Hot answers tagged transcription
12
I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system.
In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter. E. coli ...
9
I don't believe anything should change in the majority of DNA->RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing.
However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would ...
8
The NF-κB family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of RelA/p65, RelB, c-rel, NFKB1/p50, and/or NFKB2/p52 subunits. For example, the "canonical" p65/p50 dimer is activated in response to stimulants like TNF-α (tumor necrosis factor ...
8
Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled because of gene regulatory control, especially at the famous H19/Igf2 locus[1]. Here is a generally good recent review[2], note they mention that DNA methylation does not cause transcriptional silencing, and ...
7
In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory.
It is possible to design various bistable switches using protein pathways, RNAi, or other means that will latch a particular state. In that way, an organism could effectively ...
7
The techniques used to do this are ChIP-seq and ChIP-chip.
Basically, you
let the pathogen bind to the (highly replicated) DNA
cut up the DNA into little random pieces by sonication
enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen
sequence the thus enriched DNA
map the sequenced fragments back to ...
6
Still if you change your question as (If histidine is abundant, HisP's job is to stop the histidine pathway as a "repressor." If HisP binds less tightly to promotors, the pathway should not produce as much histidine.)
Then it should be under another assumption that what is the effect of HisP binding promoter of enzyme's gene. Is it suppressing the ...
6
There are two mechanisms of transcriptional termination in prokaryotes. The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase. Check out [1] which shows a model for how rho multimers move through the RNA.
The other mechanism involves ...
5
A large number of prokaryotes do indeed have nucleosome-like structures. The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria. H-NS like molecules have also been found in mycoplasma (Lsr2). One of its roles is to bind AT-rich DNA and silence transcription. The binding is usually to suppress the expression of foreign DNA ...
5
As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.
The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), ...
4
A quick search on T7 cysteines gave some clues:
Bacteriophage T7-induced DNA polymerase is composed of a 1: 1
complex of phage-induced gene 5 protein and Escherichia coli
thioredoxin. Preparation of active subunits in the absence of
sulfhydryl reagents indicates the reduced form of thioredoxin is
sufficient for formation of the active ...
4
Someone is almost sure to prove me wrong about 30 seconds after I post this, but I don't think that the mechanistic aspects of learning are really all that well known in these study systems. The idea that it is occurring at all is recent enough (I've enjoyed Tanya Latty's Ph.D. work on this, for instance: http://www.tanyalatty.com/Home/research) that I ...
3
ChIP-exo does seem to be the "ChIP-seq killer." I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed.
One thing I'd do if I were of the "experimental bent" would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the "peaks" in ChIP-exo seem to be quite ...
3
If gene B makes a protein product, you can try designing a morpholino against the 5'-UTR of gene B. This can prevent translation initiation at the ribosome as the morpholino occludes mRNA entry into the ribosome. You can detect this by western blotting.
If gene B makes some sort of regulator RNA, you will need to target expression of gene B at the DNA ...
3
How well is gene A annotated? Do you have the gene A sequence (after post-transcriptional modifications)? If you do, you can order it from a company like DNA2.0 and they will synthesize it for you for like $0.35/base. Then you can transform the cells with this plasmid and do a knockout of gene B by inserting some sequence at the ~200bases overlap.
Also, I ...
3
Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt ...
2
A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix).
Now that the ...
2
The RNA hairpin transcription terminator in prokaryotes is terminated by the GC rich hairpin followed by 4+ uracil bases as you describe it.
The original reference describing the hairpin, described the sequence requirements as being for the thermodynamic stability of the hairpin, but the protein nusA has also been found to stimulate termination.
You ...
2
There was a paper published in Cell last year that has shown that the binding motif of a Hox transcription factor will change depending on whether there's a co-factor bound to the Hox.
link to paper
2
Sorry, but you started on the right track. What you're looking for is called the central dogma of protein synthesis.
Genomic DNA is transcribed in the nucleus into messenger RNA (mRNA) by RNA polymerase. RNA polymerase is DNA-dependent; it needs a DNA template to make an RNA version of the message.
The messenger RNA moves into the cytoplasm where it gets ...
1
I can't find any transcriptome data, but I did find miRNAome data from GEO at NCBI and Array Express at EMBL.
1
Try YEASTRACT http://www.yeastract.com/
YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus
Tracking) is a curated repository of more than 48333 regulatory
associations between transcription factors (TF) and target genes in
Saccharomyces cerevisiae, based on more than 1200 bibliographic
references. It also includes the ...
1
I'd like to add regulonDB which is not as integrated, but has a tremendous map of the e coli regulome which would be useful for any bacterial model.
I agree with @DanielStandage that this is not a well understood and there don't even appear to be standard representations for this sort of data.
1
There is an article in PNAS Conservation and divergence in eukaryotic DNA methylation who used:
next-generation sequencing to investigate the DNA methylation patterns
in eight divergent species, including green algae, flowering plants,
insects, and vertebrates. Their data allowed a comprehensive
comparison of whole-genome methylation profiles ...
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