Polycomb group heterochromatin-associated protein HP1-like protein

Overview
NamePolycomb group heterochromatin-associated protein HP1-like protein
Smed IDSMED30005341
Length (bp)1660
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Polycomb group heterochromatin-associated protein HP1-like protein (SMED30005341) t-SNE clustered cells

Violin plots show distribution of expression levels for Polycomb group heterochromatin-associated protein HP1-like protein (SMED30005341) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Polycomb group heterochromatin-associated protein HP1-like protein (SMED30005341) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Polycomb group heterochromatin-associated protein HP1-like protein (SMED30005341) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30005341

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30005341SMESG000079834.1 PL05004B2C08ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005341SMESG000079834.1 PL030012B10F05ncbi_smed_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30005341SMESG000079834.1 dd_Smed_v4_945_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30005341SMESG000079834.1 dd_Smed_v4_945_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30005341SMESG000079834.1 dd_Smed_v4_945_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30005341SMESG000079834.1 dd_Smed_v6_945_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. TrEMBL
Match: A0A5J6BTI0 (Polycomb group heterochromatin-associated protein HP1-like protein OS=Dugesia japonica OX=6161 GN=hp1 PE=2 SV=1)

HSP 1 Score: 214.927 bits (546), Expect = 4.160e-57
Identity = 120/188 (63.83%), Postives = 146/188 (77.66%), Query Frame = 3
Query: 1005 GFYSIYNGFENHKASNKQFDKDRYSLKDKETKSKNGFNFFKTLENVVDPSKALIEEYENIILEQLKINSQISRNDIEEEEFNSYLYRWNSITLRKSEILRLLVNQSEAKFINEKLKYFNSICYQRKYHDCLPESEIYYXXXXXXXXXXXXXXXXCCMVVSDTHETGRKGLKHLKNTLFSTWYVTLENS 1568
            GFYS+YNG EN K   K ++ DRYSLK+ ETKSKNGFNFFKT   + DP K L +EYE II++Q +IN+Q+SRNDI+ EEF + L +WNSITLRKSEILR L+NQSE K ++EKL+YFN+I YQ+KY DCLPES+IY+STQS +SSQSE SD+S  + VSD  E   K  KH  + LFSTWYV LENS
Sbjct:  624 GFYSVYNGTENRKNPIKLYEADRYSLKETETKSKNGFNFFKT---ITDPMKPLTDEYEKIIMDQFEINNQMSRNDIQNEEFKNCLTKWNSITLRKSEILRTLLNQSETKTVSEKLRYFNAIYYQKKYQDCLPESDIYHSTQSQQSSQSEASDNSYNIAVSDNREISGKETKHFGHGLFSTWYVKLENS 808          
BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Planmine SMEST
Match: SMESG000079834.1 (SMESG000079834.1)

HSP 1 Score: 816.224 bits (2107), Expect = 0.000e+0
Identity = 432/434 (99.54%), Postives = 433/434 (99.77%), Query Frame = 3
Query:  267 MKDITKLARRGWWKAMIHQRTLSLILTLDNFLLSGPHILFDCKQLESSDPNVFFVRGRGTQSLIQSELDKEENQNSLSNAHTYYVMRSFIRGILFGLNPLYQISLYVPCNDPKQIQLYREIITKIDIGGQFFQDRIYWNLESLQRDIMDERLACLIYADNLNYIKNDWLKKISIEVKPFVATIDSDMTTNNNLFDLVEMRSFLEEMHERYFSIVNECKSTHFVNMIKFYITXXXXXXXXXXXXXXXGFYSIYNGFENHKASNKQFDKDRYSLKDKETKSKNGFNFFKTLENVVDPSKALIEEYENIILEQLKINSQISRNDIEEEEFNSYLYRWNSITLRKSEILRLLVNQSEAKFINEKLKYFNSICYQRKYHDCLPESEIYYXXXXXXXXXXXXXXXXCCMVVSDTHETGRKGLKHLKNTLFSTWYVTLENS 1568
            MKDITKLARRGWWKAMIHQRTLSLILTLDNFLLSGPHILFDCKQLESSDPNVFFVRGRGTQSLIQSELDKEENQNSLSNAHTYYVMRSFIRGILFGLNPLYQISLYVPCNDPKQIQLYREIITKIDIGGQFFQDRIYWNLESLQRDIMDERLACLIYADNLNYIKNDWLKKISIEVKPFVATIDSDMTTNNNLFDLVEMRSFLEEMHERYFSIVNECKSTHFVNMIKFYITENNNNKSKENYFNPNGFYSIYNGFENHKASNKQFDKDRYSLKDKETKSKNGFNFFKTLENVVDPSKALIEEYENIILEQLKIN QISRNDIEEEEFN+YLYRWNSITLRKSEILRLLVNQSEAKFINEKLKYFNSICYQRKYHDCLPESEIYYSTQSHRSSQSEQSDSSCCMVVSDTHETGRKGLKHLKNTLFSTWYVTLENS
Sbjct:    1 MKDITKLARRGWWKAMIHQRTLSLILTLDNFLLSGPHILFDCKQLESSDPNVFFVRGRGTQSLIQSELDKEENQNSLSNAHTYYVMRSFIRGILFGLNPLYQISLYVPCNDPKQIQLYREIITKIDIGGQFFQDRIYWNLESLQRDIMDERLACLIYADNLNYIKNDWLKKISIEVKPFVATIDSDMTTNNNLFDLVEMRSFLEEMHERYFSIVNECKSTHFVNMIKFYITENNNNKSKENYFNPNGFYSIYNGFENHKASNKQFDKDRYSLKDKETKSKNGFNFFKTLENVVDPSKALIEEYENIILEQLKINGQISRNDIEEEEFNNYLYRWNSITLRKSEILRLLVNQSEAKFINEKLKYFNSICYQRKYHDCLPESEIYYSTQSHRSSQSEQSDSSCCMVVSDTHETGRKGLKHLKNTLFSTWYVTLENS 434          
The following BLAST results are available for this feature:
BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A5J6BTI04.160e-5763.83Polycomb group heterochromatin-associated protein ... [more]
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Polycomb group heterochromatin-associated protein HP1-like protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000079834.10.000e+099.54SMESG000079834.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005341 ID=SMED30005341|Name=Polycomb group heterochromatin-associated protein HP1-like protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1660bp
TCATATTGAAATTTCGTTCTTATGATTTAGTTTTAATTCATTATTATTTA
TAGAATTATTAAGGTCATTAAAGATCATAGTTAATTTGTCAGATGACGAC
GTCAGTTGGTTTGTAGAATTTGCACTTTGTACATTTTATAAAAAAACATG
ATTTAACTAAAGAGGCTATTGATTTTCACTTATAAATTTTTTTATTTACA
AAACACAGACTCTATTCAATGGAAATGAAGTTTGTTTTTTATTATTAAGA
CATTCAGTATTTTTAGATGAAAGATATTACTAAATTAGCTAGACGTGGAT
GGTGGAAAGCAATGATACATCAGCGAACTTTATCGCTTATTTTAACTTTG
GATAATTTTCTTTTGTCTGGACCTCATATTCTATTTGATTGTAAGCAGCT
AGAATCATCAGATCCGAATGTTTTTTTCGTCAGAGGTCGAGGAACTCAGT
CTTTAATTCAGTCAGAATTGGATAAAGAAGAAAATCAAAATTCACTATCC
AACGCTCACACATATTATGTAATGCGATCATTCATTCGGGGTATATTGTT
TGGATTAAATCCTCTGTACCAAATTTCACTTTATGTTCCTTGTAATGACC
CAAAACAAATCCAGCTTTACCGAGAAATAATAACGAAAATAGATATTGGT
GGACAATTTTTTCAAGATCGTATTTATTGGAATTTGGAGAGTTTGCAGCG
AGACATTATGGATGAAAGATTGGCTTGTTTGATTTATGCGGATAATTTGA
ATTACATAAAAAATGATTGGCTTAAAAAAATAAGTATTGAAGTAAAACCT
TTCGTTGCCACGATCGATAGTGACATGACAACGAATAATAACCTTTTCGA
TCTCGTTGAAATGCGAAGTTTTCTTGAAGAAATGCATGAGAGATATTTCA
GTATTGTTAATGAATGTAAATCTACTCATTTTGTCAACATGATAAAATTT
TATATCACTGAAAATAATAACAATAAATCTAAAGAAAATTATTTCAACCC
AAATGGATTTTATTCTATTTATAATGGATTCGAAAATCATAAAGCTTCCA
ATAAACAATTTGATAAGGATCGATATTCATTGAAAGACAAAGAAACCAAA
TCGAAAAATGGATTTAATTTTTTCAAAACTCTAGAAAACGTTGTCGATCC
ATCTAAAGCTTTGATTGAAGAATATGAAAACATCATTCTTGAACAATTGA
AAATTAATAGTCAAATAAGTAGAAACGATATTGAAGAAGAAGAATTTAAT
AGTTATCTTTATCGCTGGAACAGTATAACTTTACGAAAATCGGAAATTCT
TCGACTTCTCGTCAATCAAAGTGAAGCAAAATTTATCAATGAAAAGTTAA
AATATTTCAATTCAATTTGTTATCAAAGGAAATATCACGATTGCTTACCA
GAATCAGAAATCTATTATTCGACACAATCTCACAGATCCAGTCAGAGTGA
ACAATCGGATAGTAGTTGTTGTATGGTCGTATCAGATACTCATGAAACAG
GCAGAAAGGGATTGAAGCATCTAAAGAATACTTTGTTTTCTACTTGGTAT
GTAACATTAGAGAATAGTTAGGTTGCGTTGGTGGTCGATTTCCAGATTAC
TATTGTTCTGTACAAGATTTATTTTATTAATAAATAATTTTGCTATTTTA
AAAAAAAAGA
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protein sequence of SMED30005341-orf-1

>SMED30005341-orf-1 ID=SMED30005341-orf-1|Name=SMED30005341-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=435bp
MKDITKLARRGWWKAMIHQRTLSLILTLDNFLLSGPHILFDCKQLESSDP
NVFFVRGRGTQSLIQSELDKEENQNSLSNAHTYYVMRSFIRGILFGLNPL
YQISLYVPCNDPKQIQLYREIITKIDIGGQFFQDRIYWNLESLQRDIMDE
RLACLIYADNLNYIKNDWLKKISIEVKPFVATIDSDMTTNNNLFDLVEMR
SFLEEMHERYFSIVNECKSTHFVNMIKFYITENNNNKSKENYFNPNGFYS
IYNGFENHKASNKQFDKDRYSLKDKETKSKNGFNFFKTLENVVDPSKALI
EEYENIILEQLKINSQISRNDIEEEEFNSYLYRWNSITLRKSEILRLLVN
QSEAKFINEKLKYFNSICYQRKYHDCLPESEIYYSTQSHRSSQSEQSDSS
CCMVVSDTHETGRKGLKHLKNTLFSTWYVTLENS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005719nuclear euchromatin
Vocabulary: biological process
TermDefinition
GO:0045892negative regulation of transcription, DNA-templated
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell