Lab Notes

Back to Andy Ultimate goal: Identify genes that are trisomy-related but differentially expressed based on parent-of-origin. 1) Identify trisomic genes 2)

Methods followed for various experiments: Workflow for candidate gene identification: Start with P_PT and M_MT gene lists -> find all overlapping genes (these should represent all trisomic genes plus some noise) -> Identify genes that are up-regulated in one parent and down-regulated in another

Identified the overlapping genes with the top and bottom 10% logFC values and we are especially interested in genes that have an inverse correlation for M v P.

Fold change is First/Second, so a -FC for a PT/MT comparison means the PT is less than the MT

Some Ensembl IDs map to the same gene but represent alternative splicing events (http://vega.sanger.ac.uk/Mus_musculus/Gene/Summary?db=core;g=OTTMUSG00000028340;r=16:91647506-91679221)

Dimentia/AD in DS- "there is a subset of aged DS persons who do not appear to develop clinical signs of dementia at any age." AD in Down

Excel: Gene names need to be truncated using command- left(A1, 18)
Andy Genes:
Up/Down and in P_M:

• Gabpa - This gene encodes one of three GA-binding protein transcription factor subunits which functions as a DNA-binding subunit. Because of its chromosomal localization and ability to form heterodimers with other polypeptides, this gene may play a role in the Down Syndrome phenotype.
  
• Dyrk1a - Dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family; localized in the Down syndrome critical region of chromosome 21, and is considered to be a strong candidate gene for learning defects associated with Down syndrome; It catalyzes its autophosphorylation on serine/threonine and tyrosine residues. It may play a significant role in a signaling pathway regulating cell proliferation and may be involved in brain development.
  
• Cryzl1
  
• Scaf8 (HSA6)
  
• Jam2
  

Jam2 and Gabpa are proximal to one another:

Up/Down and not in P_M:

• Ets2 - HSA 21 - This gene encodes a transcription factor which regulates genes involved in development and apoptosis. The encoded protein is also a protooncogene and shown to be involved in regulation of telomerase.
  
• Dscr3 - HSA21 - The DSCR3 (Down syndrome critical region gene 3) gene is found in this region and is predictated to contain eight exons. DSCR3 is expressed in most tissues examined. (this link also characterized the critical region).
  
• Chaf1b- HSA21 - Chromatin assembly factor I (CAF-I) is required for the assembly of histone octamers onto newly-replicated DNA. CAF-I is composed of three protein subunits, p50, p60, and p150. The protein encoded by this gene corresponds to the p60 subunit and is required for chromatin assembly after replication. The encoded protein is differentially phosphorylated in a cell cycle-dependent manner. In addition, it is normally found in the nucleus except during mitosis, when it is released into the cytoplasm. This protein is a member of the WD-repeat HIR1 family and may also be involved in DNA repai.
  
• Rcan1 - HSA21 - The protein encoded by this gene interacts with calcineurin A and inhibits calcineurin-dependent signaling pathways, possibly affecting central nervous system development. This gene is located in the minimal candidate region for the Down syndrome phenotype, and is overexpressed in the brain of Down syndrome fetuses. Chronic overexpression of this gene may lead to neurofibrillary tangles such as those associated with Alzheimer disease.-- Interestingly enough, there is a negative correlation with the expression of this gene in paternal trisomy, while a positive expression change is found in Maternal trisomy.*** Double check fold change*** Chronic overexpression is suspected to play a role in alzheimers.
  
• Atp5o
• Paxbp1
• Wrb
• Rps6ka2
• Fgfr1op
• Bach1
• Cct8
• Fcgr2b
• Ice2
• Tdgf1
• Rwdd2b
• Ltn1
• Srrt
• Hmgn1
• Ezr
• Tmem181a
• Mis18a
• Gtf2h5
• Brwd1
• Son
• Mrpl39
• Ttc3
• Paxbp1
• Son
• Prdx2
• Hk1
• Son
• Urb1
• Son
• Psmg1
• Ggnbp2
• Gart
• Atxn1
• Cct8
• Cct8
• Dynlt1b

Ben Genes:

• RIPK4- mutations cause severe phenotype (wrinkly skin, fused eyelids, small mouth, no nose) and babies do not survive. The gene is implicated in keratinocyte differentiation. RIPK4 directly regulates IRF6-> differentiation in keratinocytes. (Not very promising for trisomy)

• Usp16- triplication of Usp16 reduces the self-renewal of haematopoietic stem cells and the expansion of mammary epithelial cells, neural progenitors and fibroblasts.Usp16 can remove ubiquitin from histone H2A on lysine 119, a critical mark for the maintenance of multiple somatic tissues. Downregulation of Usp16, either by mutation of a single normal Usp16 allele or by short interfering RNAs, largely rescues all of these defects.Furthermore, in human tissues overexpression of USP16 reduces the expansion of normal fibroblasts and postnatal neural progenitors, whereas downregulation of USP16 partially rescues the proliferation defects of Down's syndrome fibroblasts. Taken together, these results suggest that USP16 has an important role in antagonizing the self-renewal and/or senescence pathways in Down's syndrome and could serve as an attractive target to ameliorate some of the associated pathologies.