Creación de una célula bacteriana controlada por un genoma sintetizado químicamente.

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Craig Venter

We report the design, synthesis and assembly of the 1.08-
Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting
from digitized genome sequence information and its
transplantation into a Mycoplasma capricolum recipient
cell to create new Mycoplasma mycoides cells that are
controlled only by the synthetic chromosome. The only
DNA in the cells is the designed synthetic DNA sequence,
including “watermark” sequences and other designed
gene deletions and polymorphisms, and mutations
acquired during the building process. The new cells have
expected phenotypic properties and are capable of
continuous self-replication.

RNAs en todos lados.

A series of reports over the last few years have indicated that a much larger portion of the mammalian genome is transcribed than can be accounted for by currently annotated genes, but the quantity and nature of these additional transcripts remains unclear. Here, we have used data from single- and paired-end RNA-Seq and tiling arrays to assess the quantity and composition of transcripts in PolyA+ RNA from human and mouse tissues. Relative to tiling arrays, RNA-Seq identifies many fewer transcribed regions (“seqfrags”) outside known exons and ncRNAs. Most nonexonic seqfrags are in introns, raising the possibility that they are fragments of pre-mRNAs. The chromosomal locations of the majority of intergenic seqfrags in RNA-Seq data are near known genes, consistent with alternative cleavage and polyadenylation site usage, promoter- and terminator-associated transcripts, or new alternative exons; indeed, reads that bridge splice sites identified 4,544 new exons, affecting 3,554 genes. Most of the remaining seqfrags correspond to either single reads that display characteristics of random sampling from a low-level background or several thousand small transcripts (median length = 111 bp) present at higher levels, which also tend to display sequence conservation and originate from regions with open chromatin. We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported.

Citation: van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most “Dark Matter” Transcripts Are Associated With Known Genes. PLoS Biol 8(5): e1000371. doi:10.1371/journal.pbio.1000371

The DNA-binding landscape

GENE REGULATION

The DNA-binding landscape

Proteins or small molecules designed to bind certain DNA sequences and to regulate target genes have much promise in both basic and applied research. Aseem Ansari and colleagues at the University of Wisconsin, Madison, therefore tested the specificity of factor binding to DNA. They used custom DNA arrays displaying every possible 10-mer sequence—almost a half a million of them—to examine the binding profiles of engineered hairpin polyamides and protein transcription factors, as well as of several natural DNA-binding proteins, across sequence space. They quickly ran into a problem. The data were just too complex to understand intuitively. “We had this comprehensive binding dataset,” says Ansari, “and the first question was, how do you look at these data? If you use colors or tables or graphs to represent it, things begin to get very complicated very quickly.” They saw that protein transcription factors, in particular, bind fairly broadly across sequence space and that, although it is possible to extract a consensus binding motif, this often did not tell the whole story. What is more, the consequences of changing particular residues in a binding motif were not always simple or additive. So they had to find a new way of visualizing the data.

Nature Methods 7, 254 - 255 (2010)
doi:10.1038/nmeth0410-254a

Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter
Constitutive promoters are used routinely to drive ectopic gene expression. Here, we carried out a systematic comparison of eight commonly used constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian systems, and COPIA and ACT5C for Drosophila systems). We also included in the comparison the TRE promoter, which can be activated by the rtTA transcriptional activator in a doxycycline-inducible manner. To make our findings representative, we conducted the comparison in a variety of cell types derived from several species. We found that these promoters vary considerably from one another in their strength. Most promoters have fairly consistent strengths across different cell types, but the CMV promoter can vary considerably from cell type to cell type. At maximal induction, the TRE promoter is comparable to a strong constitutive promoter. These results should facilitate more rational choices of promoters in ectopic gene expression studies.
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Deciphering the splicing code

Artículo