Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins

Ghosh, Subhanita; Kakumani, Pavan Kumar; Kumar, Ajit; Malhotra, Pawan; Mukherjee, Sunil K; Bhatnagar, Raj K

doi:10.1186/1471-2164-15-775

BMC Genomics

Table 1 Putative RNAi factors of Sf21 quantified by gfp reversion assay

From: Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins

Gene	% gfpreversion	Identity %
Gene	% gfpreversion	Bm	Tc	Dm
Core RNAi factors
Argonaute-1	48.6	94	88	83
Argonaute-3	12.25	69	44	43
Dicer-2	43.61	64	38	30
Dicer-1	25.43	68	43	40
Aubergine	41.42	69	49	44
Drosha	39.97	84	66	60
Pasha	45.56	69	53	38
Loquacious	16.56	84	66	56
R2D2	23.74	60	28	30
Auxilliary RNAi factors
DEAD RNA helicase domain proteins
Dbp45A subfamily	24.22	87	56	57
VASA subfamily	31.08	80	59	58
DDX18/HAS1 subfamily	61.54	74	53	52
RNA processing module
U1A snRNP	36.87	90	83	73
SmG	23.79	94	83	77
Integrator complex subunit (Int11)	76.11	99	92	91
Zn finger protein	38.7	69	35	33
Regulator of nonsense transcripts 1 homolog (smg-2 like)	11.45	97	81	76
Protein Kinase family of signalling allied components
CaM Kinase	25.86	96	84	83
Serine/threonine p21-activated kinase (PAK) mbt like protein	31.32	86	62	79
cAMP-dependent protein kinase C1	39.3	99	98	95
Protein Kinase C	21.58	97	92	87
IKK-beta	30.39	66	36	30
STE20/Fray	40.41	86	75	73
MAPKK4	39.96	90	75	73
Multi drug resistance cassette transporter
MDR1A	67.51	73	51	46
Tudor domain protein
Tudor**	-	79	56	54
Sid like protein
Sil-2	9.23	65	33
Chromatin factors
Histone3 Lysine4 N-methyltransferase	38.57	82	45	60
Histone deacetylase 3 like	26.71	94	85	79
Gas41	26.92	88	71	70
Translational unit
eIF2B-gamma	30.55	79	48	41
eIF4AII	24.16	96	83	80
eIF4AIII	30.92	99	93	96
RPL23P	28.09	98	93	84
Cell division associated elements
KIF18A-like	24.97	76	63	59
Cyclin-dependent kinase 5 homolog	23.61	99	91	80
KIF3A-like	44.75	96	58	69
Metabolic factor
Isocitrate dehydrogenase [NAD] subunit alpha	67.32	82	79	72
Others
Myosin VIIa-like	26.44	95	88	84
Nucleolar complex protein 2 homolog	35.81	69	53	55
WD 40 like repeat domain	30.55	97	94	90
S-phase kinase-associated protein (SkpA)	35.7	98	93	83

The table contains 42 Sf21 RNAi factors with their respective percentage of gfp reversion in the functional assay. Comparative genomics analyses for identity of each Sf21 candidate with other insects Bombyx mori (Bm), Tribolium castaneum (Tc) and Drosophila melanogaster have been done by homology based search.
**Several RNAi related studies reveal Tudor as one of the conventional RNAi factor. Although reversion assay did not show expected outcome in our study; we consider Tudor as one of the potential RNAi candidate thus mentioning 42 RNAi candidates in the present study.

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ISSN: 1471-2164

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