Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

Accurate functional annotation of protein sequences is hampered by important factors such as the failure of sequence search methods to identify relationships and the inherent diversity in function of proteins related at low sequence similarities. Earlier, we had employed intermediate sequence search approach to establish new domain relationships in the unassigned regions of gene products at the whole genome level by taking Mycoplasma gallisepticum as a specific example and established new domain relationships. In this paper, we report a detailed comparison of the conservation status of the domain and domain architectures of the gene products that bear our newly predicted domains amongst 14 other Mycoplasma genomes and reported the probable implications for the organisms. Some of the domain associations, observed in Mycoplasma that afflict humans and other non-human primates, are involved in regulation of solute transport and DNA binding suggesting specific modes of host-pathogen interactions

FRA2A is a CGG repeat expansion associated with silencing of AFF3

Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5-12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship

Computational characterization of modes of transcriptional regulation of nuclear receptor genes

Background: Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, development and reproduction. They are activated through the binding of small ligands, which can be replaced by drug molecules, making nuclear receptors promising drug targets. Transcriptional regulation of the genes that encode them is central to gaining a deeper understanding of the diversity of their biochemical and biophysical roles and their role in disease and therapy. Even though they share evolutionary history, nuclear receptor genes have fundamentally different expression patterns, ranging from ubiquitously expressed to tissue-specific and spatiotemporally complex. However, current understanding of regulation in nuclear receptor gene family is still nascent. Methodology/Principal Findings: In this study, we investigate the relationship between long-range regulation of nuclear receptor family and their known functionality. Towards this goal, we identify the nuclear receptor genes that are potential targets based on counts of highly conserved non-coding elements. We validate our results using publicly available expression (RNA-seq) and histone modification (ChIP-seq) data from the ENCODE project. We find that nuclear receptor genes involved in developmental roles show strong evidence of long-range mechanism of transcription regulation with distinct cis-regulatory content they feature clusters of highly conserved non-coding elements distributed in regions spanning several Megabases, long and multiple CpG islands, bivalent promoter marks and statistically significant higher enrichment of enhancer mark around their gene loci. On the other hand nuclear receptor genes that are involved in tissuespecific roles lack these features, having simple transcriptional controls and a greater variety of mechanisms for producing paralogs. We further examine the combinatorial patterns of histone maps associated with dynamic functional elements in order to explore the regulatory landscape of the gene family. The results show that our proposed classification capturing long-range regulation is strongly indicative of the functional roles of the nuclear receptors compared to existing classifications. Conclusions/Significanc: We present a new classification for nuclear receptor gene family capturing whether a nuclear receptor is a possible target of long-range regulation or not. We compare our classification to existing structural (mechanism of action) and homology-based classifications. Our results show that understanding long-range regulation of nuclear receptors can provide key insight into their functional roles as well as evolutionary history; and this strongly merits further study

Statistical significance test for H3K4me1 around different genomic distributions.

<p>A) H3K4me1 distribution in different clusters across ±10 kb TSS against the random background distribution. B) H3K4me1 distribution in different clusters across ±1 Mb TSS with respect to random background distribution. C) H3k4me1 distribution in different clusters across ±2 Mb TSS with respect to random background distribution. This figure shows that cluster 1 (shown by red bar) has significantly higher distribution of H3K4me1 in comparison to random selected background region (marked by black bars), CpG and non-CpG region (shown by blue and green bar respectively) and cluster 2 genes (shown by pink bar).</p

The bubble plots for bivalent promoter mark for each gene in human embryonic stem cell line.

<p>The x-axis shows read counts for repression (H3K27me3) mark around ±10 KB TSS. The y-axis shows read counts for active promoter (H3K4me3) mark around ±10 KB TSS. The size of the bubble (yellow) shows RPKM value for respective gene. The left section of the plot comprises all of the genes (black) in cluster 2 (except few cases where cluster 1 gene have very high expression). This shows that cluster 2 genes does not have any enrichment of repression mark around their TSS irrespective of their expression. The top and bottom right sections consist of genes from cluster 1 (red). This shows that when genes in cluster 1 are not expressed they have higher read counts for repression mark while still some of the genes retain repression mark even when they are expressed.</p

The dissimilarity matrix of HCNE content among nuclear receptors and its clustering.

<p>Nuclear receptor genes broadly divided in to two clusters on the basis of higher and lower enrichment of HCNEs around 2(shown below) consists of 25 genes having higher enrichment of HCNE, while cluster 2 consists of the remaining 23 genes.</p

Classification comparison of nuclear receptors gene family with respect to sequence homology and transcriptional mechanism and function based.

<p>The GRB target genes (cluster 1 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088880#pone-0088880-t001" target="_blank">Table 1</a>) are shown in red, while non-targets are in blue. Nuclear hormone receptors are presented in normal bold text while orphan receptors are underlined and in italics. There are in total 23 nuclear receptor GRB target genes and 25 nuclear receptor non-GRB target nuclear receptor genes. It is clear from the figure that both GRB target and non-target nuclear receptors are dispersed among seven families classified on the basis of sequence homology.</p

The GRB Model.

<p>GRB has developmental and/or transcription factor gene (target gene, orange) spanned by a cluster of highly conserved non-coding elements (red ovals), which regulates the target gene expression by acting as enhancers/insulators and other un-related neighboring genes (bystander genes, green).</p

Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration.

The intestinal epithelium is largely maintained by self-renewing stem cells but with apparently committed progenitors also contributing, particularly following tissue damage. However, the mechanism of, and requirement for, progenitor plasticity in mediating pathological response remain unknown. Here we show that phosphorylation of the transcription factor Atoh1 is required for both the contribution of secretory progenitors to the stem cell pool and for a robust regenerative response. As confirmed by lineage tracing, Atoh1+ cells (Atoh1(WT)CreERT2 mice) give rise to multilineage intestinal clones both in the steady state and after tissue damage. In a phosphomutant Atoh1(9S/T-A)CreERT2 line, preventing phosphorylation of ATOH1 protein acts to promote secretory differentiation and inhibit the contribution of progenitors to self-renewal. Following chemical colitis, Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenicity that affects overall regeneration. Progenitor plasticity maintains robust self-renewal in the intestinal epithelium, and the balance between stem and progenitor fate is directly coordinated by ATOH1 multisite phosphorylation.Cancer Research UK Welcome Trust Rosetrees Trust Stoneygate Trus

Additional file 2 of BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Supplementary Table S1. (XLS 24 kb