TGD | Gene Details

Identifiers and Description

Gene Model Identifier
TTHERM_01109990

Standard Name
PDD3 (Programmed DNA Degradation )

Aliases
PreTt17969 | 239.m00048 | 3802.m00189

Description
Programmed DNA degradation 3 protein; developmentally regulated chromodomain protein; localizes to DNA elimination structures during programmed DNA elimination; binds methylated Lys-9 of histone H3

Genome Browser

Gene Ontology Annotations

Cellular Component
macronucleus (IDA) | GO:0031039 | Ref:10805754
Molecular Function
methylated histone residue binding (IDA) | GO:0035064 | Ref:12297044

Domains

No Data fetched for Domains

Gene Expression Profile

Tetrahymena Functional Genomics Database: TTHERM_01109990

Homologs (v.2006 protein sequences)

No Data fetched for Homologs

General Information

Paragraph No Gene Name Paragraph Text
2 TWI1,
HHT2,
PDD1,
PDD3,
DCL1 A proposed model for the mechanism of programmed DNA elimination in Tetrahymena is based on the timing of expression, cellular distribution, mutant phenotypes, and predicted functions of the protein and RNA components involved. In this model, both strands of the micronuclear genome (or perhaps only the portions containing internal eliminated sequences) are transcribed early in conjugation to produce large non-genic, double-stranded RNAs. This transcription is likely performed by RNA Polymerase II, based on the localization of its subunit Rpb3p to the micronucleus during this time. These transcripts pass to the cytoplasm where they are processed into short (~28 nucleotide) scan RNAs (scnRNA) by the dicer-like protein Dcl1p, similar to the production of the small inhibitory RNAs (siRNA) central to the RNA interference (RNAi) pathway of other eukaryotes. The scnRNAs complex with Twi1p, a member of the PPD (PAZ and Piwi Domain) protein family, whose members are commonly involved in RNAi and related processes. The scnRNA/Twi1p complexes enter the old macronucleus, where scnRNAs homologous to DNA sequences found there are degraded. The remaining scnRNAs, comprised of micronuclear-restricted sequences, are transferred to the developing macronucleus. There, histone H3 proteins (Hht1p, Hht2p) that are bound to sections of the genome sharing identity to the scnRNAs are methylated on lysine-9. This modification, which is often associated with the formation of heterochromatin, is recognized by one or more of the chromodomains belonging to Pdd1p and Pdd3p. Regions of DNA associated with these modified histones are eliminated from the developing macronuclear genome.

Associated Literature

Ref:12297044: Taverna SD, Coyne RS, Allis CD (2002) Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell 110(6):701-11
Ref:10805754: Nikiforov MA, Gorovsky MA, Allis CD (2000) A novel chromodomain protein, pdd3p, associates with internal eliminated sequences during macronuclear development in Tetrahymena thermophila. Molecular and cellular biology 20(11):4128-34

Sequences

>TTHERM_01109990(coding)
ATGTAATTAGAAACAAACATTCCCTTAACTAAAATGAAGATGAGTAAGGAAGAAGATTAC
TAGCCTATTAAGAAAGCTCCTAAAAAAAAAACAAATAAAAGAAAAAACGATGAAAATTCT
GTAAGTACCAGAAGGTCAAACAAGAAACAGCATAACGAGGTTAGTGAAGTATCTGATGAA
AGACAGAAAAAGCAAAACGATGCTGAAGAATCACAAAAGTACACTAGATTCTTATCAAAA
GGAAGAGCAAAGTATGTTATCAAAAAATTCTTTAAAAATAATTCTGGTGTTTGGATGATA
GATTTCTAGTAATAGTAGCTAGGAAATGTCATTAATATGTGCAAGAACATTGATGAATCT
CTTGAATACTTAGAACCTAAGTTAATTATCACGTACCTTTTTATTGCTTTGATAAAGTTA
GAATAAAACTGCTTTGAAGTTAAAAGAATTGCTGATGATATGCAATAGTAAGTTGAGTAA
GTAAAAAGTAGCTATAAGATTATATAAATAAATAGAGACCTCAAGACAGCATAGCTTTCA
AAAGATTAAATGCAGAATATACTATTAGAATTCTAGCAAAAGCTGAGTTATTTGGAATGC
ATGATGAATCAAATTATGGGATTAAAAGATATATTTACTTTTAATTTAAATCAACTATTA
GAATCAGAATTGAATGATAGCTAAAAGAGTTACAACTAAAAGAGTCCGAATGTCCATATA
GAGTATTACTTGGAGAGAGATTAAAAATAAAATTAAAATGATATTAAAATTGAAGAAAAT
CAATTTGATGATAATAAAATATTTTATTCTTCTTTCTCCTCTTCTAAAAAGAAAAGTAAT
AATGATTCAATTTAAAAGGAGCAAACTGATCAAAAAAATTAAGATGAATAAGTGCAAGAG
TTCGATGATGATTACTTATTTGAAAGTGGGAGTAAATTACCTTAAGATACTCAAAAACCT
AATTTAAATTTAAATGAAAATGAATAGTATTCTCATCTTAATTTATTCAATCGTAAGATT
GTTAAGAAACAACCTTACAAAGTCCCAGAAAAAATTCTTGATGAAAAAATTTAACACTAT
AGTATAAAAAATTTGTATGATGCTAATGTTTTTGACATGGATTAGAGCAAGTTGAGAAAG
TAAAAAGATAATAAAAAATTTTCAAATGATTCGATAGCTCAATGCATAGATTACTTGTAA
AAAAATAAATAAATTGATTGGGGAAAAGTTTATGAAAGTTGGAGATAGTTAGAATAAATA
TCAAAAATGAAAATTCCTAACTATTTTTACACAGCAGATTTTAGAAATAACTTAAAAATT
AAAGGAGTCACATCAAATCTTTCAAAGTAGGAGATTCTCGATCTTTTTGAATTATCTAAA
CTTTTTAGGAGCCAATCAGCTTTTTCAAAATTTTTATAGCTTTCTAGAGATTAAATTGGC
AAAATGTTTAAGAGAAAACTCGGGGTAAAGTTAGTTGAGTAAAAATCAATTTTCTAATGT
TTCAATTAAAAATGA

>TTHERM_01109990(protein)
MQLETNIPLTKMKMSKEEDYQPIKKAPKKKTNKRKNDENSVSTRRSNKKQHNEVSEVSDE
RQKKQNDAEESQKYTRFLSKGRAKYVIKKFFKNNSGVWMIDFQQQQLGNVINMCKNIDES
LEYLEPKLIITYLFIALIKLEQNCFEVKRIADDMQQQVEQVKSSYKIIQINRDLKTAQLS
KDQMQNILLEFQQKLSYLECMMNQIMGLKDIFTFNLNQLLESELNDSQKSYNQKSPNVHI
EYYLERDQKQNQNDIKIEENQFDDNKIFYSSFSSSKKKSNNDSIQKEQTDQKNQDEQVQE
FDDDYLFESGSKLPQDTQKPNLNLNENEQYSHLNLFNRKIVKKQPYKVPEKILDEKIQHY
SIKNLYDANVFDMDQSKLRKQKDNKKFSNDSIAQCIDYLQKNKQIDWGKVYESWRQLEQI
SKMKIPNYFYTADFRNNLKIKGVTSNLSKQEILDLFELSKLFRSQSAFSKFLQLSRDQIG
KMFKRKLGVKLVEQKSIFQCFNQK

>TTHERM_01109990(gene)
ATGTAATTAGAAACAAACATTCCCTTAACTAAAATGAAGATGAGTAAGGTAATTAATCTG
ATAGTAGTAGTAATTCTTAGGAAGAAGATTACTAGCCTATTAAGAAAGCTCCTAAAAAAA
AAACAAATAAAAGAAAAAACGATGAAAATTCTGTAAGTACCAGAAGGTCAAACAAGAAAC
AGCATAACGAGGTTAGTGAAGTATCTGATGAAAGACAGAAAAAGCAAAACGATGCTGAAG
AATCACAAAAGTACACTAGATTCTTATCAAAAGGAAGAGCAAAGTATGTTATCAAAAAAT
TCTTTAAAAATAATTCTGGTGTTTGGATGATAGATTTCTAGTAATAGTAGCTAGGAAATG
TCATTAATATGTGCAAGAACATTGATGAATCTCTTGAATACTTAGAACCTAAGTTAATTA
TCACGTACCTTTTGTAAAAATTTGAACCTAGCAGTCAAAGCTGAATATATTATAAAAAAT
ACTCTTTTACAAATACCTATAAAATTTAAACAGTTAATAAATTAATTATATATACCTTGT
GAAAAATAAATGATGCATTTATTACTTATTAGTATTTATTTATATAATTAATATTTGAAT
GATAATTTTTACCTTTTTGTTGAAATTTATTTTTTTAGAATTTATTTAATTAATTAGAAA
TTTCTGTTGGTCAGATTAAAAATAATTTTAAATAAAATAATCTCTTTTTATTTTTTATAA
ATATTAAGATTTTAATTAATTAGGTAAAATAAAAAAATTAATAAAAAAACAAAATGCTAA
GTATTGCTTTGATAAAGTTAGAATAAAACTGCTTTGAAGTTAAAAGAATTGCTGATGATA
TGCAATAGTAAGTTGAGTAAGTAAAAAGTAGCTATAAGATTATATAAATAAATAGAGACC
TCAAGACAGCATAGCTTTCAAAAGATTAAATGCAGAATATACTATTAGAATTCTAGCAAA
AGCTGAGTTATTTGGAATGCATGATGAATCAAATTATGGGATTAAAAGATATATTTACTT
TTAATTTAAATCAACTATTAGAATCAGAATTGAATGATAGCTAAAAGAGTTACAACTAAA
AGAGTCCGAATGTCCATATAGAGTATTACTTGGAGAGAGATTAAAAATAAAATTAAAATG
ATATTAAAATTGAAGAAAATCAATTTGATGATAATAAAATATTTTATTCTTCTTTCTCCT
CTTCTAAAAAGAAAAGTAATAATGATTCAATTTAAAAGGAGCAAACTGATCAAAAAAATT
AAGATGAATAAGTGCAAGAGTTCGATGATGATTACTTATTTGAAAGTGGGAGTAAATTAC
CTTAAGATACTCAAAAACCTAATTTAAATTTAAATGAAAATGAATAGTATTCTCATCTTA
ATTTATTCAATCGTAAGATTGTTAAGAAACAACCTTACAAAGTCCCAGAAAAAATTCTTG
ATGAAAAAATTTAACACTATAGTATAAAAAATTTGTATGATGCTAATGTTTTTGACATGG
ATTAGAGCAAGTTGAGAAAGTAAAAAGATAATAAAAAATTTTCAAATGATTCGATAGCTC
AATGCATAGATTACTTGTAAAAAAATAAATAAATTGATTGGGGAAAAGTTTATGAAAGTT
GGAGATAGTTAGAATAAATATCAAAAATGAAAATTCCTAACTATTTTTACACAGCAGATT
TTAGAAATAACTTAAAAATTAAAGGAGTCACATCAAATCTTTCAAAGTAGGAGATTCTCG
ATCTTTTTGAATTATCTAAACTTTTTAGGAGCCAATCAGCTTTTTCAAAATTTTTATAGC
TTTCTAGAGATTAAATTGGCAAAATGTTTAAGAGAAAACTCGGGGTAAAGTTAGTTGAGT
AAAAATCAATTTTCTAATGTTTCAATTAAAAATGAGATTAAAATAAATATGATGACCCTA
TATATAAATTATATAAAAATAGAAAAAGTATCTGATATCCTTCTAATATTTAGAATAATT
AGTTAATTCATAAATTAATTTCCAAAAAAGCTTAAGAATTCTTAAATAATAAATTTATAT
TTCAATCCTTTAAATTGTTTTCAAATATGAAATAGCTAGAAAATTATTATTTATTGAATT
ATCAAAAATTTATTAATCGGTCCAATAGAAATTATAACAAATATTTTTTGTTGTTTTGCA
GTAATAT

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Identifiers and Description

Gene Model Identifier

Standard Name

Aliases

Description

Genome Browser

Gene Ontology Annotations

Cellular Component

Molecular Function

Domains

Gene Expression Profile

Homologs (v.2006 protein sequences)

General Information

Associated Literature

Sequences

Wiki Links

External Links

Paragraph No	Gene Name	Paragraph Text
2	TWI1, HHT2, PDD1, PDD3, DCL1	A proposed model for the mechanism of programmed DNA elimination in Tetrahymena is based on the timing of expression, cellular distribution, mutant phenotypes, and predicted functions of the protein and RNA components involved. In this model, both strands of the micronuclear genome (or perhaps only the portions containing internal eliminated sequences) are transcribed early in conjugation to produce large non-genic, double-stranded RNAs. This transcription is likely performed by RNA Polymerase II, based on the localization of its subunit Rpb3p to the micronucleus during this time. These transcripts pass to the cytoplasm where they are processed into short (~28 nucleotide) scan RNAs (scnRNA) by the dicer-like protein Dcl1p, similar to the production of the small inhibitory RNAs (siRNA) central to the RNA interference (RNAi) pathway of other eukaryotes. The scnRNAs complex with Twi1p, a member of the PPD (PAZ and Piwi Domain) protein family, whose members are commonly involved in RNAi and related processes. The scnRNA/Twi1p complexes enter the old macronucleus, where scnRNAs homologous to DNA sequences found there are degraded. The remaining scnRNAs, comprised of micronuclear-restricted sequences, are transferred to the developing macronucleus. There, histone H3 proteins (Hht1p, Hht2p) that are bound to sections of the genome sharing identity to the scnRNAs are methylated on lysine-9. This modification, which is often associated with the formation of heterochromatin, is recognized by one or more of the chromodomains belonging to Pdd1p and Pdd3p. Regions of DNA associated with these modified histones are eliminated from the developing macronuclear genome.