Talk:Chromosome conformation capture

Molecular Biology: Genetics / MCB / COMPBIO

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Wiki Education Foundation-supported course assignment[edit]

This article was the subject of a Wiki Education Foundation-supported course assignment, between 27 August 2019 and 6 December 2019. Further details are available on the course page. Student editor(s): Cseibert832.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 19:04, 17 January 2022 (UTC)[reply]

Wiki Education Foundation-supported course assignment[edit]

This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Ds17b.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 17:40, 16 January 2022 (UTC)[reply]

Where's the beef?[edit]

I don't know enough about 3C to write this myself. In the introduction, there needs to be some sort of brief explanation of how 3C actually works. --aciel (talk) 01:24, 2 February 2009 (UTC)[reply]

unsigned comment added by 88.97.10.166 talk) 15:55, 6 June 2009 (UTC)[reply]

I agree; there should be a very broad big-picture overview of the process (1-2 sentences) before the step-by-step discussion of digestion and ligation. Additionally, the section on ligation is very hard to read and not very clear. --chodges (talk) 19:56, 26 June 2009 (UTC)[reply]

Please read and heed[edit]

…the messages contained in the article and section tags, clicking on the links continued therein. The primacy of discovery is supported by secondary sources, not primary, and the appearance of Step 1, etc., in the various sections violates the aims of the article to be encyclopedic (prose, descriptive, conceptual), and not "how to" guides to procedures. The bold intrusions in each method section should be removed, and the sections edited to contain a conceptual description, in prose, of the methods, aims, and possibly, applications. Secondary sources should be used to provide this, with the primary sources used as further information and flavour (not as the only source for a whole paragraph or section. These are all in WP:VERIFY and other guidelines. Cheers. Leprof 7272 (talk) 00:02, 24 April 2016 (UTC)[reply]

Lede paragraphed move here[edit]

The following paragraph is so laden with abbreviations and undefined and unsourced terms that is is moved here, for the editor placing it to edit it to make it encyclopedic:

Several techniques have been developed from 3C to increase the throughput of quantifying a chromosome’s interactions with other chromosomes and with proteins, including (1) 3C and ChIP version of 3C (ChIP-loop assay), (2) 4C and ChIP version of 4C (enhanced 4C), (3) 5C and 3D assays and (4) Genome conformation capture (GCC) related (Hi-C), ChIP version of GCC as 6C. The application of analyzing DNA segments by microarray and high-throughput sequencing in the 4C, 5C and Hi-C methodologies has brought the assessment of chromosome interactions to the genome-wide scale.

Note, no sources. Those abbreviations that could be defined from the main article were kept in the lede, in a shortened paragraph. No technique should appear in the lede that is not fully defined and sourced in the main article. When it is defined, every technique should be stated in full name, followed by its abbreviation, and a clear definition of what the method entails (followed by a secondary source). Regarding which: ChIP, GCC, 3D, Hi-C, and 6C are incompletely defined or unsourced, as far as I can tell. Leprof 7272 (talk) 01:25, 24 April 2016 (UTC)[reply]

Remove history?[edit]

I've started a major overhaul of this article. I'll be adding a lot and may also remove some sections. Maybe history should be removed or put in another section. I don't know how typical it is for a relatively new molecular biology method article like this to have a history section. Lrieber (talk) 01:37, 30 May 2016 (UTC)[reply]

I agree, it's out of place and should be either moved to Chromatin or Nuclear organization or just removed altogether. Goatsnstoats (talk) 03:37, 1 October 2021 (UTC)[reply]

Medical impact[edit]

I removed the following unsupported sentence from the article:

This technology was described^{[by whom?]} as giving possible beneficial insights into the complex interplay of genetic factors that contribute to such debilitating disorders such as cancer, Duchenne muscular dystrophy (DMD), Rett syndrome and Alzheimer's disease.^{[citation needed]}

I think some description of the medical impact of 3C methods is warranted - however, I think it would be better to find some concrete examples. If we're sticking with a general description like the above, I think it makes sense to talk about that in the "Biological function" section, as a consequence of generally understanding looping interactions. Any opinions? Jmc200 (talk) 12:21, 3 August 2016 (UTC)[reply]

Categorisation[edit]

While I like the identification of each experiment as "enrichment for specific loci", "enrichment for all loci" etc, I didn't think these should be section headings. Firstly, we're not making a distinction between "one" and "many". Considering all combinations of "one", "many", and "all" (e.g. one-vs-one, one-vs-many) would lead to too many section headings, most of which would be a bit sparse, and there is already a pretty large ratio of header to text. Secondly, I think the difference between 3C/4C/5C/Hi-C, capture-based methods, and ChIP-based methods is much larger and merits being the top-level categorization. Then, individual methods can be labelled as one-vs-one etc. I'm going to start making this change but I wanted to lay out my reasoning for doing so. Jmc200 (talk) 15:20, 3 August 2016 (UTC)[reply]

structural modelling[edit]

This sentence was out of place in the lede:

These methods assume that the observed interaction frequency between two loci is inversely proportional to the average distance between them.^[1]

It could be useful in a section on reconstructing structures from Hi-C and single-cell Hi-C, possibly in the data analysis section? Any good reviews on structural modelling out there?

^ Varoquaux, Nelle (2014). "A statistical approach for inferring the 3D structure of the genome". Bioinformatics. 30 (12): i26–i33. doi:10.1093/bioinformatics/btu268. Retrieved 30 May 2016.

Should we mention/link Chromatin conformation signatures here[edit]

We don't have a Chromatin conformation signature, but 3C etc seem to be how they are determined. See fig 2 of Chromatin conformation signatures: ideal human disease biomarkers? - Rod57 (talk) 13:14, 17 June 2017 (UTC)[reply]

Elaborating on experimental methods[edit]

I added information to the introductory portion on the Experimental methods section. There is room for improvement on all the sub-sections as wellDs17b (talk) 20:30, 6 December 2017 (UTC)[reply]

[Varoquaux_2014-1] Varoquaux, Nelle (2014). "A statistical approach for inferring the 3D structure of the genome". Bioinformatics. 30 (12): i26–i33. doi:10.1093/bioinformatics/btu268. Retrieved 30 May 2016.

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