Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed repres...

BACKGROUND The role of long non-coding RNAs (lncRNAs) in controlling gene expression has garnered increased interest in recent years. Sequencing projects, such as Fantom3 for mouse and H-InvDB for human, have generated abundant data on transcribed components of mammalian cells, the majority of which appear not to be protein-coding. However, much of the non-protein-coding transcriptome could mer...

Entry into meiosis is a key developmental decision. We show here that meiotic entry in Saccharomyces cerevisiae is controlled by antisense-mediated regulation of IME4, a gene required for initiating meiosis. In MAT a/alpha diploids the antisense IME4 transcript is repressed by binding of the a1/alpha2 heterodimer at a conserved site located downstream of the IME4 coding sequence. MAT a/alpha di...

Kaposi's sarcoma-associated herpesvirus (KSHV) is a gamma-2 herpesvirus with a genome containing a long unique coding region (LUR) flanked by GC-rich terminal repeat sequences. The LUR encodes approximately 90 annotated open reading frames (ORFs) with complex patterns of gene expression during viral latency, reactivation, and de novo infection. To identify unannotated KSHV genes, we examined th...

Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene (CDKL5) cause early onset infantile spasms and subsequent severe developmental delay in affected children. Deleterious mutations have been reported to occur throughout the CDKL5 coding region. Several studies point to a complex CDKL5 gene structure in terms of exon usage and transcript expression. Improvements in molecular diagnosis ...

DNA from the scarlet (st) region of Drosophila melanogaster has been cloned by chromosome walking, using the breakpoints of a new X-ray-induced third chromosome inversion (In(3LR)st-a27) which breaks in the scarlet (73A3.4) and rosy (87D13-14) regions. Two spontaneous mutants of st(st1 and stsp) contain insertions of non-st DNA located within 3.0 kb of the site of the inversion breakpoint used ...

Research into new methods to identify genes in anonymous genomic sequences has been going on for more than 15 years. Over this period of time, the field has evolved from the designing of programs to identify protein coding regions in compact mitochondrial or bacterial genomes, to the challenge of predicting the detailed organization of multi-exon vertebrate genes. The best program currently ava...

ABA-INSENSITIVE (ABI)4 is a transcription factor implicated in response to ABA in maturing seeds, and seedling responses to ABA, salt, and sugar. Previous studies have shown that ABI4 transcripts are high in seeds and in seedlings exposed to high concentrations of glucose and, to a lesser extent, osmotic agents and ABA, but that transcript levels are very low through most of vegetative growth. ...

Metabolic engineering and multisubunit protein production necessitate the expression of multiple genes at coordinated levels. In bacteria, genes for multisubunit proteins or metabolic pathways are often expressed in operons under the control of a single promoter; expression of the genes is coordinated by varying transcript stability and the rate of translation initiation. We have developed a sy...