Gene Details:

• Gene ID: AT2G40030
• Gene Symbol: ATNRPD1B, DMS5, DRD3, NRPD1B, NRPE1, POLV
• Gene Name: DEFECTIVE IN MERISTEM SILENCING 5, nuclear RNA polymerase D1B
• Description: nuclear RNA polymerase D1B;(source:Araport11)
• TAIR Accession:
• Genome: Araport11_genome_release
• Species: Arabidopsis thaliana

Transcripts:

• AT2G40030.1     AT2G40030.2

Plant Ontology Annotations:

• PO:0000037  — shoot axis apex — ápice del epiblasto (epiblastema) (Spanish, exact), シュート頂、茎頂 (Japanese, exact)
• PO:0008019  — leaf lamina base — base de la lámina de la hoja (Spanish, exact), 葉身基部 (Japanese, exact)
• PO:0009005  — root — raíz (Spanish, exact), radices (exact, plural), radix (exact), 根 (Japanese, exact), aerial root (narrow), climbing root (narrow)
• PO:0009006  — shoot system — sistema de epiblasto (epiblastema) (Spanish, exact), シュート系、苗条系 (Japanese, exact), Poaceae crown (related), shoot (related), thalli (related), thallus (related), tree crown (narrow)
• PO:0009009  — plant embryo — embrión (Spanish, exact), 植物胚 (Japanese, exact), germ (related), embryo (broad)
• PO:0009025  — vascular leaf — foliage leaf (exact), hoja vascular (Spanish, exact), leaf, vascular (exact), vascular leaves (exact, plural), 維管束のある葉, または維管束植物の葉 (Japanese, exact), crozier (related), macrophyll (related), megaphyll (related), ascidia (narrow), ascidium (narrow), fiddlehead (narrow), frond (narrow), needle-like leaf (narrow), pitcher (narrow), pitcher blade (narrow), pitcher-blade (narrow), scale-like leaf (narrow), sterile frond (narrow), trophophyll (narrow)
• PO:0009029  — stamen — estambre (Spanish, exact), 雄蕊 (Japanese, exact), Poaceae stamen (narrow), Zea stamen (narrow)
• PO:0009031  — sepal — sépalo (Spanish, exact), がく片 (Japanese, exact)
• PO:0009046  — flower — flor (Spanish, exact), 花 (Japanese, exact), floret (related), Asteraceae floret (narrow), basal flower (narrow), double flower (narrow), hermaphrodite flower (narrow), monoclinous flower (narrow), perfect flower (narrow)
• PO:0009052  — inflorescence flower pedicel — 小花柄 (Japanese, related), pedicelo (Spanish, broad)
• PO:0020030  — cotyledon — cotiledón (Spanish, exact), seed leaf (exact), 子葉 (Japanese, exact)
• PO:0020038  — petiole — pecíolo (Spanish, exact), 葉柄 (Japanese, exact)
• PO:0020100  — hypocotyl — hipocótile (Spanish, exact), 胚軸 (Japanese, exact)
• PO:0020137  — leaf apex — ápice de la hoja (Spanish, exact), 葉先 (Japanese, exact), leaf lamina apex (narrow), phyllid apex (narrow)
• PO:0025022  — collective leaf structure — estructura colectiva de hoja (Spanish, exact), leaf series (exact), 葉が集まった構造 (Japanese, exact), leaf whorl (narrow), rosette (narrow), cycle (broad), verticil (broad)
• PO:0000084  — plant sperm cell — célula espermática o esperma (Spanish, exact), male gamete (exact), microgamete (exact), 植物精子細胞 (Japanese, exact), sperm nucleus (related), sperm cell (broad)

Germplasm Phenotype:

• CS66152  — Late flowering under short day conditions
• CS69543  — No visible phenotype.
• CS69544  — No visible phenotype.

Function-related keywords:

• shoot axis apex ,  leaf lamina base ,  root ,  shoot system ,  plant embryo ,  vascular leaf ,  stamen ,  sepal ,  flower ,  inflorescence flower pedicel ,  cotyledon ,  petiole ,  hypocotyl ,  leaf apex ,  collective leaf structure ,  plant sperm cell

Literature:

• Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.   DOI:  10.1016/j.cell.2005.02.007 ;  PMID:  15766525
• Atypical RNA polymerase subunits required for RNA-directed DNA methylation.   DOI:  10.1038/ng1580 ;  PMID:  15924141
• Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.   DOI:  10.1101/gad.348405 ;  PMID:  16140984
• An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.   DOI:  10.1016/j.cell.2006.05.032 ;  PMID:  16839879
• The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.   DOI:  10.1016/j.cell.2006.05.031 ;  PMID:  16839878
• Two-step recruitment of RNA-directed DNA methylation to tandem repeats.   DOI:  10.1371/journal.pbio.0040363 ;  PMID:  17105345
• RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants.   DOI:  10.1016/j.bbaexp.2007.03.001 ;  PMID:  17449119
• Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components.   DOI:  10.1101/gad.451207 ;  PMID:  17938239
• PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.   DOI:  10.1073/pnas.0709632105 ;  PMID:  18287047
• NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.   DOI:  10.1111/j.1365-313X.2008.03525.x ;  PMID:  18433438
• A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.   DOI:  10.1038/ng.119 ;  PMID:  18425128
• Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.   DOI:  10.1016/j.molcel.2008.12.015 ;  PMID:  19110459
• NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.   DOI:  10.1101/gad.1765209 ;  PMID:  19204117
• Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana.   DOI:  10.1371/journal.pgen.0040027 ;  PMID:  18266474
• PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit.   DOI:  10.1073/pnas.0810310106 ;  PMID:  19141635
• Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis.   DOI:  10.1093/nar/gkq162 ;  PMID:  20338883
• The RNA silencing enzyme RNA polymerase v is required for plant immunity.   DOI:  10.1371/journal.pgen.1002434 ;  PMID:  22242006
• DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene.   DOI:  10.1111/j.1365-313X.2011.04714.x ;  PMID:  21771120
• Systematic identification of functional plant modules through the integration of complementary data sources.   DOI:  10.1104/pp.112.196725 ;  PMID:  22589469
• RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.   DOI:  10.4161/epi.20290 ;  PMID:  22647529
• Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.   DOI:  10.1073/pnas.1208557109 ;  PMID:  22733760
• DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.   DOI:  10.1038/nsmb.2354 ;  PMID:  22864289
• Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.   DOI:  10.1016/j.cell.2012.10.054 ;  PMID:  23313553
• The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis.   DOI:  10.1038/emboj.2013.49 ;  PMID:  23524848
• The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs.   DOI:  10.1093/nar/gkt639 ;  PMID:  23877244
• The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci.   DOI:  10.1371/journal.pgen.1003948 ;  PMID:  24465213
• DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis.   DOI:  10.1186/s13059-014-0458-3 ;  PMID:  25228471
• High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis.   DOI:  10.1016/j.plaphy.2014.12.022 ;  PMID:  25576840
• RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway.   DOI:  10.1111/nph.13727 ;  PMID:  26522658
• The role of DNA (de)methylation in immune responsiveness of Arabidopsis.   DOI:  10.1111/tpj.13252 ;  PMID:  27341062
• A Role for MINIYO and QUATRE-QUART2 in the Assembly of RNA Polymerases II, IV, and V in Arabidopsis.   DOI:  10.1105/tpc.17.00380 ;  PMID:  29352065
• APURINIC/APYRIMIDINIC ENDONUCLEASE2 and ZINC FINGER DNA 3'-PHOSPHOESTERASE Play Overlapping Roles in the Maintenance of Epigenome and Genome Stability.   DOI:  10.1105/tpc.18.00287 ;  PMID:  30135084
• The RNA Export Factor ALY1 Enables Genome-Wide RNA-Directed DNA Methylation.   DOI:  10.1105/tpc.18.00624 ;  PMID:  30814259
• Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis.   DOI:  10.1111/mpp.12850 ;  PMID:  31274236
• Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis.   DOI:  10.1093/nar/gkz636 ;  PMID:  31372641
• Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana.   DOI:  10.1371/journal.pgen.1008492 ;  PMID:  31887137
• Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis.   DOI:  10.1186/s13059-021-02359-2 ;  PMID:  33957942
• Roles of IDM3 and SDJ1/2/3 in Establishment and/or Maintenance of DNA Methylation in Arabidopsis.   DOI:  10.1093/pcp/pcab091 ;  PMID:  34185870
• Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation.   DOI:  10.1111/jipb.13406 ;  PMID:  36354145
• RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.   DOI:  10.1007/s00425-023-04135-x ;  PMID:  37120771
• RNA polymerase IV directs silencing of endogenous DNA.   DOI:  10.1126/science.1106910 ;  PMID:  15692015
• An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.   DOI:  10.1016/j.cell.2006.05.032 ;  PMID:  16839879
• NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.   DOI:  10.1111/j.1365-313X.2008.03525.x ;  PMID:  18433438
• NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.   DOI:  10.1101/gad.1765209 ;  PMID:  19204117

Sequences: