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
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
Up/Down and not in P_M:
- Ets2
- Dscr3
- Chaf1b
- Rcan1
- 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.
