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Questions tagged [gene-regulation]

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

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What is the "anatomy" of transcriptional regulation in Archaea?

I want to know what are the DNA elements that are recognized by transcription factors in Archaea and so what is the "anatomy" of transcriptional regulation in this case. I found in this ...
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Conservation Law in Gene Regulatory Network modelling

I was going through the GRN modelling from Chemical and enzyme kinetics by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/...
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Review paper on gene expression regulatory mechanisms

I'm a junior grad student in bioinformatics with CS background. I am involved in a project around discovering gene regulatory networks in some data, which got me curious about the gene expression ...
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What is the difference between "dysregulation" and "deregulation" of miRNA?

I've started to study the role of miRNA in cancer. Wikipedia says: Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with ...
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How does the phosphorylation state of 4E-BPs affect translation of nuclear-encoded mitochondrial transcripts?

A 2020 review paper about mTOR (ref. 1) says: because biomass accumulation demands vast reserves of energetic currency, mTORC1 enhances translation of nuclear-encoded mitochondrial transcripts ...
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Consensus sequence for selection of initiation codon in eukaryotes

In bacteria the AUG (or other) codon at which translation of mRNA is initiated is preceded at a precise distance by a sequence known as the Shine and Dalgarno sequence, to which the 30S subunit ...
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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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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 possible ...
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Number of regulators required for specify the total state of genes

My course notes make the following claim: If the regulation of each gene could include all transcription regulators available, then in principle the total state of all genes could be specified with ...
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Are there limitations in using DNase I hypersensitive sites (DHSs) to identify candidate enhancers?

Candidate enhancer regions are often defined in studies by DHSs and/or certain chromatin marks. I was wondering if DHSs are exhaustive for identifying possible enhancer regions, and if there is any ...
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response elements in transcription regulation

I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA ...
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How is the breakdown of lactose regulated at the gene level?

How is the breakdown of lactose regulated at the gene level? This is my answer: Without lactose in the cell, the repressor protein binds to the operator and prevents the read through of RNA ...
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Length of upstream and downstream of tss important for gene regulation o

I want to find SNPs in the upstream and downstream regions of transcription start sites of some 42 genes implicated in a disease (on which I am working). Are there any suggestions on what length ...
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Do transcription factors need to undergo extensive post-translational modification?

Some proteins need additional processing to become fully functional, for example NiFe-hydrogenases need to be cleaved by endopeptidases for some of their subunits to be active. Is it known whether ...
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Is there a difference between "genetic cross regulation" and "crosstalk"?

What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "Wanner BL. ...
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what happens when you put enhancer and caat box in prokaryotes

what happens when you put enhancer and caat box in prokaryotes
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