Molecular Biology: Open Access

DJ-1, a cancer- and Parkinson’s disease-associated protein, works as a coactivator to various transcription factors. In this study, DNA fragments that bind to DJ-1 complexes were obtained by a chromatin immunoprecipitation sequencing with an anti-human DJ-1 antibody using chromatin from SH-SY5Y cells. We identified 60 different sequences as potential DJ-1 complex-binding sites in genes. Of sequences identified, expression levels of DJ-1-associated sitecontaining genes for DNA polymerase N, estrogen receptor α and S-adenosylhomocysteine hydrolase like-2 were decreased in DJ-1-knockdown cells and in 6-OHDA-treated cells. These studies suggest that DJ-1 regulates the expression of versatile genes at the transcriptional level and that some of the genes are regulated by DJ-1 in an oxidative status-dependent manner.

Functional MRI studies have revealed connectivity changes in several brain networks in patients with neurodegenerative diseases and imaging genomics is an emerging field to investigate the role of genetics in brain function. A hexanucleotide repeat expansion in open reading frame in chromosome 9 (C9ORF72) is a common cause of familial frontotemporal dementia. The aim of this study was to evaluate resting state networks in behavioral variant frontotemporal dementia (bvFTD) patients with the C9ORF72 expansion by using functional MRI. Seven patients and matched healthy controls were examined. The group specific resting state networks were identified by independent component analysis and the dual regression technique was used to detect between-group differences in the resting state networks with p<0.05 threshold corrected for multiple comparisons. Increased anti-correlation between bilateral thalamic parts of the salience network and anterior sub-network of the Default mode network (DMN) was found in patients with the C9ORF72 expansion. In addition, increased resting state connectivity was detected in the right-sided dorsal attention network. The changes in these cognitive networks may explain executive dysfunction as well as neuropsychiatric symptoms in patients with bvFTD.

Secretory proteins that are involved in modulating hosts are called as effectors. Lately, finding these important proteins from a large array of other gene products have been a focus area in many high funding research programs. However, since the biological data is accumulating at a much faster rate now than ever before, this search process can be compared to finding a needle in the haystack. Conventional laboratory-based methods require critical experiments, extended time and high cost which in many cases result in failure of testing hypothesis. Using high throughput sequencing technologies, whole genome sequences are generated much more quickly and efficiently. The avalanche of genomics data has ushered new opportunities into discovery of large number of novel extra cellular secretory proteins that usually lie undetected with conventional methods. Recently powerful bioinformatics methods have emerged that can predict effectors from whole genome data of pathogens, commensal, symbiotic and environmental microorganisms much easily. In this review, we present a broad overview of these biological molecules that modulates host response in different ways in many organisms – pathogenic, non-pathogenic and commensal. We also catalogue the motifs associated with many secretory mechanisms and their prediction algorithms.