The processes by which gene products (largely RNA and proteins) are increased or decreased.

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

My Background: I'm a mathematics graduate student with a physics background. I have a very little biology knowledge and a little knowledge of machine learning and statistics. Topic: I recently ...
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325 views

Percentage of genome devoted to regulating gene expression

Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 ...
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Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
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231 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 ...
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1k views

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

When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently ...
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121 views

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

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
8
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276 views

Hill's function for translational regulation

Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics): $$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$ Where $m_X$ is the mRNA ...
7
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1answer
192 views

Number of transcription factor genes in the human genome

What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. ...
7
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87 views

Do DNA repressors exist?

I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am ...
7
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97 views

How do nuclear receptors locate each other to form a DNA loop?

Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (Rubina et al.; J Mol Bio 2004). I am not sure how exactly the receptors first attach ...
7
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199 views

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

Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of ...
7
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1answer
162 views

What is the mechanism by which lamins regulate gene expression?

The heterochromatin is generally localized at the nuclear periphery (also near nuclear lamina), whereas active genes are preferentially found in the nuclear interior. Children with Hutchinson-...
6
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1answer
114 views

DNA methylation and genome size

Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability ...
6
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1answer
74 views

“Enhancers” of enhancers?

I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to ...
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212 views

High frequency human genetic oscillators?

The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles ...
5
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2answers
138 views

What are some atypical examples of positive transcriptional cooperativity?

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...
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55 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?
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69 views

What regulates these two methods of splicing?

Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can ...
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1answer
39 views

How much time do the different mechanisms of gene regulation need to take effect?

I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference. If non-active regulator genes using each of the different ...
4
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1answer
141 views

Do nucleosomes ever completely unwrap during transcription?

In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.
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How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_{R1}$, $O_{R2}$, $O_{R3}$ - ...
4
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1answer
230 views

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

One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression. I have always been told that most of transcription ...
3
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2answers
48 views

enhancers in cell-type-specific signatures

I was reading an article in nature : Epigenomics: Roadmap for regulation and was confused by the definition or/and interpretation of enhancers. Enhancers are activated through interactions with ...
3
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2answers
49 views

Heterochromatin production limitations

Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce ...
3
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1answer
68 views

How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
3
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1answer
206 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
3
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1answer
32 views

Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like: -Ptet-(Gene1)-PLacO-(Gene2)- I want to express each gene using ...
3
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1answer
69 views

Regulation of V. cholerae virulence factors

So I know that several different environmental signals, such as pH, bile, and temperature, regulate virulence gene expression in V. cholerae. Specifically, they control expression of the genes ...
3
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1answer
49 views

mutant down but not out

I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from ...
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832 views

Promoter in the lac operon

Here is the question: Suppose an experimenter becomes proficient with a technique that allows her to move DNA sequences within a prokaryotic genome. If she moves the promoter for the lac operon to ...
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1answer
38 views

Do the phage repressors CI and Mnt exhibit crosstalk?

I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. ...
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107 views

Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the ...
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475 views

Gene perturbation, what is it used for, explain to computer scientists? [closed]

I am trying to build a gene regulation network, and I need some basic knowledge of it. So, in gene research, we perturb genes. Such as knock down them? Can people tell 2 or 3 experiment methods to ...
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1answer
118 views

Do “transcription factor binding site” and “operator” mean the same thing?

Can the terms "transcription factor binding site" and "operator" be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding ...
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1answer
23 views

Ways to identify that proteins are regulating different genes experimentally

As part of my study I have been given this hypothesis: HIF 1a and HIF 2a regulate different genes in multiple myeloma What ways do we have to identify that these proteins are regulating ...
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1answer
16 views

How are constitutive enzymes regulated?

I found that inducible enzymes can be regulated by many ways, but I cannot find how constitutive enzymes are regulated...
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1answer
39 views

Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
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1answer
118 views

Why is the gene regulation in eukaryotic cells needs multiple level of control than in prokaryotic cells?

That "eukaryotic cells are more complex" and "compartmentalized" are used to justify the need of more level of control of gene expression. I get the basic idea but can't convince myself why complexity ...
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39 views

Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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Regulation of Cra protein level in E coli

Catabolite Activator/Repressor, Cra protein (formerly known as Fructure Repressor FruR) plays a significant role in central carbon metabolism of E coli. Its activity is inhibited by fructose-1,6-...
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Does a gene that regulates itself necessarily be a transcription factor?

I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? ...
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1answer
21 views

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

Operons are often described using all or nothing language. A repressor binding to the operator is usually presented as "turning off" the regulated genes. Case in point, Scitable at Nature.com says: ...
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1answer
168 views

How does the enzyme Dicer function in the RISC complex?

I know that the RISC (RNA-induced silencing complex) is one of the primary complexes involved in gene regulation through RNAi. What I want to know is, what role exactly does Dicer play in this ...
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Feedback mechanisms for the dynorphin-kappa opioid system?

(this is all happening in the brain). Also it's best to go context-first I think (1) Normally if you take an agonist drug that hits a receptor "x", eventually the brain will downregulate the density ...
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What's the regulation of natural antisense transcripts?

By running an in silico approach on TF binding site prediction, I've discovered binding motif similarity on a nucleotide sequence within the EGFR-AS1. I was quite surprised, given that the ...
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0answers
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Are there any monomeric repressors in prokaryotes?

I'm looking for a monomeric repressor protein in E. coli, but all of the usual repressors are homodimers or tetramers. Are there any known prokaryotic repressors that repress as a monomer?