of T cells reactive with hematopoiesis-restricted mHag may help to separate the GVT and GVHD effects of allo-SCT. However, the number of attractive mHag identified to date remains limited. In this study we aimed to determine whether it is feasible to perform genome-wide identification of hematopoiesis-restricted minor histocompatibility antigens. Successful development of such a technology could allow the rapid identification of sets of hematopoiesis-restricted minor histocompatibility antigens required to make antigen-selective adoptive T cell therapy a realistic option. To this purpose we performed microarray analyses of hematopoietic progenitor and non-hematopoietic restricted cell types and merged our data with a microarray database to select approximately 80 genes with a hematopoiesis-restricted gene expression pattern. Subsequently, 322 single nucleotide polymorphism (SNPs) were identified in this set of genes and HLA-A2 binding peptides were predicted in both the normal and alternative reading frames using four different HLA-binding algorithms. The resulting set of 1300 putative HLA-A2 ligands was synthesized and tested for binding affinity using a MHC-peptide exchange technology based on UV-sensitive conditional ligands. Binding affinity was determined based on the ability of the peptides to induce MHC-complex recovery after photo cleavage of the conditional ligand. Based on these affinity measurements 400 high- to medium affinity HLA-A2 binding peptides were selected and used to generate tetramers by MHC-ligand exchange. To enable screening with this vast number of tetramers we developed a combinatorial coding method that allows the detection of up to 25 different T-cell populations in one sample. Furthermore, to overcome the problem of limited availability of patient PBMC and low-frequent T cell responses we performed an in vitro T-cell enrichment and expansion step. In this method tetramer positive lymphocytes are isolated with magnetic cell separation columns and cultured in presence of cytokines, feeders and anti-CD3/28 coated beads. Using this technological platform, we have begun to analyze hematopoiesis-restricted mHag responses in transplant recipients with different hematologic malignancies. This screen confirmed the existence of a known hematopoiesis-restricted mHag response and suggested the presence of a number of novel hematopoiesis-restricted mHag responses. Our data indicate that the technology developed within this project is likely to be of value to the identification of collections of novel minor histocompatibility antigens with potential clinical value.

A Combinatorial Code for Pattern Formation in Drosophila Oogenesis

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Neuromancer1 and Neuromancer2 regulate cell fate specification in the developing embryonic CNS of Drosophila melanogaster

T-box genes encode a large family of transcription factors that regulate many developmental processes in vertebrates and invertebrates. In addition to their roles in regulating embryonic heart and epidermal development in Drosophila, we provide evidence that the T-box transcription factors neuromancer1 (nmr1) and neuromancer2 (nmr2) play key roles in embryonic CNS development. We verify that nmr1 and nmr2 function in a partially redundant manner to regulate neuronal cell fate by inhibiting even-skipped (eve) expression in specific cells in the CNS. Consistent with their redundant function, nmr1 and nmr2 exhibit overlapping yet distinct protein expression profiles within the CNS. Of note, nmr2 transcript and protein are expressed in identical patterns of segment polarity stripes, defined sets of neuroblasts, many ganglion mother cells and discrete populations of neurons. However, while we observe nmr1 transcripts in segment polarity stripes and specific neural precursors in early stages of CNS development, we first detect Nmr1 protein in later stages of CNS development where it is restricted to discrete subsets of Nmr2-positive neurons. Expression studies identify nearly all Nmr1/2 co-expressing neurons as interneurons, while a single Eve-positive U/CQ motor neuron weakly co-expresses Nmr2. Lineage studies map a subset of Nmr1/2-positive neurons to neuroblast lineages 2–2, 6–1, and 6–2 while genetic studies reveal that nmr2 collaborates with nkx6 to regulate eve expression in the CNS. Thus, nmr1 and nmr2 appear to act together as members of the combinatorial code of transcription factors that govern neuronal subtype identity in the CNS.