AMD, an automated motif discovery tool using stepwise refinement of gapped consensuses

Characterization of gene expression in the kidney of renal tubular cell-specific NFAT5 knockout mice

Nuclear factor of activated T cells 5 (NFAT5; also called TonEBP/OREBP) is a transcription factor that is activated by hypertonicity and induces osmoprotective genes to protect cells against hypertonic conditions. In the kidney, renal tubular NFAT5 is known to be involved in the urine concentration mechanism. Previous studies have suggested that NFAT5 modulates the immune system and exerts various effects on organ damage, depending on organ and disease states. Pathophysiological roles of NFAT5 in renal tubular cells, however, still remain obscure. We conducted comprehensive analysis by performing transcription start site (TSS) sequencing on the kidney of inducible and renal tubular cell-specific NFAT5 knockout (KO) mice. Mice were subjected to unilateral ureteral obstruction to examine the relevance of renal tubular NFAT5 in renal fibrosis. TSS sequencing analysis identified 722 downregulated TSSs and 1,360 upregulated TSSs, which were differentially regulated ≤-1.0 and ≥1.0 in log2 fold, respectively. Those TSSs were annotated to 532 downregulated genes and 944 upregulated genes, respectively. Motif analysis showed that sequences that possibly bind to NFAT5 were enriched in TSSs of downregulated genes. Gene Ontology analysis with the upregulated genes suggested disorder of innate and adaptive immune systems in the kidney. Unilateral ureteral obstruction significantly exacerbated renal fibrosis in the renal medulla in KO mice compared with wild-type mice, accompanied by enhanced activation of immune responses. In conclusion, NFAT5 in renal tubules could have pathophysiological roles in renal fibrosis through modulating innate and adaptive immune systems in the kidney.NEW & NOTEWORTHY TSS-Seq analysis of the kidney from renal tubular cell-specific NFAT5 KO mice uncovered novel genes that are possibly regulated by NFAT5 in the kidney under physiological conditions. The study further implied disorders of innate and adaptive immune systems in NFAT5 KO mice, thereby exacerbating renal fibrosis at pathological states. Our results may implicate the involvement of renal tubular NFAT5 in the progression of renal fibrosis. Further studies would be worthwhile for the development of novel therapy to treat chronic kidney disease.

BML: a versatile web server for bipartite motif discovery

Motif discovery and characterization are important for gene regulation analysis. The lack of intuitive and integrative web servers impedes the effective use of motifs. Most motif discovery web tools are either not designed for non-expert users or lacking optimization steps when using default settings. Here we describe bipartite motifs learning (BML), a parameter-free web server that provides a user-friendly portal for online discovery and analysis of sequence motifs, using high-throughput sequencing data as the input. BML utilizes both position weight matrix and dinucleotide weight matrix, the latter of which enables the expression of the interdependencies of neighboring bases. With input parameters concerning the motifs are given, the BML achieves significantly higher accuracy than other available tools for motif finding. When no parameters are given by non-expert users, unlike other tools, BML employs a learning method to identify motifs automatically and achieve accuracy comparable to the scenario where the parameters are set. The BML web server is freely available at http://motif.t-ridership.com/ (https://github.com/Mohammad-Vahed/BML).

C/EBPα is indispensable for PML/RARα-mediated suppression of long non-coding RNA NEAT1 in acute promyelocytic leukemia cells

Better understanding of the transcriptional regulatory network in acute promyelocytic leukemia (APL) cells is critical to illustrate the pathogenesis of other types of acute myeloid leukemia. Previous studies have primarily focused on the retinoic acid signaling pathway and how it is interfered with by promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion protein. However, this hardly explains how APL cells are blocked at the promyelocytic stage. Here, we demonstrated that C/EBPα bound and transactivated the promoter of long non-coding RNA NEAT1, an essential element for terminal differentiation of APL cells, through C/EBP binding sites. More importantly, PML/RARα repressed C/EBPα-mediated transactivation of NEAT1 through binding to NEAT1 promoter. Consistently, mutation of the C/EBP sites or deletion of retinoic acid responsive elements (RAREs) and RARE half motifs abrogated the PML/RARα-mediated repression. Moreover, silencing of C/EBPα attenuated ATRA-induced NEAT1 upregulation and APL cell differentiation. Finally, simultaneous knockdown of C/EBPα and C/EBPβ reduces ATRA-induced upregulation of C/EBPε and dramatically impaired NEAT1 activation and APL cell differentiation. In sum, C/EBPα binds and transactivates NEAT1 whereas PML/RARα represses this process. This study describes an essential role for C/EBPα in PML/RARα-mediated repression of NEAT1 and suggests that PML/RARα could contribute to the pathogenesis of APL through suppressing C/EBPα targets.

Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana

Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized protein sequence signatures for three family members in the HRGP superfamily: the hyperglycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). However, the mechanism of pollen-specific HRGP gene expression remains unexplored. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences to identify cis-regulatory motifs responsible for pollen-specific expression of HRGP genes in Arabidopsis thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery identified 15 conserved promoter elements between A.thaliana and A. lyrata. Motif scanning revealed two pollen related transcription factors: GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Finally, we performed a regression analysis and demonstrated that the 15 motifs provided a good model of HRGP gene expression in pollen (R = 0.61). In conclusion, we performed the first integrative analysis of cis-regulatory motifs in pollen-specific HRGP genes, revealing important insights into transcriptional regulation in pollen tissue.

The C. elegans GATA transcription factor elt-2 mediates distinct transcriptional responses and opposite infection outcomes towards different Bacillus thuringiensis strains

The nematode Caenorhabditis elegans has been extensively used as a model for the study of innate immune responses against bacterial pathogens. While it is well established that the worm mounts distinct transcriptional responses to different bacterial species, it is still unclear in how far it can fine-tune its response to different strains of a single pathogen species, especially if the strains vary in virulence and infection dynamics. To rectify this knowledge gap, we systematically analyzed the C. elegans response to two strains of Bacillus thuringiensis (Bt), MYBt18247 (Bt247) and MYBt18679 (Bt679), which produce different pore forming toxins (PFTs) and vary in infection dynamics. We combined host transcriptomics with cytopathological characterizations and identified both a common and also a differentiated response to the two strains, the latter comprising almost 10% of the infection responsive genes. Functional genetic analyses revealed that the AP-1 component gene jun-1 mediates the common response to both Bt strains. In contrast, the strain-specific response is mediated by the C. elegans GATA transcription factor ELT-2, a homolog of Drosophila SERPENT and vertebrate GATA4-6, and a known master regulator of intestinal responses in the nematode. elt-2 RNAi knockdown decreased resistance to Bt679, but remarkably, increased survival on Bt247. The elt-2 silencing-mediated increase in survival was characterized by reduced intestinal tissue damage despite a high pathogen burden and might thus involve increased tolerance. Additional functional genetic analyses confirmed the involvement of distinct signaling pathways in the C. elegans defense response: the p38-MAPK pathway acts either directly with or in parallel to elt-2 in mediating resistance to Bt679 infection but is not required for protection against Bt247. Our results further suggest that the elt-2 silencing-mediated increase in survival on Bt247 is multifactorial, influenced by the nuclear hormone receptors NHR-99 and NHR-193, and may further involve lipid metabolism and detoxification. Our study highlights that the nematode C. elegans with its comparatively simple immune defense system is capable of generating a differentiated response to distinct strains of the same pathogen species. Importantly, our study provides a molecular insight into the diversity of biological processes that are influenced by a single master regulator and jointly determine host survival after pathogen infection.

Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting

Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, and they go through a number of developmental molts. While whole genome sequences of parasitic worms are now available, very little is known about transcription factor (TF) binding sites and their cognate transcription factors that play a role in regulating development. To address this gap, we developed a novel motif prediction pipeline, Emotif Alpha, that integrates ten different motif discovery algorithms, multiple statistical tests, and a comparative analysis of conserved elements between the filarial worms Brugia malayi and Onchocerca volvulus, and the free-living nematode Caenorhabditis elegans. We identified stage-specific TF binding motifs in B. malayi, with a particular focus on those potentially involved in the L3-L4 molt, a stage important for the establishment of infection in the mammalian host. Using an in vitro molting system, we tested and validated three of these motifs demonstrating the accuracy of the motif prediction pipeline.

Diseases caused by parasitic worms such as the filariae are among the leading causes of morbidity in the developing world. Very little is known about how development is regulated in these vector-transmitted parasites. We have developed a computational method to identify motifs that correspond to transcription factor binding sites in the genome of the parasitic worm, Brugia malayi, one of the causative agents of lymphatic filariasis. Using this approach, we were able to predict stage-specific transcription factor binding sites involved in a stage of the molting process important for the establishment of the infection. We validated the role of these motifs using an in vitro molting system.

Sex chromosome evolution in parasitic nematodes of humans

Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.

DIpartite: A tool for detecting bipartite motifs by considering base interdependencies

It is extremely important to identify transcription factor binding sites (TFBSs). Some TFBSs are proposed to be bipartite motifs known as two-block motifs separated by gap sequences with variable lengths. While position weight matrix (PWM) is commonly used for the representation and prediction of TFBSs, dinucleotide weight matrix (DWM) enables expression of the interdependencies of neighboring bases. By incorporating DWM into the detection of bipartite motifs, we have developed a novel tool for ab initio motif detection, DIpartite (bipartite motif detection tool based on dinucleotide weight matrix) using a Gibbs sampling strategy and the minimization of Shannon’s entropy. DIpartite predicts the bipartite motifs by considering the interdependencies of neighboring positions, that is, DWM. We compared DIpartite with other available alternatives by using test datasets, namely, of CRP in E. coli, sigma factors in B. subtilis, and promoter sequences in humans. We have developed DIpartite for the detection of TFBSs, particularly bipartite motifs. DIpartite enables ab initio prediction of conserved motifs based on not only PWM, but also DWM. We evaluated the performance of DIpartite by comparing it with freely available tools, such as MEME, BioProspector, BiPad, and AMD. Taken the obtained findings together, DIpartite performs equivalently to or better than these other tools, especially for detecting bipartite motifs with variable gaps. DIpartite requires users to specify the motif lengths, gap length, and PWM or DWM. DIpartite is available for use at https://github.com/Mohammad-Vahed/DIpartite.

The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life

The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.

Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.

TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct

Metabolic acidosis often results from chronic kidney disease; in turn, metabolic acidosis accelerates the progression of kidney injury. The mechanisms for how acidosis facilitates kidney injury are not fully understood. To investigate whether low pH directly affects the expression of genes controlling local homeostasis in renal tubules, we performed transcription start site sequencing (TSS-Seq) using IN-IC cells, a cell line derived from rat renal collecting duct intercalated cells, with acid loading for 24 h. Peak calling identified 651 up-regulated and 128 down-regulated TSSs at pH 7.0 compared with those at pH 7.4. Among them, 424 and 38 TSSs were ≥ 1.0 and ≤ -1.0 in Log₂ fold change, which were annotated to 193 up-regulated and 34 down-regulated genes, respectively. We used gene ontology analysis and manual curation to profile the up-regulated genes. The analysis revealed that many up-regulated genes are involved in renal fibrosis, implying potential molecular mechanisms induced by metabolic acidosis. To verify the activity of the ubiquitin-proteasome system (UPS), a candidate pathway activated by acidosis, we examined the expression of proteins from cells treated with a proteasome inhibitor, MG132. The expression of ubiquitinated proteins was greater at pH 7.0 than at pH 7.4, suggesting that low pH activates the UPS. The in vivo study demonstrated that acid loading increased the expression of ubiquitin proteins in the collecting duct cells in mouse kidneys. Motif analysis revealed Egr1, the mRNA expression of which was increased at low pH, as a candidate factor that possibly stimulates gene expression in response to low pH. In conclusion, metabolic acidosis can facilitate renal injury and fibrosis during kidney disease by locally activating various pathways in the renal tubules.

Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1

Background

The invertebrate immune system comprises physiological mechanisms, physical barriers and also behavioral responses. It is generally related to the vertebrate innate immune system and widely believed to provide nonspecific defense against pathogens, whereby the response to different pathogen types is usually mediated by distinct signalling cascades. Recent work suggests that invertebrate immune defense can be more specific at least at the phenotypic level. The underlying genetic mechanisms are as yet poorly understood.

Results

We demonstrate in the model invertebrate Caenorhabditis elegans that a single gene, a homolog of the mammalian neuropeptide Y receptor gene, npr-1, mediates contrasting defense phenotypes towards two distinct pathogens, the Gram-positive Bacillus thuringiensis and the Gram-negative Pseudomonas aeruginosa. Our findings are based on combining quantitative trait loci (QTLs) analysis with functional genetic analysis and RNAseq-based transcriptomics. The QTL analysis focused on behavioral immune defense against B. thuringiensis, using recombinant inbred lines (RILs) and introgression lines (ILs). It revealed several defense QTLs, including one on chromosome X comprising the npr-1 gene. The wildtype N2 allele for the latter QTL was associated with reduced defense against B. thuringiensis and thus produced an opposite phenotype to that previously reported for the N2 npr-1 allele against P. aeruginosa. Analysis of npr-1 mutants confirmed these contrasting immune phenotypes for both avoidance behavior and nematode survival. Subsequent transcriptional profiling of C. elegans wildtype and npr-1 mutant suggested that npr-1 mediates defense against both pathogens through p38 MAPK signaling, insulin-like signaling, and C-type lectins. Importantly, increased defense towards P. aeruginosa seems to be additionally influenced through the induction of oxidative stress genes and activation of GATA transcription factors, while the repression of oxidative stress genes combined with activation of Ebox transcription factors appears to enhance susceptibility to B. thuringiensis.

Conclusions

Our findings highlight the role of a single gene, npr-1, in fine-tuning nematode immune defense, showing the ability of the invertebrate immune system to produce highly specialized and potentially opposing immune responses via single regulatory genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2603-8) contains supplementary material, which is available to authorized users.

Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury

Background

Glaucoma is characterized by progressive loss of the visual field and death of retinal ganglion cells (RGCs), a process that is mediated, in part, by axonal injury. However, the molecular pathomechanisms linking RGC death and axonal injury remain largely unknown. Here, we examined these mechanisms with a cap analysis of gene expression (CAGE), which allows the comprehensive quantification of transcription initiation across the entire genome. We aimed to identify changes in gene expression patterns and to predict the resulting alterations in the protein network in the early phases of axonal injury in mice.

Results

We performed optic nerve crush (ONC) in mice to model axonal injury. Two days after ONC, the retinas were isolated, RNA was extracted, and a CAGE library was constructed and sequenced. CAGE data for ONC eyes and sham-treated eyes was compared, revealing 180 differentially expressed genes. Among them, the Bcat1 gene, involved in the catabolism of branched-chain amino acid transaminase, showed the largest change in expression (log2 fold-change = 6.70). In some differentially expressed genes, alternative transcription start sites were observed in the ONC eyes, highlighting the dynamism of transcription initiation in a state of disease. In silico pathway analysis predicted that ATF4 was the most significant upstream regulator orchestrating pathological processes after ONC. Its downstream candidate targets included Ddit3, which is known to induce cell death under endoplasmic reticulum stress. In addition, a regulatory network comprising IFNG, P38 MAPK, and TP53 was predicted to be involved in the induction of cell death.

Conclusion

Through CAGE, we have identified differentially expressed genes that may account for the link between axonal injury and RGC death. Furthermore, an in silico pathway analysis provided a global view of alterations in the networks of key regulators of biological pathways that presumably take place in ONC. We thus believe that our study serves as a valuable resource to understand the molecular processes that define axonal injury-driven RGC death.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-982) contains supplementary material, which is available to authorized users.

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

Underlying the complexity of the mammalian brain is its network of neuronal connections, but also the molecular networks of signaling pathways, protein interactions, and regulated gene expression within each individual neuron. The diversity and complexity of the spatially intermingled neurons pose a serious challenge to the identification and quantification of single neuron components. To address this challenge, we present a novel approach for the study of the ribosome-associated transcriptome-the translatome-from selected subcellular domains of specific neurons, and apply it to the Purkinje cells (PCs) in the rat cerebellum. We combined microdissection, translating ribosome affinity purification (TRAP) in nontransgenic animals, and quantitative nanoCAGE sequencing to obtain a snapshot of RNAs bound to cytoplasmic or rough endoplasmic reticulum (rER)-associated ribosomes in the PC and its dendrites. This allowed us to discover novel markers of PCs, to determine structural aspects of genes, to find hitherto uncharacterized transcripts, and to quantify biophysically relevant genes of membrane proteins controlling ion homeostasis and neuronal electrical activities.

Discriminative motif optimization based on perceptron training

MOTIVATION

Generating accurate transcription factor (TF) binding site motifs from data generated using the next-generation sequencing, especially ChIP-seq, is challenging. The challenge arises because a typical experiment reports a large number of sequences bound by a TF, and the length of each sequence is relatively long. Most traditional motif finders are slow in handling such enormous amount of data. To overcome this limitation, tools have been developed that compromise accuracy with speed by using heuristic discrete search strategies or limited optimization of identified seed motifs. However, such strategies may not fully use the information in input sequences to generate motifs. Such motifs often form good seeds and can be further improved with appropriate scoring functions and rapid optimization.

RESULTS

We report a tool named discriminative motif optimizer (DiMO). DiMO takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. We use area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. Using DiMO, on a large test set of 87 TFs from human, drosophila and yeast, we show that it is possible to significantly improve motifs identified by nine motif finders. The motifs are generated/optimized using training sets and evaluated on test sets. The AUC is improved for almost 90% of the TFs on test sets and the magnitude of increase is up to 39%.

AVAILABILITY AND IMPLEMENTATION

DiMO is available at http://stormo.wustl.edu/DiMO

Structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia

Background

Transcription factor PU.1, a member of the ETS family, is a master regulator of myeloid differentiation whose functional disruption is often associated with acute myeloid leukemia (AML). Although much has been learned about PU.1 over the past decades, relatively little is known about cis-elements that interact with this factor under physiological or pathological conditions, especially in the whole-genome scale. We aimed to define the cistrome of PU.1 in acute promyelocytic leukemia (APL) cells and characterize the cis-elements bound by PU.1.

Methods

Chromatin immunoprecipitation with specific antibody coupled with deep sequencing (ChIP-seq) was used to investigate the in vivo PU.1 binding sites at the whole-genome scale in APL-derived NB4 cells. The ChIP-quantitative (q)-PCR and luciferase reporter assays were used to validate the binding events and trans-activity, respectively. Various computational analyses, including motif mining, evolutionary conservation analysis and functional enrichment analysis, were performed to characterize the cis-elements that interacted with PU.1.

Results

A total of 26,907 significantly enriched binding regions of PU.1 were identified under the false discovery rate 0.1% in NB4 cells. PU.1 bound to various types of genomic regions and acted as a promoter-enhancer dual binding transcription factor. Based on the sequence length and composition, two types of representative motifs were identified in PU.1 binding sites: a long and a short motif. The long motif, characterized by high sequence specificity and binding affinity, predominantly resided in the promoter-distal regions. In contrast, the short one, with strong evolutionary constraint, represented the primary PU.1 cis-elements in the promoter-proximal regions. Interestingly, the short one showed more preference to be correlated with the binding of other factors, especially PML/RARα. Moreover, genes targeted by both PU.1 and PML/RARα were significantly involved in categories associated with oncogenesis, hematopoiesis and the pathogenesis of acute myeloid leukemia.

Conclusions

Our results demonstrate that structurally differentiated cis-elements that interact with PU.1 are functionally distinguishable in APL, suggesting that the sequence diversity of cis-elements might be a critical mechanism by which cells interpret the genome, and contribute to distinct physiological and/or pathological function.

Computational approaches, databases and tools for in silico motif discovery

Motifs are the biologically significant fragments of nucleotide or peptide sequences in a specific pattern. Motifs are categorized as structural motifs and sequence motifs. These are discovered by phylogenetic studies of similar genes across species. Structural motifs are formed by three dimensional arrangements of amino acids consisting of two or more α helices or β strands whereas sequence motifs are formed by the nucleotide fragments appearing in the exons of a gene. The arrangement of residues in structural motifs may not be continuous while it is continuous in sequence motifs. Sequence motifs may encode to the structural motifs. The algorithms used for motif discovery are important part of the bio-computational studies. The purpose of motif discovery is to identify patterns in biopolymer (nucleotide or protein) sequences to understand the structure and function of the molecules and their evolutionary aspects. The main aim of this paper is to provide systematic compilation of a review on different approaches, databases and tools used in motif discovery.