14

The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding proteins obviously bind one strand but they do this in a non-specific manner. RNA-binding proteins recognise the sequence on a single strand by inserting ...


5

As the number of human TFs have been discussed by the previous answers, I'll limit myself to Anopheles gambiae. In the same issue of Science in which Holt et al. published a genome sequence for Anopheles gambiae (1), Zdobnov et al. published a comparison of the A. gambiae and Drosophila melanogaster genomes.(2) While the two species diverged about 250 ...


5

This is the Curated database of mouse and human transcription factors. And this is the paper in which they describe how they curated the database. In summary, there are 3230 putative mouse TF, 1200 of which are described in scientific papers.


4

Pretty interesting question. There are a few numbers out, I remember that round about 10% of the human genes are coding for transcription factors (unfortunately I don'T remember the source for that). This paper from 2002 estimates between 2000 and 3000 factors: Signal transduction and the control of gene expression. This paper from 2009 states a number of ...


4

The average number of auto-regulatory motifs (self-edges), is equal to the number of edges E times the probability that an edge is a self-edge which is $p_{self}=1/N$, with N being the total number of nodes. Therefore, $<N_{self}>_{rand} \approx E/N$ & 3. According to U.Alon's book ("Introduction to Systems Biology"), the mean number of times that ...


4

There are different kinds of DNA binding domains; the ones involved in base identification in the major groove can differentiate between different base pairs of the same nucleotides i.e. AT vs TA because they bind to functional groups on a nucleotide and not the base-pair per se. The stereochemistry i.e. which nucleotide is in the major groove, is important. ...


3

How can I detect transcription factors and preferably master TFs (master regulators) in an organism? The easiest approach to find transcription factors for any given organism would be based on sequence homology with other transcription factors. In order for this to work your organism of interest does have to be sequences, you can check this (e.g.) on the ...


3

In addition to the other answer, the following is some historical context on the naming of these genes. 1980 October: Discovery of pair-rule genes in Drosophila. Nusslein-Volhard C, Wieschaus E. 1980. Mutations affecting segment number and polarity in Drosophila. Nature 287:795-801. We have undertaken a systematic search for mutations that affect the ...


3

According to InterPro, a paired domain is a DNA-binding element consisting of paired N-terminal and C-terminal subdomains, separated by a linker. PAX proteins follow this motif, and as such typically represent a class of helix-turn-helix transcription factors. Box is the more interesting term here. In genetics, a box can be used to describe any regulatory ...


3

N is the IUPAC code for any nucleotide, so in DNA sequence an N signifies any one of the four bases could be in that position. The {4} means 4 of the previous character in the pattern, or NNNN. In Perl regular expressions \d{4} means match 4 digits in a row, so the notation is quite similar.


3

So what you need is basically your data expressed as counts instead of proportions. Even if you do not have the matrix of counts as raw data, these proportions only needs to be multiplied by the total number of binding sites used in the study (e.g. the number of sequences that have been analysed) to get the counts (since proportion = count/total number of ...


2

I can answer this question only based on guesses because I am not really sure about your claim that activators are higher in number than repressors. So consider this as an extended comment. While activators can interact directly or indirectly with the core machinery of transcription through enhancer binding, repressors predominantly recruit co-...


2

I haven't found 1.5 Mb, but 1 Megabase. This is the case for the shh gene in chicken, where the enhancer element is located 1 Mb upstream. The original article can be found here: "A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly." There are two reviews which are also interesting in ...


2

Amos Bairoch, of SWISSProt/UniProt fame has set up the nextprot database, a manually curated repository of knowledge for human proteins. While that won't help you get a number for the mosquito, it does make it easy to retrieve a list of human proteins that are annotated as transcription factors. Searching for "Transcription Factor" in the "Function" tab ...


2

In Drosophila, Toll receptors are used during embryonic development as well as innate immunity. See The Drosophila Toll Signaling Pathway by Valance, et. al. Toll-like Receptors are pattern recognition receptors found in organisms other than Drosophila that recognize common motifs found on pathogens. Toll receptors were first discovered in Drosophila and ...


2

When we say trans we mean that a diffusible factor, or agent is involved. So a molecule synthesized at one location, that can have a regulatory role in another location in the cell is said to be a "trans-acting" factor. When we say cis we mean physically linked to, in such a way that the biological regulation only affects other molecules that are attached (...


2

Transcription factors are a very heterogeneous group of proteins. Their two main objectives are to bind DNA & to recruit polymerase to that site. There are a of ways for them to accomplish these tasks. To bind DNA, all they need is a pocket of positive charge, which are found in several structural motifs across many proteins. The wikipedia page ...


2

Addition to the answer provided by Teige. Transcription factors bind to both the strands however your question also included proteins in general. DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) ...


2

No, eQTLs and transcption factor are very different things. Like you described TFs are proteins that control the expression level of genes. eQTLs are nothing that is physically present in the cell. An eQTL is the conceptual influence of an allele-specific DNA locus (a SNP) on the expression of a certain gene. Explained with an example this means that some ...


2

This has been studied this in Drosophila, and a lot of development hinges on where the cell is in the body. An initial asymmetry of mRNA in the pre-fertilized ovum leads to the establishment of the anterior-posterior axis (which end is the head, which is the tail) So cells are told what to develop into based on what mRNA signals they receive which depends ...


1

This subject is actually both complicated and incompletely understood. For example, there is evidence that some enhancers don't result in loops at all — instead their influence travels along the chromatin to a nearby promoter. You can think of enhancers as being staging areas where protein complexes that promote transcription are assembled. In some cases ...


1

If all cells have identical genomes and, therefore, identical transcription factors Important comment: all cells do indeed have identical genomes, and all cells are therefore equipped with DNA that codes for transcription factors, but that does not mean that all cells have the same state of the genome. It is well understood that different cell types have ...


1

If you were interested in human targets, one easy way is GeneCards, which aggregates other resources, and combines computational and (some) experimental data: In this case the inverse problem is particularly well accessible: e.g.: scroll down to section of Genomics (e.g.: for the gene called NOTCH http://www.genecards.org/cgi-bin/carddisp.pl?gene=NOTCH1&...


1

Short answer - yes but probably somewhat rarely. Transcription factors aren't necessarily limited to being either repressors or activators. In practice they mostly do one a lot more than the other - e.g. if they have an 'activation' domain then they will mostly activate, but they can still do the opposite, directly or indirectly. A single TF will often ...


1

Of course it's never 100%. The protein still has a measurable Kd for the DNA, meaning that there's always some part that's not bound (or some time that it's not bound. Besides that, you're talking about repressors. There are also activators, and they use many different mechanisms. The same regulator protein can even recognize different sequences of DNA and ...


1

The first transcription factors for the first transcription after fertilization are already present in the ovum (egg) before it is fertilized. Generally, all the machinery needed for transcription, translation, and the rest of the many necessary cellular functions are already present in a cell before it divides and develops. This chain of dependency goes ...


1

So databases like TRANSFAC are of somewhat... variable quality. Those matrices maybe have been derived from a program that just doesn't output a count matrix, but instead outputs a frequency matrix directly. What I would do, and what i have seen people do in published papers, is just multiply the matrix by 100 and round down. It's a kludge, but you'd better ...


1

In case anybody ever has the same question: I found the answer in this paper by Ow et al. 1987 (fig1) http://www.pnas.org/content/84/14/4870.full.pdf Just to clarify, I did not want to boost expression of the enhancer element in my algae, it needed boosting in tobacco protoplasts/leaves.


1

Nice question! First of all make sure that you have multiple transcription stop / terminator sequences at the end of your first gene . This is quite standard procedure. Also in your case the phenomenon called transcription interference (TI) comes handy. Here's a review on TI. In short: the term TI usually refers to the direct negative impact of one ...


1

General transcriptional factor complexes bind to DNA at promoters of genes via DNA binding proteins such as TATA-binding protein. It is quite clear that it is trans-acting.


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