21 votes

120-year-old gene regulation problem independently solved by a computer. How?

The paper by Lobo and Levin is an attempt to learn a model that represents the inner workings of a biological system by fitting parameters to data. This is a common topic in "systems biology", a model-...
  • 5,605
20 votes
Accepted

120-year-old gene regulation problem independently solved by a computer. How?

The fruit, sadly, does not hang so low. Short version Lobo et al (the work you refer to) is a nice and not especially novel application of basic Systems Biology modeling approaches to the wound ...
  • 3,751
13 votes
Accepted

Number of transcription factor genes in the human genome

Here I will assume we are talking about eukaryotic sequence specific transcription factors (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive ...
  • 1,720
11 votes

How to validate the regulatory interactions inferred from gene expression data?

You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput ...
  • 35.1k
10 votes
Accepted

Do nucleosomes ever completely unwrap during transcription?

Yes, nucleosomes are completely unwound. Histone chaperones such as FACT (for H2A/H2B) and ASF1, CAF-1, HIRA, Nucleophosmin etc (for H3/H4), associate with RNA Pol II and handle the displaced ...
9 votes
Accepted

Do DNA repressors exist?

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen. In the "classical" way the silencer is ...
  • 49.4k
8 votes
Accepted

What's the term for "Amino acid regulating the expression of components used to synthesize it"?

The method of inhibition of the operation an anabolic metabolic pathway by the final product synthesized is called: End-product Inhibition or Feedback Inhibition Of more biochemical interest is the ...
  • 22.7k
7 votes

What is it about the housekeeping genes that makes them almost immune to gene regulation?

Housekeeping genes aren't clustered on a single chromosome. It is perhaps not that 'housekeeping' genes - broadly expressed genes - are 'above the laws of regulation'; rather that their regulation is ...
  • 766
6 votes

What is it about the housekeeping genes that makes them almost immune to gene regulation?

The problem with housekeeping genes is that they are often not stable and their expression depends on the cell types as well as the conditions. They can be stable under one condition, but are not ...
  • 49.4k
6 votes
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High frequency human genetic oscillators?

Here are some examples: electric oscillators: neural activity cardiac automatism (0.8 ... 1 Hz) mechanical oscillators (as a result of neural activity): heart beats breathing (0.2 ... 0.3 Hz) ...
  • 7,097
5 votes
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How much time do the different mechanisms of gene regulation need to take effect?

People often imprecisely say that type of regulation takes place on the order of many minutes to hours, and that may be as precise as you can get given the variable kinetics of any given pathway. ...
  • 470
5 votes

Difference between viral and native RNA

There is no fundamental difference between viral RNA and and native cellular RNA other than the sequence of RNA bases in them. The sequence differences are not biochemically apparent in the RNA, only ...
  • 8,759
5 votes
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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?

I believe that what you are aiming to do is not possible with the mechanisms that you propose. In most transcriptional and translational genetic circuits, the limiting factor for switching state is ...
  • 6,957
4 votes
Accepted

Hill's function for translational regulation

Your logic looks correct to me. Essentially, what you are doing is uniformly distributing the regulator among the available mRNA. Note that even when using Hill functions to model transcription, the ...
  • 511
3 votes

120-year-old gene regulation problem independently solved by a computer. How?

Christian, great idea to ask this question here before taking important decisions. Are those media articles a hype? Yes. Over the last 10 years I constantly see those hype stories in media about "...
3 votes

Databases for gene regulatory network graphs?

I highly recommend you to visit Pathguide to get a sense of how vast is the catalog of Pathway Databases. Looking into the category Pathway Diagrams or in Transcription Factors / Gene Regulatory ...
3 votes
Accepted

What are some atypical examples of positive transcriptional cooperativity?

Positive co-operativity without feedback from the downstream genes: I guess Polycomb/Trithorax complexes will fit this criterion nicely. Polycomb group (PcG) represses Hox and other differentiation ...
  • 35.1k
3 votes

what are the nodes and edges in gene regulatory networks

You're asking for a short answer to an entire field of research. You won't get a comprehensive one that fits in a SE answer. Generally, yes the genes/their products (which are often treated as the ...
  • 37.1k
2 votes

What are some atypical examples of positive transcriptional cooperativity?

Interesting question. I think I have two examples for you which might be interesting. The first is the co-regulation of the microphthalmia-associated transcription factor (MITF) in pigmentation by ...
  • 49.4k
2 votes

How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?

Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact ...
  • 35.1k
2 votes
Accepted

Why are most transcription factors enhancing the expression rather than repressing?

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 ...
  • 35.1k
2 votes
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enhancers in cell-type-specific signatures

You nailed down what enhancers are (canadianer give a good explanation too, while not answering the question in my opinion). For understanding the authors statement you first need to know that: ...
  • 2,873
2 votes

enhancers in cell-type-specific signatures

Enhancer is a just a term for a regulatory region distant from a gene that contains specific sites where transcription factors bind. As it happens, a single enhancer can contain DNA binding sites for ...
  • 17.5k
2 votes

Ways to identify that proteins are regulating different genes experimentally

Chromatin immunoprecipitation (ChIP) or ChIP-Seq are the first methods that pop into my mind. Essentially, DNA is cross-linked to bound proteins (transcription factors, histones, etc.) by various ...
  • 14.9k
2 votes

Does a gene that regulates itself necessarily be a transcription factor?

First of all you need to clarify what exactly is the output that needs to be regulated. We often say regulation of expression of a gene but what expression ultimately leads to is the activity of the ...
  • 35.1k
2 votes
Accepted

Are the subordinate genes of a repressed operon really "turned off"?

There are several mechanisms by which the expression of a gene can be completely turned off. Certain network architectures can ensure foolproof repression (for e.g. by using multiple repressors ...
  • 35.1k
2 votes
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Can the brain influence gene expression?

As has been pointed out in comments, the brain can certainly affect gene expression; but so can anything in our bodies, because the blood stream is super good at carrying stuff around the body to ...
2 votes

Can a miRNA be upregulated and downregulated in the same disease

Since diseases are frequently complex, it is not surprising to find specific genes (both miRNA coding genes or protein coding genes) being deferentially regulated when different studies of similar-...
  • 390
2 votes
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On enhancers, strands, and zygosity

...an enhancer sits on just one of DNA's two strands (usually the same strand as the protein-coding DNA gene itself). Yes and no. Enhancers are in fact sometimes palindromic, so they're mirrored on ...
  • 7,620
2 votes
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Books on machine learning applications in Biology

At NIPS 2016 most ANN implementations I saw were related to biology were trained on imaging data, thus the kind of comprehensive book you are looking for probably doesn't exist yet. However, if you ...

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