User:Ccharro22/sandbox

NF1
Available structures
PDB	Ortholog search: PDBe RCSB
Identifiers
Aliases
External IDs
Gene Location (Human)
Chr.	Chromosome 17 (Human)
Band	17q11.2
Gene Location (Mouse)
Chr.	Chromosome 11 (Mouse)
Band	11 B5; 11 46.74 cM
Gene Ontology
Cellular Component	Axon
	Cytoplasm
	Cytosol
	Dendrite
	Intrinsic component of the cytoplasmic side of the plasma membrane
	Membrane
	Nucleolus
	Nucleus
	Presynapse
Molecular Function	GTPase activator activity
	Phosphatidylcholine binding
	Phosphatidylethanolamine binding
	Protein binding
Biological Process	MAPK cascade
	Ras protein signal transduction
	Schwann cell development
	Actin cytoskeleton organization
	Adrenal gland development
	Amygdala development
	Artery morphogenesis
	Brain development
	Camera-type eye morphogenesis
	Cell communication
	Cellular response to heat
	Cerebral cortex development
	Cognition
	Collagen fibril organization
	Extracellular matrix organization
	Extrinsic apoptotic signalling pathway via death domain receptors
	Forebrain astrocyte development
	Forebrain morphogenesis
	Gamma-aminobutyric acid secretion neurotransmission
	Glutamate secretion, neurotransmission
	Hair follicle maturation
	Heart development
	Liver development
	Metanephros development
	Myelination in peripheral nervous system
	Negative regulation of MAP kinase activity
	Negative regulation of MAPK cascade
	Negative regulation of Rac protein signal transduction
	Negative regulation of Ras protein signal transduction
	Negative regulation of angiogenesis
	Negative regulation of astrocyte differentiation
	Negative regulation of cell migration
	Negative regulation of cell-matrix adhesion
	Negative regulation of endothelial cell proliferation
	Negative regulation of fibroblast proliferation
	Negative regulation of neuroblast proliferation
	Negative regulation of neurotransmitter secretion
	Negative regulation of oligodendrocyte differentiation
	Negative regulation of osteoclast differentiation
	Negative regulation of protein kinase activity
	Negative regulation of transcription factor import into nucleus
	Neural tube development
	Observational learning
	Osteoblast differentiation
	Peripheral nervous system development
	Phosphatidylinositol 3-kinase signalling
	Pigmentation
	Positive regulation of GTPase activity
	Positive regulation of adenylate cyclase activity
	Positive regulation of apoptotic process
	Positive regulation of endothelial cell proliferation
	Positive regulation of extrinsic apoptotic signalling pathway in the absence of ligand
	Positive regulation of extrinsic apoptotic signalling pathway via death domain receptors
	Positive regulation of neuron apoptotic process
	Regulation of GTPase activity
	Regulation of angiogenesis
	Regulation of blood vessel endothelial cell migration
	Regulation of bone resorption
	Regulation of cell-matrix adhesion
	Regulation of gene expression
	Regulation of glial cell differentiation
	Regulation of long-term neuronal synaptic plasticity
	Regulation of long-term synaptic potential
	Regulation of synaptic transmission, GABAergic
Response to hypoxia
Skeletal muscle tissue development
Smooth muscle tissue development
Spinal cord development
Sympathetic nervous system development
Visual learning
Wound healing
Orthologs
Species	Human	Mouse
Entrez	4763	18015
Ensembl	ENSG00000196712	ENSMUSG00000020716
UniProt	P21359	Q04690
RefSeq (mRNA)	NM_000267.3 NM_001042492.2 NM_001128147.2	NM_010897.2
RefSeq (protein)	NP_000258.1 NP_001035957.1 NP_001121619.1	NP_035027.1

Article Draft

Neurofibromin 1

Neurofibromin 1 (NF1) is a gene in humans that codes for neurofibromin, a GTPase-activating protein that negatively regulate Ras pathway activity (2) through accelerating Ras-bound GTP hydrolysis, which is the active form of Ras (8). Mutations in the NF1 gene affecting GTPase activity can alter cellular growth control, and neural development, resulting in neurofibromatosis type 1 (also known as von Recklinghausen syndrome) (2). Complications include cutaneous neurofibromas, café au lait pigment spots, plexiform neurofibromas, skeletal defects and optic nerve gliomas (1)(2). 

Gene 

The NF1 gene encodes the protein neurofibromin, a tumor suppressor protein, which primarily regulates the protein ras (9). NF1 is located on the long arm of chromosome 17, position q11.2 (2) and was identified in 1990 through positional cloning(14). NF1 spans over 350-kb of genomic DNA and contains 62 exons (3). 58 of these exons are constitutive and 4 exhibit alternative splicing ( 9a, 10a-2, 23a, and 28a) (3). The genomic sequence starts 4,951-bp upstream of the transcription start site and 5,334-bp upstream of the translation initiation codon, with the length of the 5’ UTR being 484-bp long (5). 

There are three genes that are present within intron 27b of NF1. These genes are EVI2B, EVI2A and OMG, which are encoded on the opposite strand and are transcribed in the opposite direction of NF1 (5). EVI2A and EVI2B are human homologs of the Evi-2A and Evi-2B genes in mice that encode proteins related to leukemia in mice (14). OMG is a membrane glycoprotein that is expressed in the human central nervous system during myelination of nerve cells (5). 

Promoter

Early studies of the NF1 promoter found that there is great homology between the human and mouse NF1 promoters (5). The major transcription start site has been confirmed, as well as well as two minor transcription start sites in both the human and mouse gene (5). 

The major transcription start is 484-bp upstream of the translation initiation site (22). The open reading frame is 8,520-bp long and begins at the translation initiation site (22). The NF1 exon 1 is 544-bp long and it contains the 5’ UTR and encodes the first 20 amino acids of neurofibromin (5). The NF1 promoter lies within a CpG island that is 472-bp long, consisting of 43 CpG dinucleotides, and extends into the start of exon 1 (5)(22). This CpG Island begins 731-bp upstream of the promoter and no core promoter element, such as a TATA or CCATT box, has been found within it (22). Although no core promoter element has been found, consensus binding sequences have been identified in the 5’ UTR for several transcription factors such as Sp1 and AP2 (5).

A methylation map of five regions of the promoter in both mouse and human was published in 1999. This map showed that three of the regions (at approximately – 1000, – 3000, and – 4000) were frequently methylated, but the cytosines near the transcription start site were unmethylated (5).  Methylation has been shown to functionally impact Sp1 sites as well as a CREB binding site (21).  It has been shown that the CREB site must be intact for normal promoter activity to occur and methylation at the Sp1 sites may affect promoter activity (21).

Proximal NF1 promoter/5’ UTR methylation has been analyzed in tissues from NF1 patients, with the idea that reduced transcription as a result of methylation could be a “second hit” mechanism equivalent to a somatic mutation (5). There are some sites that have been detected to be methylated at a higher frequency in tumor tissues than normal tissues (5). These sites are mostly within the proximal promoter, however some are in the 5’ UTR as well and there is a lot of interindividual variability in the cytosine methylation in these regions (5).

3' UTR

A study in 1993 compared the mouse Nf1 cDNA to the human transcript and found that both the untranslated regions and coding regions were highly conserved (5). It was verified that there are two NF1 polyadenylated transcripts that differ in size because of the length of the 3’ UTR, which is consistent with what has been found in the mouse gene (5). 

A study conducted in 2000, examined whether the involvement of the 3’ UTR in posttranscriptional gene regulation had an effect on the variation of NF1 transcript quantity both spatially and temporally (5). Five regions of the 3’ UTR that appear to bind proteins were found, one of which is HuR, a tumor antigen (20). HuR binds to AU-rich elements which are scattered throughout the 3' UTR and are thought to be negative regulators of transcript stability (20). This supports the idea that posttranscriptional mechanisms may influence the levels of NF1 transcript (20).

Mutations

The NF1 gene has one of the highest mutation rates amongst known human genes (7), however mutation detection is difficult because of its large size, the presence of pseudogenes, and the variety of possible mutations (18). The NF1 locus has a high incidence of de novo mutations, meaning that the mutations are not inherited maternally or paternally. Approximately 50% of mutations associated with Neurofibromatosis type 1 are de novo (14). Although the mutation rate is high, there are no mutation “hot spot” regions. Mutations tend to be distributed within the gene, although exons 3, 5, and 27 are common sites for mutations (14). 

The Human Gene Mutation Database contains 1,347 NF1 mutations, but none are in the “regulatory” category (5). There have not been any mutations conclusively identified within the promoter or untranslated regions. This may be because such mutations are rare, or they do not result in a recognizable phenotype (5). 

There have been mutations identified that affect splicing, in fact 286 of the known mutations are identified as splicing mutations (7). About 78% of splicing mutations directly affect splice sites, which can cause aberrant splicing to occur (7). Aberrant splicing may also occur due to mutations within a splicing regulatory element (7). Intronic mutations that fall outside of splice sites also fall under splicing mutations, and approximately 5% of splicing mutations are of this nature (7). Point mutations that effect splicing are commonly seen and these are often substitutions in the regulatory sequence. Exonic mutations can lead to deletion of an entire exon, or a fragment of an exon if the mutation creates a new splice site (14). Intronic mutations can result in the insertion of a cryptic exon, or result in exon skipping if the mutation is in the conserved 3’ or 5’ end (14). 

Protein

 The NF1 gene encodes neurofibromin, which is a 320-kDa protein that contains 2,818 amino acids (2). Neurofibromin is a GTPase-activating protein (GAP) that negatively regulates Ras pathway activity (2) by accelerating hydrolysis of Ras-bound guanosine triphosphate (GTP) (8). Neurofibromin localizes in the cytoplasm, however some studies have found neurofibromin or fragments of it in the nucleus (8). Neurofibromin does contain a nuclear localization signal that is encoded by exon 43, but whether or not neurofibromin plays a role in the nucleus is currently unknown (3).  Neurofibromin is ubiquitously expressed, but expression levels vary depending on the tissue type and developmental stage of the organism (2). Expression is at its highest level in adult neurons, Schwann cells, astrocytes, leukocytes, and oligodendrocytes (3)(8).

The catalytic RasGAP activity of neurofibromin is located in a central portion of the protein, that is called the GAP-related domain (GRD)(8). The GRD is closely homologous to p120GAP (8) and represents about 10% (229 amino acids (8)) of the neurofibromin sequence (2). The GRD is made up of a central portion called the minimal central catalytic domain (GAPc) as well as an extra domain (GAPex) that is formed through the coiling of about 50 residues from the N- and C- terminus (8). The Ras-binding region is found in the surface of GAPc and consists of a shallow pocket that is lined by conserved amino acid residues (8). 

In addition to the GRD, neurofibromin also contains a Sec14 homology-like region as well as a pleckstrin homology-like (PH) domain (8). Sec14 domains are defined by a lipid binding pocket that resembles a cage and is covered by a helical lid portion that is believed to regulate ligand access (8). The PH-like region displays a protrusion that connects two beta-strands from the PH core that extend to interact with the helical lid found in the Sec14 domain (8). The function of the interaction between these two regions is presently unclear, but the structure implies a regulatory interaction that influences the helical-lid conformation in order to control ligand access to the lipid binding pocket (8). 

Isoforms

There are five isoforms of neurofibromin (II, 3, 4, 9a, and 10a-2) and these isoforms are generated through the inclusion of exons that exhibit alternative splicing (9a, 10a-2, 23a, and 48a), but do not alter the reading frame (3). These five isoforms are expressed in distinct tissues and are each detected by specific antibodies (3). 

Neurofibromin type II, also named GRD2 (domain II-related GAP), results from the insertion of exon 23a, which causes the addition of 21 amino acids in the 5’ region of the protein (3). Neurofibromin type II is expressed in Schwann cells and is essential to normal brain function, however, this isoform has reduced GAP activity (3). 

Neurofibromin type 3 (also called isoform 3’ ALT) contains exon 48a which results in the insertion of 18 amino acids into the 3’ terminal (3). Neurofibromin type 4 contains exons 23a and 48a, which results in the insertion of 21 amino acids in the 5’ region, and 18 amino acids in the 3’ terminal (3).

Neurofibromin 9a (also referred to as 9br), includes exon 9a which results in the insertion of 10 amino acids in the 5’ region. This isoform shows little neuronal expression and may play a role in memory and learning mechanisms (3). 

An isoform with insertion of exon 10a-2 has been studied introduces a transmembrane domain (19). The inclusion of exon 10a-2 causes the insertion of 15 amino acids in the 5’ region. This isoform is expressed in most human tissues, therefore it likely performs a housekeeping function in intracellular membranes (3). 

It has been suggested that the quantitative differences in expression between the different isoforms may be related to the phenotypic variability of neurofibromatosis type 1 patients (3).

Related Conditions

Neurofibromatosis Type 1 (NF1)

Neurofibromatosis 1 (NF1) is a rare autosomal dominant disease that is linked to mutations in the NF1 gene. NF1 occurs in 1 in 3000 to 4000 people worldwide (7) (9). It is a genetic disorder that results in the formation of tumors on nerve tissues, and these tumors can develop anywhere in the nervous system (6). Neurofibromatosis is usually diagnosed in childhood or early adulthood and the main diagnostic signs are café au lait spots visible on the skin and freckles of skinfolds (8) (2).

Inheritance Pattern

The inheritance pattern of neurofibromatosis type 1 is autosomal dominant, meaning that a parent with the disorder has a 50% chance of passing it on to one of their children (8). People with NF1 are born with one mutated copy of the NF1 gene present in each cell. In about 50% of NF1 cases, the mutated gene is inherited from an affected parent, and the remaining cases occur in people with no family history of the disorder and result from de novo mutations in the NF1 gene (9). 

In most autosomal dominant conditions, the presence of one altered copy of the gene in each cell is enough to cause the disorder. In NF1, two copies of the altered NF1 gene must be present to trigger tumor formation. The majority of people born with one NF1 mutation acquire a second mutation in several cells and develop tumors characteristic of neurofibromatosis type 1 (9). 

Article Evaluation

• Article on CpG site
  • I found the pictures at the start of the article ( two sequences) to be distracting and not really necessary.
  • sentence after the second paragraph on the percentage of CpG sites methylated in mammals seems out of place.
  • Sentence in 5th paragraph under "CpG islands" on imprinting seems out of place and kind of distracting. Doesn't really seem important to the overall topic.
  • First half of CpG islands section doesn't seem to flow very nicely, kind of hard to follow.
  • Written kind of choppy. A lot of lone sentences that don't really fit in with paragraphs before or after them.
  • References is a lot of older studies (2002, 2012).
  • First paragraph in "DNA repair genes with hyper/hypo-methylated promoters in cancers" section doesn't flow very nicely. A lot of short sentences.
  • Article seems very neutral, nothing seems biased.
  • There don't seem to be any viewpoints that are overrepresented or underrepresented. Covers several topics relating to CpG sites, doesn't put too much focus on any particular topic.
  • All of the 10 links that I checked worked and led to primary articles that were reputable.
  • All of the sources that I checked were scientific articles found on NCBI which seem to be unbiased and reliable sources.
  • Most facts are referenced with appropriate and reliable sources, but there are a few that don't appear to be referenced.
  • Information seems up to date, but the studies referenced are fairly dated, one from 2002 and one from 2012.
  • Could maybe add some more information on what methylation is and what it entails. Not sure if that is required or if users are just expected to go to the page on methylation to learn more.
  • The formulas for the observed and expected CpG ratio is a bit confusing. Could maybe be written out more clearly.
  • On the talk page, there are conversations going on about whether the term "CpG continents" should be used or whether "CpG islands" is more appropriate. Also discussing the reliability of references regarding stats stated in the article. Clarification of what is meant by the formulas for observed and expected CpG ratio. Someone also commented on the clarity of the picture of nucleotide sequences at the start of the article.
  • This article is rated C-class, mid-importance. It is part of three WikiProjects: WikiProject Genetics, WikiProject Molecular and Cell Biology and WikiProject Evolutionary Biology.
  • I don't find that this article discusses anything differently than how we have talked about it in class, other than it also refers to CpG sites as CG sites, which is a term I have never heard before. I think the article covers all of the key points as well as adds some additional information, I just don't think it is written as clearly as it could be or flow as nicely as it should.

Possible Topics

• NF1 gene
• Fryns-Aftimos Syndrome
• Caspase-9
• Gal operon
• Monosomy

Article on NF1

Structure of Article

Gene

- The NF1 gene encodes a tumour suppressor protein called neurofibromin (PMID 27622733)

- Located on chromosome 17, band q 11.2

- Gene spans more than 280kb

- PMID 26671924

Mutations

Structure

Function

- Protein involved in accelerating GTP hydrolysis on Ras proteins (PMID 8563751)

- Plays a role in keratinocytes and melanocytes (PMID 27622733)

- regulates melanin synthesis and keratinocyte differentiation (PMID 27622733)

- role in tumorigenesis and cancer ( PMID 27622733)

Related Conditions

- Neurofibromatosis

Good job. Keep it up! AdamCF87 (talk) 17:40, 5 October 2017 (UTC)