Syndromes associated with Homo sapiens pol II regulatory genes

Discovering candidate imprinted genes and imprinting control regions in the human genome

BACKGROUND

Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps.

RESULTS

Because of the importance of the ICRs to regulating parent-of-origin specific gene expression, I developed a genome-wide strategy for predicting their positions in the human genome. My strategy consists of creating plots to display the density of ZFBS-morph overlaps along the entire chromosomal DNA sequences. In initial evaluations, I found that peaks in these plots pinpointed several of the known ICRs/gDMRs along the DNA in chromosomal bands. I deduced that in density-plots, robust peaks corresponded to actual or candidate ICRs in the DNA. By locating the genes in the vicinity of candidate ICRs, I could discover potential imprinting genes. Additionally, my assessments revealed a connection between several of the potential imprinted genes and human developmental anomalies. Examples include Leber congenital amaurosis 11, Coffin-Siris syndrome, progressive myoclonic epilepsy-10, microcephalic osteodysplastic primordial dwarfism type II, and microphthalmia, cleft lip and palate, and agenesis of the corpus callosum.

CONCLUSION

With plots displaying the density of ZFBS-morph overlaps, researchers could locate candidate ICRs and imprinted genes. Since the datafiles are available for download and display at the UCSC genome browser, it is possible to examine the plots in the context of Single nucleotide polymorphisms (SNPs) to design experiments to discover novel ICRs and imprinted genes in the human genome.

Exploring Transcription Factor Binding Properties of Several Non-coding DNA Sequence Elements in the Human NF-IL6 Gene

We examined several DNA segments upstream of the transcription start site of the human NF-IL6 gene to evaluate the predictions of two computational models developed to identify potential regulatory elements in the non-coding regions of genes. One model, comparative genomics, is based on the hypothesis that functional regulatory sequences can be localized in alignments of genomic DNA from several species. The other model is based on the hypothesis that protein-binding sites in genomic DNA may include sequence elements that occur frequently in proximal promoters of genes. The segments selected for DNA binding and functional evaluations included: (1) two conserved regions identified in multi-species sequence alignments; (2) a region containing several localized hits with 9-mers that ranked highly in studies of proximal promoters of human genes; and (3) two regions that were either GC-rich and/or contained tracts of G. The assays were done under nearly identical experimental conditions, using a cell line (U937) representing human monocytes/macrophages. The experiments also aimed at evaluating what effect, if any, cellular stimulation could have on the interactions of nuclear proteins with naturally occurring GC-rich elements in a human genomic DNA. In DNA binding assays, several complexes were formed with the conserved regions identified in multi-species sequence alignment. Furthermore, these regions were active in functional assays. The region containing several matches with 9-mers derived from proximal promoters of human genes was not conserved but formed several complexes with nuclear proteins including Sp1, Egr-1, and an unidentified protein. In addition, this region was active in functional assays and responded to cellular stimulations. Overall, the results of the assays suggest an important role for the sequence context of genomic DNA in protein binding and selection.

Sequence patterns defining the 5' boundary of human genes

In studies of both short and relatively long human genomic DNA, we found a clustering of the consensus site for the transcription factor GCF at the 5' boundary of a subset of human genes. In studies of promoter regions with known transcription initiation site, the cluster of consensus GCF site appeared near the transcription initiation site and in some sequences it extended into the transcribed region defining the leader mRNA. We also found a detectable correlation between the 5' boundary of human genes and recognition motifs for other transcription factors that bind to GC-rich sequences. But in these cases, the correlation was not as general as the correlation observed for the consensus GCF site.

Identifying a series of candidate genes for mania and psychosis: a convergent functional genomics approach

We have used methamphetamine treatment of rats as an animal model for psychotic mania. Specific brain regions were analyzed comprehensively for changes in gene expression using oligonucleotide GeneChip microarrays. The data was cross-matched against human genomic loci associated with either bipolar disorder or schizophrenia. Using this convergent approach, we have identified several novel candidate genes (e.g., signal transduction molecules, transcription factors, metabolic enzymes) that may be involved in the pathogenesis of mood disorders and psychosis. Furthermore, for one of these genes, G protein-coupled receptor kinase 3 (GRK3), we found by Western blot analysis evidence for decreased protein levels in a subset of patient lymphoblastoid cell lines that correlated with disease severity. Finally, the classification of these candidate genes into two prototypical categories, psychogenes and psychosis-suppressor genes, is described.