Background
Methods
Identification of the US12 potential transcriptional regulation region sequences in HSV
Phylogenetic analysis of the transcriptional regulation region of the US12 gene
Prediction of US12 transcription regulatory sequences and factors
Alignment of the transcriptional regulation region sequences of US12
Results
Identification of the US12 transcription regulatory region of HSV-1-LXMW
HSV Strain | Gene Bank ID | Tax-ID | Sub-Date | US12 transcription regulatory regions | University, Country |
---|---|---|---|---|---|
HSV-1 strain XLMW | 145,851 / 148,050 | Yangtze University, Jingzhou, China | |||
HSV-1 strain 17 | JN555585 | 10,299 | 2011-08-02 | 145,869 /148,068 | RC University, Glasgow, UK |
HSV-1 strain H129 | GU734772 | 744,249 | 2010-01-18 | 145,769/ 147,968 | Princeton University, USA |
HSV-1 Strain CR38 | HM585508 | 10,298 | 2013-10-17 | 145,315 / 147,514 | MRC Virology Unit, UK |
HSV-1 strain SC16 | KX946970 | 10,309 | 2016-10-30 | 113,629/114,168 | Severo Ochoa, Spain |
HSV-1 strain KOS | JQ673480 | 10,306 | 2012-03-10 | 145,672 /147,871 | University of Kansas, USA |
HSV-1 strain Patton isolate | MF959544 | 10,308 | 2017-10-11 | 146,470 / 148,669 | NYU, New York, USA |
HSV-1 strain E19 | HM585511 | 10,298 | 2013-10-22 | 144,988 / 147,187 | University of Glasgow Centre for Virus Research, UK |
HSV-1 strain F | GU734771 | 10,304 | 2010-01-18 | 145,795 / 147,994 | Princeton University, USA |
HSV-2 strain SD90e | KF781518 | 1,177,628 | 2013-10-25 | 147,503 / 149,702 | Harvard Medical School, Boston, US |
HSV-2 strain HG52 | JN561323 | 10,310 | 2011-08-05 | 147,834 / 150,033 | University of Glasgow, UK |
HSV-2 strain H1226 | KY922720 | 16,866 | 2017-09-27 | 147,094 /149,293 | Pennslyvania State University, USA |
Phylogenetic analysis of HSV-1-LXMW and other 11 HSV strains
Identification of the US12 TRS and TRF
HSV strain | Matrix identifier | Position strand | Core match | Matrix match | Sequence | Factor name |
---|---|---|---|---|---|---|
HSV-1 strain XLMW | V$CREL_01 | 37 (+) | 1.000 | 0.982 | gggtcTTTCC | c-Rel |
V$HNF4_01 | 1020 (−) | 0.883 | 0.898 | ccctgtcCTTTTtcccacc | HNF-4 | |
V$ELK1_02 | 1875(+) | 1.000 | 0.984 | ggcgcCGGAAgccc | Elk-1 | |
V$PAX4_01 | 2029 (−) | 0.888 | 0.833 | gccacgggccgCTTCAcggcc | Pax-4 | |
HSV-1 strain 17 | V$CREL_01 | 37 (+) | 1.000 | 0.982 | gggtcTTTCC | c-Rel |
V$HNF4_01 | 1023 (−) | 0.883 | 0.898 | ccctgtcCTTTTtcccacc | HNF-4 | |
V$PAX4_01 | 2032 (−) | 0.888 | 0.833 | gccacgggccgCTTCAcggcc | Pax-4 | |
HSV-2 strain SD90e | V$HNF4_01 | 746 (−) | 1.000 | 0.928 | gctcgcaCTTTGccctaat | HNF-4 |
I$CF2II_01 | 767 (−) | 1.000 | 1.000 | tatATATAc | CF2-II | |
V$HNF4_01 | 886 (−) | 1.000 | 0.928 | gctcgcaCTTTGccctaat | HNF-4 | |
I$CF2II_01 | 907 (−) | 1.000 | 1.000 | tatATATAc | CF2-II | |
I$E74A_01 | 1076(+) | 1.000 | 0.954 | cgaaccCGGAAgggcag | E74A | |
V$OCT1_Q6 | 1120 (−) | 0.883 | 0.911 | ctcaTTAGCatcgcg | Oct-1 | |
F$STUAP_01 | 1637 (−) | 1.000 | 1.000 | ggtCGCGAtg | StuAp |
The TRS and TRF are conserved
The TRFs c-Rel and Oct-1 are functional during HSV infection
Tissue type | HSV strain | Oct-1 | c-Rel | Function | Ref. |
---|---|---|---|---|---|
Kidney: Vero cells | HSV-1 strain 17 | – | c-Rel | As a novel cause of HSE disease susceptibility. | [31] |
Hematological: Jurkat cells | HSV-1 | – | p65/c-Rel | the p65/c-Rel heterodimer is responsible for the NF-kB-dependent induction of HIV-1 LTR in HSV- 1-infected cells. | [32] |
Embryonic: WT and dOct MEF cells | HSV-1 strain F | Oct-1 | – | Oct-1 is required for the formation of HSV replication factories and late gene expression. | [33] |
Digestive: Hep2 cells | HSV-1 strain KOS | Oct-1 | – | Oct-1 directly recognizes TAATGARAT elements in promoters of IE genes. | [34] |
Urinary: COS-7 cells | HSV-1 strain KOS | Oct-1 | – | Distinct conformations of Oct-1 on the BHV IE1 sites and on the HSV IE110 sites. | [35] |
Genital: HeLa cells | HSV-1 strain F | Oct-1 | – | late in infection Oct-1 is posttranslationally modified and exhibits a reduced capacity to bind to its cognate sites. | [36] |
Genital: HeLa cells | HSV-1 strain KOS | Oct-1 | – | Ser375 is important for the interaction of VP16 with Oct-1, and that the interaction is required to enable both proteins to bind to IE promoters. | [28] |
Genital: HFF | HSV-1 strain KOS | Oct-1 | – | forms a transactivation complex with the cellular proteins HCF-1 and HSV-1 VP16 tegument protein. | [29] |
Genital: HeLa cells | HSV-2 strain 333 | Oct-1 | – | the HSV-2 protein forms a transcriptional complex with the cellular Oct-1 protein and target TAATGARAT elements from immediate-early promoters. | [37] |
The HSV-1/2 tissue tropism and TRFs expression in different tissues
System | Cell/ tissue | HSV-1 | HSV-2 | c-Rel | HNF-4 | Elk-1 | Pax-4 | CF2-II | OCT-1 |
---|---|---|---|---|---|---|---|---|---|
Blood system | CD34+ stem cell | + | _ | H | H | H | H | H | H |
721 B lymphoblasts | + | _ | H | H | H | H | M | H | |
CD19 + B cell | + | _ | H | H | H | H | M | H | |
Leukemia lymphoblastic | + | _ | M | M | M | M | L | L | |
Bonemarrow | + | _ | H | M | H | H | M | H | |
Pituitariy | + | _ | H | H | H | H | H | M | |
Head | Prefrontal Cortex | + | _ | H | H | H | H | H | H |
Pineal | + | _ | H | H | H | H | H | M | |
Tongue | + | _ | H | M | H | H | L | M | |
Tonsil | + | _ | H | M | M | H | L | L | |
Retina | + | _ | H | H | H | H | H | M | |
Trigeminal ganglion | + | _ | M | H | H | H | L | L | |
Cerebellum | + | _ | H | H | M | H | H | M | |
Viscera | Heart | + | _ | H | H | H | H | H | M |
Lung | + | _ | H | H | H | H | H | M | |
Liver | + | _ | H | H | H | H | H | M | |
Kidney | + | _ | M | M | M | M | H | L | |
Smooth Muscles | + | _ | H | H | H | H | H | M | |
Adipocyte | + | _ | H | M | M | H | L | L | |
Secretory system | Adrenalgland | + | _ | M | M | H | H | L | L |
Pancreaticlstet | + | _ | H | H | H | H | H | M | |
Genital system | Placenta | + | + | H | H | H | M | H | M |
Fetalthyroid | + | + | H | M | M | M | H | M | |
Uterus | + | + | M | M | M | M | M | L | |
Testis | + | + | M | M | M | M | H | L | |
Ovary | + | + | M | M | L | L | L | M |