Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis

<p>Abstract</p> <p>Background</p> <p>Multi-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We have developed <it>EvoPrinter</it>, a web-accessed genomics tool that provides a single uninterrupted view of conserved sequences as they appear in a species of interest. An <it>EvoPrint </it>reveals with near base-pair resolution those sequences that are essential for gene function.</p> <p>Results</p> <p>We describe here <it>EvoPrinterHD</it>, a 2^nd-generation comparative genomics tool that automatically generates from a single input sequence an enhanced view of sequence conservation between evolutionarily distant species. Currently available for 5 nematode, 3 mosquito, 12 <it>Drosophila</it>, 20 vertebrate, 17 <it>Staphylococcus </it>and 20 enteric bacteria genomes, <it>EvoPrinterHD </it>employs a modified BLAT algorithm [<it>enhanced</it>-BLAT (<it>e</it>BLAT)], which detects up to 75% more conserved bases than identified by the BLAT alignments used in the earlier <it>EvoPrinter </it>program. The new program also identifies conserved sequences within rearranged DNA, highlights repetitive DNA, and detects sequencing gaps. <it>EvoPrinterHD </it>currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An <it>EvoDifferences </it>profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, <it>EvoPrinterHD </it>incorporates options that allow for (1) re-initiation of the analysis using a different genome's aligning region as the reference DNA to detect species-specific changes in less-conserved regions, (2) rapid extraction and curation of conserved sequences, and (3) for bacteria, identifies unique or uniquely shared sequences present in subsets of genomes.</p> <p>Conclusion</p> <p><it>EvoPrinterHD </it>is a fast, high-resolution comparative genomics tool that automatically generates an uninterrupted species-centric view of sequence conservation and enables the discovery of conserved sequences within rearranged DNA. When combined with <it>cis</it>-Decoder, a program that discovers sequence elements shared among tissue specific enhancers, <it>EvoPrinterHD </it>facilitates the analysis of conserved sequences that are essential for coordinate gene regulation.</p

CASZ1b, the Short Isoform of CASZ1 Gene, Coexpresses with CASZ1a during Neurogenesis and Suppresses Neuroblastoma Cell Growth

In Drosophila, the CASZ1 (castor) gene encodes a zinc finger transcription factor and is a neural fate-determination gene. In mammals, the CASZ1 gene encodes two major isoforms, CASZ1a with 11 zinc fingers and CASZ1b with 5 zinc fingers. CASZ1b is more evolutionally conserved since it is the only homologue found in drosophila and Xenopus. Our previous study showed that full length CASZ1 (CASZ1a) functions to suppress growth in neuroblastoma tumor. However, the function of CASZ1b isoform in mammals is unknown. In this study, realtime PCR analyses indicate that mouse CASZ1b (mCASZ1b) is dynamically expressed during neurogenesis. CASZ1b and CASZ1a co-exist in all the neuronal tissues but exhibit distinct expression patterns spatially and temporally during brain development. CASZ1b and CASZ1a expression is coordinately upregulated by the differentiation agent Retinoic Acid, as well as agents that modify the epigenome in neural crest derived neuroblastoma cell lines. In contrast CASZ1b is down regulated while CASZ1a is upregulated by agents that raise intracellular cAMP levels. CASZ1b and CASZ1a have no synergistic or antagonistic activities on the regulation of their target NGFR gene transcription. Specific restoration of CASZ1b in NB cells suppresses tumor growth in vitro and in vivo. Consistent with its function role, we find that low CASZ1b expression is significantly associated with decreased survival probability of neuroblastoma patients (p<0.02). This study indicates that although their mechanisms of regulation may be distinct, both CASZ1b and CASZ1a have largely redundant but critical roles in suppressing tumor cell growth