Whole-genome microarray experiments were performed to define the Listeria monocytogenes cold growth regulon and to identify genes differentially expressed during growth at 4 and 37 degrees C. Microarray analysis using a stringent cutoff (adjusted P < 0.001; >/=2.0-fold change) revealed 105 and 170 genes that showed higher transcript levels in logarithmic- and stationary-phase cells, respectivel...

Worldwide, colorectal cancer (CRC) is the third most common cancer, with the highest mortality rates occurring in Central Europe. The use of chemotherapy to treat CRC is limited by the inter-individual variability in drug response and the development of cancer cell resistance. ATP-binding cassette (ABC) transporters play a crucial role in the development of resistance by the efflux of anticance...

Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Surprisingly...

Abstract Oritatami is a formal model of RNA co-transcriptional folding, in which an sequence (transcript) folds upon itself while being synthesized (transcribed) out its DNA template. This simple enough for further extension and also strong to study computational aspects this phenomenon. Some the structural motifs designed Turing universal computations oritatami have been demonstrated approxima...

We determined that the putative upstream promoter of the long transcript (P1) of ompA, the gene encoding the major outer membrane protein of Chlamydia trachomatis L2, is recognized in vitro by the major sigma factor of chlamydiae, sigma 66. We found no evidence that the putative downstream promoter of the short ompA transcript (P1) is functional in vitro. RNase protection of guanylyltransferase...

The GreA and GreB transcript cleavage factors of Escherichia coli suppress elongation arrest and may have a proofreading role in transcription. With the use of E. coli greA-greB- mutant, RNA polymerase is demonstrated to possess substantial intrinsic transcript cleavage activity. Mildly alkaline pH mimics the effect of the Gre proteins by inducing transcript cleavage in ternary complexes and an...

1 21 We examined the relative amounts of Na –Ca exchanger (NCX) isoform mRNAs in cultured neurons, astrocytes and developmental rat brain. NCX1 transcript was predominant in neurons and astrocytes, but NCX2 transcript was about four-fold higher than NCX1 or NCX3 transcript in adult rat cortex. NCX2 transcript in the cortex increased markedly during postnatal development, whereas NCX1 and 1 45 2...

The trp RNA-binding attenuation protein of Bacillus subtilis, TRAP, regulates both transcription and translation by binding to specific transcript sequences. The optimal transcript sequences required for TRAP binding were determined by measuring complex formation between purified TRAP protein and synthetic RNAs. RNAs were tested that contained repeats of different trinucleotide sequences, with ...

In animals, the transfer of developmental control from maternal RNAs and proteins to zygotically derived products occurs at the midblastula transition. This is accompanied by the destabilization of a subset of maternal transcripts. In Drosophila, maternal transcript destabilization occurs in the absence of fertilization and requires specific cis-acting instability elements. We show here that eg...

Continuing our quantitative analysis of rho-dependent termination at the trp t ' terminator, we here present evidence that the position of rho-dependent terminators along the template is strongly regulated by the secondary structure of the nascent RNA transcript, and that the prerequisite for establishing an effective kinetic competition between elongation and rho-dependent RNA release at a par...