Genomic Organization of Merkel cell polyomavirus (MCPyV)

Based on the provided image of the MCPyV (Merkel cell polyomavirus) genome, it appears that ALTO is positioned between the LT (Large T antigen) and sT (small T antigen) regions. However, it's not entirely clear from the diagram alone if ALTO is a distinct domain within sT, or if it's a separate gene entirely.

In the literature, the ALTO protein (A novel T antigen Open Reading Frame) of MCPyV has been described as a unique feature of the virus. While its specific function and relationship to the other T antigens (LT and sT) are still a topic of research, it is indeed distinct from the canonical LT and sT proteins.

In short, based on the diagram and typical annotations for MCPyV, ALTO does not appear to be a part of sT; rather, it's a distinct open reading frame (ORF) or protein. However, more detailed genomic annotations and experimental studies would be needed to definitively determine its relationship with other proteins encoded by the virus.

https://www.frontiersin.org/articles/10.3389/fmicb.2021.739695/full

https://www.researchgate.net/publication/328072551_The_biology_and_treatment_of_Merkel_cell_carcinoma_current_understanding_and_research_priorities

JN707599.gtf

JN707599    Genbank gene    465 1190    .   +   .   gene_id "VP2"; gene_type "protein_coding"
JN707599    Genbank transcript  465 1190    .   +   .   gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599    Genbank exon    465 1190    .   +   0   gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599    Genbank CDS 465 1190    .   +   0   gene_id "VP2"; transcript_id "tx-AEX86628.1"; gene_type "protein_coding"
JN707599    Genbank gene    600 1190    .   +   .   gene_id "VP3"; gene_type "protein_coding"
JN707599    Genbank transcript  600 1190    .   +   .   gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599    Genbank exon    600 1190    .   +   0   gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599    Genbank CDS 600 1190    .   +   0   gene_id "VP3"; transcript_id "tx-AEX86629.1"; gene_type "protein_coding"
JN707599    Genbank gene    1156    2427    .   +   .   gene_id "VP1"; gene_type "protein_coding"
JN707599    Genbank transcript  1156    2427    .   +   .   gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599    Genbank exon    1156    2427    .   +   0   gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599    Genbank CDS 1156    2427    .   +   0   gene_id "VP1"; transcript_id "tx-AEX86630.1"; gene_type "protein_coding"
JN707599    Genbank gene    2503    5387    .   -   .   gene_id "LT"; gene_type "protein_coding"
JN707599    Genbank transcript  5154    5387    .   -   .   gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank exon    5154    5387    .   -   0   gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank CDS 5154    5387    .   -   0   gene_id "LT"; transcript_id "tx1-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank transcript  2503    4722    .   -   .   gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank exon    2503    4722    .   -   0   gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank CDS 2503    4722    .   -   0   gene_id "LT"; transcript_id "tx2-AEX86632.1"; gene_type "protein_coding"
JN707599    Genbank gene    4827    5387    .   -   .   gene_id "sT"; gene_type "protein_coding"
JN707599    Genbank transcript  4827    5387    .   -   .   gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"
JN707599    Genbank exon    4827    5387    .   -   0   gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"
JN707599    Genbank CDS 4827    5387    .   -   0   gene_id "sT"; transcript_id "tx-AEX86631.1"; gene_type "protein_coding"

JN707599.fasta

>JN707599
CTTGTCTATATGCAGAAGGAGTTTGCAGAAAGAGCAGAGGAGCAAATGAGCTACCTCACTAAGGAGTGGT
TTTTATACTGCAGTTTCCCGCCCTTGGGATCTGCCCTTAGATACTGCCTTTTTTGCTAATTAAGCCTCTT
AAGCCTCAGAGGCCTCTCTCTTTTTTTTCCAGAGGCCTCGGAGGCTAGGAGCCCCAAGCCTCTGCCAACT
TGAAAAAAAAAAGTCACCTAGGCAGCCAAGTTGTGGTTACATGATTGAACTTTTATTGCTGCAGGGTTTC
TGGCATTGACTCATTTCCTGGAGAGGCGGAGTTTGACTGATAAACAAAACTTTTTTTCTTTCTGTTTGGG
AGGGAGACGGAAGACTCTTAACTTTTTTTCAACAAGGGAGGCCCGGAGGCTTTTTTTTCTCTTACAAAGG
GAGGAGGACATTAAAAGAGTAAGTATCCTTATTTATTTTTCAGGATGGGGGGCATCATCACACTGCTGGC
CAATATTGGTGAAATTGCTACTGAACTAAGTGCCACCACAGGAGTAACTTTGGAAGCTATTCTTACAGGA
GAAGCTTTAGCAGCTTTGGAAGCAGAGATCTCCAGTTTAATGACAATTGAGGGTATTTCTGGCATTGAGG
CTTTAGCTCAACTTGGGTTCACAGCTGAACAGTTTTCAAATTTCTCATTAGTGGCTTCTTTGGTTAACCA
AGGTTTAACTTATGGCTTCATTCTCCAAACTGTTAGTGGTATAGGCTCTCTAATAACTGTGGGGGTGAGG
TTGTCACGCGAGCAAGTGTCACTTGTAAAGAGGGATGTTTCGTGGGTAGGTAGTAATGAGGTTTTGAGGC
ATGCACTTATGGCCTTTAGCCTAGATCCTCTGCAGTGGGAAAATAGCTTGCTGCATTCTGTGGGGCAAGA
TATTTTTAATTCTTTATCTCCTACCTCTAGGCTGCAGATACAATCAAACCTAGTGAATCTGATACTAAAT
AGCCGGTGGGTCTTTCAGACAACTGCTTCTCAGAATCAGGGCCTTTTATCAGGAGAGGCTATATTAATTC
CTGAACATATAGGAGGAACTCTGCAGCAGCAAACTCCAGATTGGCTTCTTCCTCTGGTACTAGGCCTTAG
TGGATATATTTCTCCTGAATTACAAGTAATTGAAGATGGCACCAAAAAGAAAAGCATCATCCACCTGTAA
AACACCCAAAAGGCAATGTATACCTAAGCCGGGATGCTGCCCTAATGTTGCCTCAGTTCCAAAACTGCTT
GTTAAAGGAGGAGTGGAAGTATTATCTGTGGTTACTGGAGAAGATAGCATTACCCAAATTGAGTTGTATT
TGAATCCAAGAATGGGAGTTAATTCCCCTGATCTTCCTACTACTTCAAACTGGTATACTTATACTTATGA
CCTGCAGCCAAAGGGATCATCTCCAGATCAGCCCATCAAGGAAAATTTGCCAGCTTACAGTGTGGCAAGA
GTGTCTCTGCCAATGCTAAATGAGGATATTACCTGTGACACATTGCAGATGTGGGAGGCAATATCTGTTA
AAACAGAAGTAGTTGGAATAAGTTCTTTAATTAATGTTCATTATTGGGACATGAAAAGAGTTCATGATTA
TGGTGCTGGTATTCCTGTGTCAGGGGTAAATTACCATATGTTTGCCATTGGGGGAGAACCTCTGGATTTG
CAAGGCCTAGTTTTAGATTACCAGACTGAGTATCCAAAAACTACAAATGGTGGGCCTATTACAATTGAAA
CTGTATTGGGAAGAAAAATGACACCTAAAAATCAGGGCCTAGATCCACAAGCTAAAGCAAAATTAGATAA
AGATGGAAATTATCCTATAGAAGTATGGTGTCCTGATCCTTCTAAAAATGAAAACAGTAGATACTATGGG
TCTATTCAGACAGGCTCTCAGACTCCTACAGTTCTTCAATTTAGTAATACTCTAACTACTGTCCTTTTAG
ATGAGAATGGAGTGGGCCCTCTATGCAAAGGAGATGGCCTATTTATTAGCTGTGCAGACATAGTGGGGTT
TCTGTTTAAAACCAGTGGAAAAATGGCTCTTCATGGGTTGCCTAGATATTTTAATGTTACTTTGAGAAAA
AGATGGGTGAAAAACCCCTACCCAGTAGTTAATTTAATAAACTCACTCTTCAGCAACTTAATGCCAAAAG
TGTCAGGCCAACCTATGGAAGGAAAAGATAATCAGGTAGAAGAGGTTAGAATATATGAGGGGTCAGAACA
ATTACCTGGTGATCCTGATATTGTCAGATTTTTAGATAAATTTGGGCAGGAGAAAACTGTTTACCCAAAG
CCCTCTGTTGCCCCAGCAGCAGTAACATTCCAAAGTAATCAGCAGGATAAGGGCAAGGCGCCACTGAAAG
GACCTCAAAAGGCCTCTCAAAAAGAAAGCCAAACACAAGAATTATGAGAATTATTTCATGCATTCCTATT
CAGTTAAGTAGGCCCCAGAAAAACAAACACAGGAAATATGAAGCAGATGCCTTTATTGAGAAAAAGTACC
AGAATCTTGGGTTTCTTCAGTTTCCTCAGGGCCCTCTTCCTCAATAAGAATATTGAGCAGAGGGTCCTGA
CCAGCTTCTACATTTTCTATCATTTGACAAAATTTACCATATGATATTTCACTCTGTAAAATTTGCTTCC
AGTTTTTAATTTCTTCTTGTAAGCAAGGCTTAAAGGTTGTATCAGGCAAGCACCAAATAAGACAAAGCAA
TAAAGTGGTTCCACTTTGAAGAATTCTTCTTTTTCTTATTTCCATGTTCTGATCCAGGGAATCTCTTAGA
TTTGCCTTTGGGGAAAAGTGTAAAGTATAACTAAATCTTGCTATTAATGTTTTGGGAATAAAATAATCAT
TAGCAGTAACAATACAAGGAGGAAAAATCTGATGCTTTTTATTCACATGCTTCTTCTCTAAGCTTACAGC
TACAGCACCATCTAGATGATCTCTTAAGTTATCAAGGTTATTTATTCCTTGCCCTGGTTGCAGATCTTTA
TTTAGGCTATTTTGCCCTTTCACATCCTCAAAAACAACCATAAATTTATCCAAAGCACATCCTAGTTCAA
AAGGCAGTTTATCAGATGGACAGTTTATATTCAAGGCCTTCCCTTCTAGCAAATCTATTAAGGCTGCAGC
AAAGCTTGTTTTTCCACTGTTAATAGGCCCTTTAAACCAAATGTTTCTATACTTAGGTATATTCTCTGTT
AATAATTGAATAATTTTCTGCAGCTTCTTTTCAAACTCTTCAAATAAGCAGCAGTACCAGGCCACACCAC
CCATATAATACAGTAGATCTATTGTATCTAAATCTCTTAATCTCTCTAGGTGCTTCTTAAACTTCTTACA
TAGCATTTCTGTCCTGGTCATTTCCAGCATCTCTAACCTCCTTTTGGCTAGAACAGTGTCTGCGGCTTGT
TGGCAAATGGTTTTCTGAGATTTAGATTCATAAAATAGCTTAGCATTAGAATGATGAGCCTCATGAGCCT
TGTGAGGTTTGAGGCGAGATCTGTTTTCACACTTTTGGCAAGGAAATGGTTTTGCAAAGTCTAGATAATG
GGCTAAGATAATAAAGTGGTCGTCTAGCTCATATTCACAAGCAAATTCAGCAACTAAATTCCAATTACAG
CTGGCCTCTTTTTCTTTTTCTTGAAATTCATAATTGAGCAGTGGCTTATTCTCTTGCAGTAATTTGTAAG
GGGGCTTGCATAAATTATTATACATTTCAGGCATCTTATTCACTCCTTTACAAATTAAAAAGCTTATAGT
GCAGAAGGTAGAGCAAAAATTCTTAATAGCAGATACTCTATGCTTTGATAAAGTTATAAACAATAAAATA
CATCCTAATTCACAGGCATGCCTGCTTTTAAAATCAACTTTAAATTTCTCAATCTTATCATATAACTCTA
TAGCTTTATCAGAAGTAGTATAAATGGCAAAACAACTTACTGTTTTATTACTATATACAGCATGGCTAAG
ATAATCAGAAAGATCAATAGGAAAATCAGTAGGAACAGGAGTTTCTCTGTTCTTTTTTGGCTTTGGTGGA
GTGCTTGTAAAACTTGCTGAACTAGCAGAGCTTGCAGAGCTTCGGGACCCCCCAAATTTTCGCTTTCTTG
AGAATGGAGGAGGGGTCTTCGGGGTGGTGAAGGAGGAGGATCTGTATTCCTCATCTGTAAACTGAGATGA
CGAGGCCTCCTCGGCAGAGGAAGACGGGGGCTGCCGGGGCGAGCTTCTTGAGGAGGGGGGCTCCTCAGGC
TCCTCAGAGGACGAGGGAGGCTCAGGGGAGGAAAGTGATTCATCGCAGAAGAGATCCTCCCAGGTGCCAT
CCGTTCTGGAAGAATTTCTAGGTACACTGGTTCCATTGGGTGTGCTGGATTCTCTTCCTGAATTGGTGGT
CTCCTCTCTGCTACTGGATCCAGAGGATGAGGTGGGTTCCTCATGGTGTTCGGGAGGTATATCGGGTCCT
CTGGACTGGGAGTCTGAAGCCTGGGACGCTGAGAAGGACCCATACCCAGAGGAAGAGCTCTGGCTGTGGG
GTGGTGAGCTTCCACTGGGGGCTCCCCTGGATGCATTGGAGGAAGGCTTTCTGGATCTTGAGTTGGTCCC
GTGTGGATTGGGCCCATATTCGTATGCCTTCCCGAAGCTGAATCCTCCTGATCTCCACCATTCTTTGAAT
TTAGTGGTCCCATATATAGGGGCCTCGTCAACCTAGATGGGAAAGTACAGAAAATCTGTCATAAATAACC
TTTCTTTGATATTTTGCCTTATAGACTTTTCCATATCTAATACTTACAGAGGAAGGAAGTAGGAGTCTAG
AAAAGGTGCAGATGCAGTAAGCAGTAGTCAGTTTCTTCTAAAGTTTTTTGCCACCAGTCAAAACTTTCCC
AAGTAGGAGGAAATCCAAACCAAAGAATAAAGCACTGATAGCAAAAACACTCTCCCCACGTCAGACAGTT
TTTTTGCTTTAAAGTTTTTAGACTACAATGCTGGCGAGACAACTTACAGCTAATACAAGCGCACTTAGAA
TCTCTAAGTTGCTTAAGCATGCACCCAGGACCTCTGCAAAATCTAGCATTATATCCACTTTGCATATAAT
CCTTTAAAGTTCCATATTCTTCCCAAGGAAATTTTGTACTGACCTCATCAAACATAGAGAAGTCACTTCT
GAGCTTGTGGATATTTTGCTGGAATTTGCTCCAAAGGGTGTTCAATTCCATCATTATAACAGGATTTCCC
CCTTTATCAGGGTGATGCTTTAAGCAGCTTCTTTTGAAAGCAGCTTTCATCAGAGGGATGTTGCCATAAC
AATTAGGAGCAATCTCTAAAAGCTTGCAGAGAGCCTCTCTTTCTTTCCTATTTAGGACTAAATCCAT

| title | treatment | time | | :--- | :----: | ---: | | untreated_DonorI | untreated | Day 0 | | untreated_DonorII | untreated | Day 0 | | p601_d3_DonorII | mCherry control | Day 3 | | p604_d3_DonorII | sT | Day 3 | | p601_d8_DonorII | mCherry control | Day 8 | | p604_d8_DonorII | sT | Day 8 | | p601_d3_DonorI | mCherry control | Day 3 | | p604_d3_DonorI | sT | Day 3 | | p601_d8_DonorI | mCherry control | Day 8 | | p604_d8_DonorI | sT | Day 8 | | p600_d3_DonorII | GFP control | Day 3 | | p605_d3_DonorII | LTtr | Day 3 | | p600_d8_DonorII | GFP control | Day 8 | | p605_d8_DonorII | LTtr | Day 8 | | p600_d3_DonorI | GFP control | Day 3 | | p605_d3_DonorI | Lttr | Day 3 | | p600_d8_DonorI | GFP control | Day 8 | | p605_d8_DonorI | Lttr | Day 8 | | p602_d8_DonorII | LT | Day 8 | | p602_d8_DonorI | LT | Day 8 | | p600and601_d12_DonorI | GFP+mCherry control | Day 12 | | p604and605_d12_DonorI | sT+LTtr | Day 12 | | p600and601_d9_DonorII | GFP+mCherry control | Day 9 | | p604and605_d9_DonorII | sT+LTtr | Day 9 | | p602_d3_DonorI | LT | Day 3 | | p602_d3_DonorII | LT | Day 3 | | p602and604_d3_DonorI | sT+LT | Day 3 | | p602and604_d3_DonorII | sT+LT | Day 3 |

• untreated

• p602 LT *

• p687 LT K331A *

• p605 LTtr * (vs. p600 GFP control)

• p604 sT

• p602+604 LT+sT (vs. p601 mCherry control)

• p604+p605 sT+LTtr (vs. GFP+mCherry control p601+p600)

Filtering RNA-seq analysis results and Workbook Creation with R

    # Load required libraries
    if(!requireNamespace("readxl", quietly = TRUE)) install.packages("readxl")
    if(!requireNamespace("dplyr", quietly = TRUE)) install.packages("dplyr")
    if(!requireNamespace("writexl", quietly = TRUE)) install.packages("writexl")
    if(!requireNamespace("openxlsx", quietly = TRUE)) install.packages("openxlsx")

    library(readxl)
    library(dplyr)
    library(writexl)
    library(openxlsx)

    setwd("/media/jhuang/Seagate Expansion Drive/Data_Denise_RNASeq/results_24samples/featureCounts/degenes_2021")

    # Read the data from the specific sheet
    data <- read_excel("degenes_replicates.xls", sheet = "p604_d3_vs_p601_d3-all")
    print(data, n = 10, width = Inf)

    # Filter the data
    #filtered_data <- data %>% 
    #  filter(padj < 0.05, log2FoldChange >= 2)

    upregulated_genes <- data %>%
      filter(padj < 0.05, log2FoldChange >= 2)
    dim(upregulated_genes)

    downregulated_genes <- data %>%
      filter(padj < 0.05, log2FoldChange <= -2)
    dim(downregulated_genes)

    # Create a new Excel workbook
    wb <- createWorkbook()

    # Add sheets with data
    addWorksheet(wb, "Up-regulated")
    writeData(wb, "Up-regulated", upregulated_genes)

    addWorksheet(wb, "Down-regulated")
    writeData(wb, "Down-regulated", downregulated_genes)

    # Save the workbook
    saveWorkbook(wb, "sT_d3_up_and_down.xlsx", overwrite = TRUE)

    data <- read_excel("p604_vs_p601_d8.xls", sheet = "p604_d8_vs_p601_d8-all")
    print(data, n = 10, width = Inf)

    upregulated_genes <- data %>%
      filter(padj < 0.05, log2FoldChange >= 2)
    dim(upregulated_genes)

    downregulated_genes <- data %>%
      filter(padj < 0.05, log2FoldChange <= -2)
    dim(downregulated_genes)

    # Create a new Excel workbook
    wb2 <- createWorkbook()

    # Add sheets with data
    addWorksheet(wb2, "Up-regulated")
    writeData(wb2, "Up-regulated", upregulated_genes)

    addWorksheet(wb2, "Down-regulated")
    writeData(wb2, "Down-regulated", downregulated_genes)

    # Save the workbook
    saveWorkbook(wb2, "sT_d8_up_and_down.xlsx", overwrite = TRUE)

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