The process that produces a complementary strand of RNA from a section of DNA or (rarely) other RNA.
9
votes
2answers
102 views
Modularity of transcription factors
I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying ...
16
votes
3answers
465 views
Are single-celled organisms capable of learning?
I've read that the amoeba is capable of learning. Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the ...
1
vote
1answer
686 views
Which enzyme catalyzes transcription and which translation?
My attempt:
Transcription - RNA polymerase
Translation - aminoacyl tRNA synthetase
I know that the ribosome almost runs translation, but I don't think ribosomes are enzymes, which is why I went ...
10
votes
1answer
732 views
How does the stem-loop cause intrinsic transcription termination?
In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the ...
10
votes
1answer
182 views
How do CpG islands remain unmethylated?
In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted ...
10
votes
2answers
64 views
determining genome-wide exogenous binding of pathogens to host genome?
I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...
1
vote
1answer
28 views
Where can I find a transcriptome of a normal uveal melanocyte?
I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?
1
vote
1answer
51 views
TFBS predictions for yeast and pombe?
Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...
6
votes
1answer
372 views
ChIP-seq vs ChIP-exo
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.
As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this ...
5
votes
2answers
44 views
tools to reconstruct the transcriptional regulatory circuits?
What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
7
votes
1answer
39 views
Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?
Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based ...
14
votes
2answers
176 views
Can methylation from DNA get copied to RNA during transcription?
Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or ...
6
votes
1answer
124 views
Effect of histidine on the binding affinity of HisP
I was asked the following question by my teacher:
A gene regulatory protein called HisP regulates the enzymes for
histidine biosynthesis in the bacterium E. Coli. HisP is a protein
whoes ...
6
votes
1answer
411 views
Why does the T7 RNA Polymerase require a reducing environment ie. DTT
Every bloody protocol suggests adding in DTT when doing in vitro RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein ...
5
votes
1answer
553 views
Transcription and translation of prokaryotic operons
I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control ...
9
votes
2answers
156 views
bi-directional transcription experiment
We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic ...
4
votes
1answer
92 views
Bacterial chromatin binding data?
I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions. Can anyone point me to a source?
