User:Dmille96/sandbox

The Five Pillars according to Dmille96

1. Wikipedia is an online encyclopedia. Seems pretty straight forward.
   1. online in the sense that it is open to the public for viewing and editing
   2. encyclopedia in that it is not a dictionary or other form of academic research
2. Wikipedia has a neutral point of view. Articles must capture the entirety of an argument and remain as neutral as possible.
3. Wikipedia is free content. Free as in requiring no subscription and the opposite of Tibet.
4. Users, more specifically editors, should be mindful that the other editors are not out to ruin their day.
5. Nothing is set in stone. Just go with what you feel is best. Unless it's a bad idea, then don't do it.

Summary of Characteristics of Target Article

Our stated goal is to end up somewhere between a B and GA rated article on Wikipedia. Each article receives a rating on Wikipedia depending on the degree to which an article has been completed and with what quality it has been written. Kicking things off immediately, B and GA articles are mostly complete articles. They do not have any large pieces of information missing and only require small changes to improve their quality.

B Class

B articles have the beginnings of a good article but the thing that separates it most from lower level articles are the references. B class articles are well researched and have their important claims backed up by peer-reviewed and widely available research. These articles can be further improved by the input of professionals in the field.

GA Class

GA articles are a step up from B class articles and are approaching a professional level in writing, organization, and information quality. These articles are broken down into small, logically consistent subsections. Like a B class article, a GA article is well researched and contains several references backing up the factual claims of the author, sometimes with multiple citations for each claim. The article is well developed and encompasses all information that a reader would need about a given topic while providing easy to navigate subsections for readers searching for a small topic. Additionally, charts and pictures depicting the subject matter are included and are easy to read.

H1 Proteins and Their Role in the Cell

The H1 linker histone is the only major histone not present in the nucleosome's octamer. That group of eight rather is composed of H2A, H2B, H3, and H4 histones. The role of H1 rather is in higher order chromatin structural maintenance. Moreover, H1 proteins also have a hand in transcriptional regulation and can specifically regulate gene expression. The protein is able to accomplish this through its association with histone methylating proteins. The role to which H1 histones regulate specific genes or global transcription is still a source of much research.

Working on the Article

This article is a review of the epigenetics involved with the histone octamer. The article will provide useful infomation concerning how and when histones are modified. It provides specific examples of histone tail modification and its role on the expression of genes as well as the physical effect of such modifications. The article is useful in giving perspective of the role of histones in genetic expression.

This article also touches on gene modification but goes into more depth on how the histones are positioned throughout the chromosomes and how that lends itself to DNA packaging. This article goes over how histones are important in condensation of genetic material and ultimately play a role in higher order organization. It provides both basic and in depth information about histone interaction with DNA.

This review article also covers nucleosome positioning and its role in gene regulation. First off, this article has a lot of great figures to explain its ideas. The article is also good because it goes over how DNA attached to histones is accessed by transcriptional machinery. It covers the process of histone remodeling and removal for DNA access. This article adds some depth to the discussion of histones and gene expression as well as provides some great pictures that are free to use (the article itself is free online).

Week 8 Stuff

Goals:

1. write intro snippet for histone octamer
2. write a bit about the individual components (H2A, H2B, H3, H4)
3. get the article linked up to other relevant articles (links to nucleosome, H2A etc, histone, etc)

Introduction

A histone octamer is an octamer of the histones found at the center of a nucleosome core particle. It consists of 2 copies of each of the four core histone proteins (H2A, H2B, H3 and H4). The octamer assembles when a tetramer, containing two copies of both H3 and H4, complexes with two H2A/H2B dimers. The histone octamer can be assembled either in vivo, as the nucleosome core particle where the presence of DNA and the physiological salt concentrations allow it or without DNA under high salt concentrations. These histones of the histone octamer all contain N-terminal tails that emanate from their central histone folds, and core domains with the C-terminals. The tails comprise up to 20% of each histone and can be modified to alter the expression of the surrounding DNA. Additionally, the histone octamer interacts with the surrounding DNA through 14 points along the minor groove. These interactions, as well as hydrogen bonds and salt bridges, keep the DNA and histone octamer loosely associated and ultimately allow the two to re-position or separate entirely.

History of Histone Octamer Research

Post-translational modifications of histone were first identified and listed as having potential regulatory role on the synthesis of RNA in 1964 (1). Since then over the couple of decades chromatin theory began to evolve. Chromatin subunit models as well as a notion of nucleosome were established in 1973 and 1974, respectively (2). Richmond et al. has been able to elucidate a crystal structure of histone octamer with DNA wrapped up around it at a resolution of 7 ˚A in 1984 (3). Histone octamer structure was revisited 7 years later and at a high salt concentration 3.1 ˚A resolution was reached for octamer crystal without a DNA around it. Each peptide of a histone has an element of helix-loop helix and therefore named histone fold (4). Furthermore the details of protein-protein and protein-DNA interactions were fine tuned by X-ray crystallography studies at 2.8 and 1.9 ˚A in the 2000’s. It remains yet to crystallize the linker histone H1 in complex with H2A, H2B, H2 and H4.

Week 10 Writings

Nucleosome

The nucleosome is the most basic form of DNA compaction in mammals. Nucleosomes consist of a histone octamer surrounded by 147 base pairs wrapped in a superhelical manner. In addition to compacting the DNA, the histone octamer plays a key role in the transcription of the DNA surrounding it. The histone core and nucleosomal DNA primarily interact through two methods. First, they interact whenever the minor groove of the DNA faces the histone core. Studies have found that the histones interact more favorably with A:T enriched than G:C enriched regions in the minor grooves. Second, the histones’ N terminal tails can be modified in several ways—most commonly acetylation, phosphorylation, or methylation—to limit or increase their transcription. The interactions between the histone octamer and DNA, however, are not permanent. The two can be separated quite easily and often are during replication and transcription. Specific remodeling proteins are constantly altering the chromatin structure by breaking the bonds of the nucleosome.

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