TABLE 8

Sequences of new mutations of class B and class C synMuv proteins

ProteinClassNo. amino acidsProtein similarities and domainsa
A. Features of synMuv proteins
DPL-1B598Similar to DP family transcription factors; contains DNA- and E2F-binding domains.
EFL-1B342Similar to E2F family transcription factors; contains DNA-, DP- and Rb-binding domains.
LET-418B1829Similar to Mi-2 family ATP-dependent chromatin remodeling enzymes; contains chromodomains, PHD finger motifs, and a helicase domainb
LIN-9BLIN-9L: 644 LIN-9S: 642Similar to Drosophila Mip130 DNA replication and Aly cell cycle regulators and mammalian proteins of unknown function.
LIN-13B224824 predicted Zn-finger motifs.
LIN-35B961Similar to Retinoblastoma (pRb) family transcriptional regulators; contains “pocket” interaction domain.
LIN-36B962THAP domain, C/H-rich and Q-rich regions.
LIN-52B161Similar to Drosophila and mammalian proteins of unknown function.
LIN-53B417Similar to Drosophila p55, mammalian RbAp48 subunits of chromatin remodeling, and histone deacetylase complexes; contains WD repeats.
LIN-65B728Acid rich
MEP-1B853Six Zn-finger motifs.
MYS-1C458Similar to MYST family histone acetyltransferases; contains chromodomain and acetyltransferase domain.
SLI-1sli-1582Similar to Cbl family ubiquitination-promoting proteins; contains SH2 domain and RING finger motif.
TRR-1C4064cSimilar to mammalian TRRAP transcriptional regulator.
MutationWild-type sequenceMutant sequenceSubstitution, splice site change, or aberrationDomain affected by missense mutation
B. Allele sequences
dpl-1(n3643)dTATTAAY341ochre
GGCCGCG533RUnknown
efl-1(n3639)eCAATAAQ175ochre
let-418(n3536)CCTCTTP675LHelicase/ATPase
let-418(n3626)GGTAGTG1006SHelicase/ATPase
let-418(n3629)TCCTTCS925FHelicase/ATPase
let-418(n3634)TGGTAGW1128amber
let-418(n3635)CAGTAGQ1594amber
let-418(n3636)ACTTCTT807SHelicase/ATPase
TGGTGAW1329opal
let-418(n3719)TGGTAGW295amber
lin-9(n3631)CAATAALIN-9L: Q594ochre
LIN-9S: Q592ochre
lin-9(n3675)GATAATLIN-9L: D305NUnknown
LIN-9S: D303NUnknown
lin-9(n3767)CAGTAGLIN-9L: Q509amber
LIN-9S: Q507amber
lin-13(n3642)CATTATH832YZn finger
lin-13(n3673)CAGTAGQ1988amber
lin-13(n3674)CGATGAR1250opal
lin-13(n3726)GGAGAAG229EUnknown
lin-35(n3763)fGCAGTAA555VPocket
TTG AAA AAGTTG AAA AAA GK594 frameshift and truncation after 611 a.a.
lin-36(n3671)CATCCTH284PC/H-rich region
GAAAAAE424KUnknown
lin-36(n3672)CAGTAGQ467amber
lin-36(n3765)gGCTGTTA242VC/H-rich region
lin-52(n3718)hCAGTAGQ31amber
lin-53(n3448)AGTATTS384IWD repeat
lin-53(n3521)GAAAAAE174KWD repeat
lin-53(n3622)AAG/gtatgtgtAAG/atatgtgtExon 1 donor
lin-53(n3623)TGGTAGW337amber
lin-65(n3441)TGGTGAW534amber
lin-65(n3541)TGGTGAW534amber
lin-65(n3543)TCGTTGS720LUnknown
mep-1(n3680)AGTAATS309NUnknown
mep-1(n3702)CAGTAGQ706amber
mep-1(n3703)CTT/gtaagtttCTT/ataagtttExon 3 donor
mys-1(n3681)iGGAAGAG341RAcetyltransferase
sli-1(n3538)TCATTAS305LSH2
sli-1(n3544)ttttccag/AAAttttccaa/AAAExon 6 acceptor
sli-1(n3683)ttttttag/GATttttttaa/GATExon 4 acceptor
trr-1(n3630)jTGGTAGW2064amber
trr-1(n3637)jCAGTAGQ3444amber
trr-1(n3704)jCAATAAQ694ochre
trr-1(n3708)jCGATGAR1248opal
trr-1(n3709)jCGATGAR2550opal
trr-1(n3712)jTGGTAGW2505amber
  • The synMuv proteins described are limited to those for which we obtained mutant allele sequence; this is not a comprehensive listing of synMuv proteins. In the “Wild-type sequence” and “Mutant sequence” columns, exon and intron sequences are denoted by uppercase and lowercase letters, respectively. Nucleotides altered by the mutations are underlined.

  • a Molecular descriptions of the proteins listed were obtained from the following sources: DPL-1, and EFL-1, Ceol and Horvitz (2001) and Page et al. (2001); LET-418, Solari and Ahringer (2000) and von Zelewsky et al. (2000); LIN-9, Beitel et al. (2000); LIN-13, Melendez and Greenwald (2000); LIN-35 and LIN-53, Lu and Horvitz (1998); LIN-36, Thomas and Horvitz (1999) and Reddy and Villeneuve (2004); LIN-52, Thomas et al. (2003); MEP-1, Belfiore et al. (2002); SLI-1, Yoon et al. (1995); MYS-1 and TRR-1, Ceol and Horvitz (2004).

  • b The predicted LET-418 protein contains a sequence that is annotated as a helicase domain (see www.wormbase.org). This domain was originally identified in helicases but has since been found in nonhelicase proteins. Many of these proteins share a common ATPase activity, and this domain contains residues that are important for ATP binding and hydrolysis.

  • c Because of alternative splicing, trr-1 encodes proteins that may range in length between 4054 and 4064 amino acids (Ceol and Horvitz 2004).

  • d These data are from Figure 1 of Ceol and Horvitz (2001).

  • e These data are from Figure 4 of Ceol and Horvitz (2001).

  • f The adenosine inserted by the lin-35(n3763) frameshift mutation is not underlined, because it is unclear which adenosine in the adenosine repeat was inserted.

  • g In addition to the missense mutation described, we found an additional mutation associated with lin-36(n3765). This mutation, AG/gtaagaagaaaagc to AG/gtaagaagaaaagt, is present in the third intron of lin-36 and creates a possible splice-donor sequence. If this splice-donor were used, an in-frame ochre (TAA) stop codon would be encountered, truncating the LIN-36 protein after 261 amino acids.

  • h These data are from Figure 3 of Thomas et al. (2003).

  • i These data are from Figure 2 of Ceol and Horvitz (2004).

  • j These data are from Figure 1 of Ceol and Horvitz (2004).