wiki:ChromosomeSegregation

Version 362 (modified by vw253, 5 years ago) (diff)

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Annotation Priorities

  • 1. Issues on the curation tracker
  • 2. Annotation improving networks inferred from GO:
    • i) substrates
    • ii) physical interactions
    • iii) complexes
  • 3. Phenotype screens see ​canto (big bang for buck)
  • 4. Processes mature enough to build pathways: usually those which have a large percentage of functionally characterised genes (for example mitochondrion organization has 40 published genes/294, so is low priority, compared to cytokinesis 136/139)
    • chromosome segregation (Val)
    • DNA metabolism (Midori)
    • cytokinesis (Val)
    • regulation of mitotic cell cycle (All)
    • signaling pathways (Antonia)
    • chromatin organization (All)
    • cell polarity
  • 5. New gene characterizations -These should be sent out for community curation, but followed up

Process priorities

Mitotic Chromosome Segregation (Val)

process chromosome segregation: genes 195 of which ??? published ​esyN
gene/complexstatusDate
Mis6-Sim4 complex (12) --
fta1 Mis6-Sim4 complex annotation complete6/1/2015
fta2 Mis6-Sim4 complex annotation complete 6/1/2015
fta3 Mis6-Sim4 complex annotation complete 6/1/2015
fta4 Mis6-Sim4 complex annotation complete 15/1/2015
fta6 Mis6-Sim4 complex annotation complete 15/1/2015
fta7 Mis6-Sim4 complex annotation complete except CC PMID:2478970820/1/2015
mis6 Mis6-Sim4 complex annotation complete except CC PMID:24789708 PMID2537524020/1/2015
mis15 Mis6-Sim4 complex annotation complete 6/1/2015
mal2 Mis6-Sim4 complex annotation complete except PMID: 24789708 9/03/2016
sim4 Mis6-Sim4 complex annotation complete 20/1/2015
mis17 Mis6-Sim4 complex annotation complete 6/1/2015
cnl2 Mis6-Sim4 complex --
NMS/Ndc80 complex (10) - -
ndc80 NMS complex/Ndc80 annotation complete needs annotation to ndc80 complex -
mis12 NMS complexannotation complete1/03/2016
mis13 NMS complexannotation complete 20/1/2015
mis14 NMS complexannotation complete 6/1/2015
sos7 NMS complex annotation complete 6/1/2015
spc25 NMS complex/ Ndc80 complexannotation complete needs annotation to ndc80 complex20/1/2015
spc7 NMS complex in progress IS THIS TURNING SAC SIGNALLING OFF? PMID:17035632-
nnf1 NMS complex PMID:17035632 -
nuf2 Ndc80 complex 2 plus PMID:23770679 (out for CC) needs annotation to ndc80 complex-
spc24 Ndc80 complex annotation complete needs annotation to ndc80 complex20/1/2015
CENP-A recruiting complex(4)- -
mis16 CENP-A recruiting complex annotation complete except CC PMID:22771823 and scm3* papers-
mis18 CENP-A recruiting complex annotation complete except CC PMID:24789708 15/1/2015
mis19 CENP-A recruiting complex annotation complete except CC PMID:25375240 15/1/2015
mis20 CENP-A recruiting complex annotation complete 20/1/2015
DASH complex(10)- -
dad1 DASH complex annotation complete1/3/2016
ask1 DASH complex PMID: 16079915-
dad2 DASH complex PMID: 9748434 PMID: 11193425 PMID: 17352737 -
dad3 DASH complex annotation complete17/3/2016
dad4 DASH complex annotation complete17/3/2016
dad5 DASH complex PMID: 9748434 PMID: 10879493 PMID: 25342311??? -
dam1 DASH complex PMID: 18029449 PMID: 18256284 PMID: 18262494 PMID: 18632983 PMID: 19037096 PMID: 20624975 PMID: 20730753 PMID: 22084306 PMID: 22375062 PMID: 23770679 PMID: 24239120 -
duo1 DASH complex PMID: 16079915 PMID: 21901484-
spc19 DASH complex annotation complete17/3/2016
spc34 DASH complex PMID: 16079915 -
condensin complex (5- -
cnd1 condensin complex non-SMC subunit annotation complete CC-PMID:2576418323/10/2015
cnd2 condensin complex non-SMC subunit annotation complete CC PMID:21633354,PMID:257641833/10/2015
cnd3 condensin complex non-SMC subunit annotation complete CC-PMID:2576418323/10/2015
cut14 condensin complex SMC subunit Smc2PMID: 8395535 PMID: 7957061 PMID: 9285594 PMID: 9802907 PMID: 10485849 PMID: 12966087 PMID: 15331764 PMID: 15485909 PMID: 17030601 PMID: 20709788 PMID: 21540296 PMID: 22645654 CC PMID: 25847133 -
cut3 condensin complex SMC subunit Smc4 PMID: 7957061 PMID: 9285594 PMID: 10485849 PMID: 11927594 PMID: 12750522 PMID: 12966087 PMID: 15148393 PMID: 15485909 PMID: 19910488 PMID: 20709788 PMID: 24362309 PMID: 26832414-
monopolin complex (2)- -
csm1 monopolin complex annotation complete 1/3/2016
mde4 monopolin complex annotation complete1/3/2016
mitotic spindle checkpoint proteins (7)- -
bub1--
bub3--
dma1--
mad1--
mad2--
mad3--
mph1??--
chromosome passenger complex (4)- -
ark1--
bir1--
nbl1--
pic1--
kinesins/dynein (6)- -
cut7--
klp2--
klp5--
klp6--
pkl1--
dlc1--
dhc1--
TACC TOG + dis(3)- -
alp7--
alp14--
dis1--
misc mainly inner?(8)- -
clp1--
cnp1 in progress-
cnp20 annotation complete 6/1/2015
cnp3PMID:15791413 PMID:24449889 autonomous-
nsk1abnormal clustering of kinetochores to spindle pole bodies-
plo1--
sgo2--
wip1--
cohesin complex (5)- -
pds5 mitotic cohesin-associated protein Pds5--
psc3 mitotic cohesin-associated protein Pds5--
psm1 mitotic cohesin-associated protein Pds5--
psm3 mitotic cohesin-associated protein Pds5--
mitotic cohesin complex, non-SMC subunit Rad21 (kleisin)--
APC complex (14)- -
cut4/apc1 APC subunit, platform subcomplex CC-PMID:24948786 PMID:8918880-
apc4/cut5 APC subunit, platform subcomplex ???-
apc5/cut5 APC complex subunit PMID:19584054-
apc15 APC, platform subcomplex annotation complete24/11/2015
apc8 APC TPR lobe subcomplex PMID:18354085 PMID:23583778-
cut9/apc6 APC TPR lobe subcomplex PMID:16453724 (rad PMID:8668127 PMID:947572) PMID:12653962 CC PMID:24948786-
apc3 APC TPR lobe subcomplex ???-
apc12/hcn1 APC subunit TPR lobe accessory factor Hcn1annotation complete
apc13 APC subunit TPR lobe accessory factorannotation complete24/18/2015
apc10 APC substrate recognition subunit Apc10PMID: 9736616 PMID: 12653962 only-
apc2 APC cullin family subunitannotation complete24/4/2015
apc11 APC ubiquitin protein-ligase E3 subunit annotation complete24/4/2015
apc14 APC (might be apc16 ortholog)annotation complete24/4/2015
APC inhibitor (1)- -
slp1Cdc20 OX > securin can be degraded during interphase, whereas other destruction box proteins will remain stable. In cells lacking Cdc20, securin remains stable, and sister chromatids will not separate (Visintin et al., 1997).-
gamma tubulin complex- -
alp4 gamma tubulin complex subunitannotation complete CC-PMID:24704079 CC-PMID:2388693923/10/2015
alp6 gamma tubulin complex Alp6annotation complete CC-PMID:24704079 CC-PMID:2388693923/10/2015
alp16 gamma tubulin complex Alp16annotation complete23/4/2015
gfh1 gamma tubulin complex Gfh1annotation complete23/10/2015
gtb1 gamma tubulin Gtb1annotation complete28/4/2015
mod21 gamma tubulin complexannotation complete28/4/2015
proteasome complex (39)- -
separase securin complex- -
cut1PMID: 9635190 (HIGH PRIORITY cut2 substrate) PMID: 9649518 PMID: 9802907 PMID: 10651900 REVIEW PMID: 12653962 screen PMID: 15161942 PMID: 15329725 PMID: 15507118 PMID: 16483313 PMID: 16861909 PMID: 16904908 PMID: 18239448-
cut2 PMID: 8632802 PMID: 9264466 PMID: 9312055 PMID: 9755167 PMID: 10459014 PMID: 1052623 PMID: 11029045 PMID: 11084332 PMID: 11598020 PMID: 11967147 PMID: 12390246 PMID: 12553909 PMID: 12783882 PMID: 15146064 PMID: 15791259 PMID: 16303848 PMID: 16483313 PMID: 19117951 PMID: 22084378 PMID: 22645648 -
? remaining 54 including (list on desktop):- -
misc kinase/phosphatase- -
ppe1 to do PMID:12773390 -
sds22 phosphatase PMID:1846086 PMID:15335873 PMID:8374168 -
sds23 PP2A-type phosphatase inhibitor--
cdc13 G2/M B-type cyclin Cdc13--
dis2 serine/threonine protein phosphatase PP1--
cdc2 cyclin-dependent protein kinase Cdk1/Cdc2--
fin1 serine/threonine protein kinase- -
cek1 serine/threonine protein kinase Cek1 --
gsk3 serine/threonine protein kinase Gsk3 --
ekc1 protein phosphatase regulatory subunit - -
ubiquitin related- -
ubc11 ubiquitin conjugating enzyme E2- annotation complete 18/11/2015
ubc4 PMID: 7698660 PMID: 8972853 PMID: 19423874 PMID:19584054 PMID_21389117 CC PMID: 24454826 -
cut8 tethering factor for nuclear proteasome PMID:12653962 (more about repair, mah PMID:17178839)-
pop1PMID:14970237-
pop2PMID:14970237-
pop3--
mlo2 ubiquitin protein ligase E3 component human N-recognin 7 homolog Mlo2 --
cdc48 AAA family ATPase --
cohesion- -
mis4PMID:9808627, required in S-phase, not destroyed in G1-
dfp Hsk1-Dfp1 kinase complex regulatory subunit Dfp1--
ssl3 cohesin loading factor Ssl3--
eso1 sister chromatid cohesion protein--
swi6 HP1 family chromodomain protein Swi6 --
prw1 Clr6 histone deacetylase complex subunit--
clr6 histone deacetylase (class I) Clr6 --
rmi1 RecQ mediated genome instability protein Rmi1--
wpl1 Wings apart-like homolog Wpl1--
hta2 histone H2A beta--
hta1 histone H2A alpha--
spindle- -
mto1 MT organizer Mto1--
msd1 microtubule-anchoring factor Msd1--
mal3 PMID: 11086011???-
wdr8 mitosis-specific spindle pole body WD repeat protein--
klp9 kinesin-like protein--
ppc89 spindle pole body protein --
SUMO --
alp11 tubulin specific chaperone cofactor Bannotation complete 01/3/2016
alp21 tubulin specific chaperone cofactor Eannotation complete 01/3/2016
alp31 tubulin specific chaperone cofactor Aannotation complete 01/3/2016
alp1 tubulin specific chaperone cofactor Dannotation complete 9/3/2016
alp41 GTP-binding protein (beta-tubulin folding)annotation complete 01/3/2016
mzt1 mitotic spindle organizing protein Mzt1 annotation complete23/4/2015
misc cenp- -
cbh1 CENP-B homolog Cbh1 -
cbh2 CENP-B homolog Cbh2-
cbp1 CENP-B homolog Cbp1-
misc- -
scm3 PMID:19217404 PMID:15316103 PMID:24186062 (also mis16) CC PMID:24789708 PMID: 26921242-
csi1annotation complete01/3/2016
hos2PMID:17352737 plus-
pcs1PMID:20935472 plus... -
ams2PMID:12535531 cenp-a loading PMID:20604974 CC PMID:23195958 PMID:23267073 -
orc5 origin recognition complex subunit Orc5 -
cdc31 centrin -
nud3 nuclear distribution protein NUDC homolog -
ams2 cell cycle regulated GATA-type transcription factor Ams2 -
dcc1 Ctf18 RFC-like complex subunit Dcc1 -
sfc3 transcription factor TFIIIC complex B box binding subunit Sfc3 -
top1 DNA topoisomerase I -
ctf8 DNA replication factor C complex subunit Ctf8 -
gpn2 conserved ATP binding protein -
rna1 Ran GAP Rna1 -
top3 DNA topoisomerase III -

===

dis1 PMID:16920624 plus…XMAP215/ TOG/Stu2-family homolog, binds microtubules and localizes to kinetochores (Nakaseko et al., 2001). Mutants in dis1 lack the chromosome alignment phase in metaphase and arrest with elongated spindles and segregated but unseparated chromosome pairs (Nabe- shima et al., 1998; Ohkura et al., 1988).dis1 mutants arrest with an activated spindle checkpoint and appear to ex- perience an increase in sister chromatid cosegregation (70%) at full restrictive temperature. Such cosegregation results when mono-oriented attachment of sister kineto- chores to microtubules from the same SPB is not corrected. Since dis1 mutants lack the phase of constant spindle length when chromosomes are properly aligned -
dis2 phosphatase (PMID:14765108 - describes checkpoint termination Dis2 abrogates Chk1 phosphorylation and activation in vivo, ) PMID:2245912 PMID:8389306 PMID:8305731 PMID:7983142 PMID:7957097 PMID:9264466 PMID:9790575 PMID:10668632 PMID:11085271 PMID:16411888 PMID:17895368 PMID:19592249 PMID:21664573 (Out for CC PMID:21703453 PMID:21965289 PMID:23333317) (Iain Hagan PMID:25487150) -
cut7In the temperature-sensitive cut7 mutant, spindle formation is blocked shortly after duplication of the SPB. The mitotic spindle radiating from the opposite poles cannot interdigitate and thus remains as a V shape (Hagan and Yanagida, 1992). The cut7- specific defect generates a condition whereby the bipolar attachment of the spindle to kinetochores is not achieved. Previously, we demonstrated that this defect causes an arrest in a mad2+-dependent manner (Kim et al., 1998). At the restrictive temperature the majority of Mad2-GFP was found on condensed chromosomes as one or more speckles (Fig. 4).
skp1PMID:15147872-

Notes and annotation questions on chromosome segregation

  • read review PMID: 23512483
  • is CENP-A containing nucleosome assembly part of kinetochore assembly? Although the outer repeats play an important role in sister centromere cohesion and possibly help to properly orient the multiple kinetochore microtubule attachment sites (Pidoux and Allshire, 2004
  • Centromeres: getting a grip of chromosomes. Curr. Opin. Cell Biol. 12, 308–319., the central region is needed for the assembly of the kinetochore per se and the interaction with the mitotic spindle fibers
  • what is the relationship between kinetochoe assembly, spindle elongation and chromosome segregation (currently disjoint)
  • reannotate ndc80 and MIND subcomplexes annotate PAS complex
  • ask expert to look at CENP_A assembly vs CENP-A assembly phenotype
  • no substrates currently annotated for APC, look for motifs ABBA, KENm D-Box, C-BOX, F-box, 2BR, LRRL
    • I think from humanUbc11 is the APC E2, has some substrates assigned (cdc13 direct, slp1 indirect), but sc imlies ubc4 and ubc1 (amybe all)
  • possible substrates to annotate mitotic securin and cylin; late mitosis cdh1 , cytokinesis aurora, cyclins, cdc29; G1 geminin, cdc6, skp2,ubcH10(ubc11)
  • check all know APC targets annotated

Cytokinesis but feel free to do any genes or complexes that I haven't started

process cytokinesis: 139 of which 136 published ​esyN
gene/complexstatus date
lsk1 in progress-
mac1 annotation complete 22/1/2014
lkh1 chained 12565823 -

Notes and annotation questions on cytokinesis

  • previously considered to be linear assembly mid1- rng2- others. But if you can ectopically localize rng2 you can get all of the others (any one of the 3 will work)
  • check should mid1 be ring assemlby or localization only?
check mid1 NOT assembly? positioning
main target of mid1 is rng2 rng3- myosin specific chaperone add to wiki with mohan paper details

Regulation of mitotic cell cycle

process regulation of mitotic cell cycle: l genes 258 of which 231 published ​esyN
gene/complexstatus date
psk1 annotation complete (except PMID: 22976295 out for CC) 16/2/2015

Notes and annotation questions on cell cycle regulation

  • Only include gene products here not covered in chromosome segregation, cytokinesis or DNA metabolism
  • genes which should be annotated to "signalling" based on the signalling components of the cell cycle regulation network
  • Need to do cytokinesis checkpoint, G1 cell size control checkpoint, DNA damage checkpoint (ask experts to check specific checkpoint lists)
Misc other annotation complete
gene/complexstatus date
mcp60 annotation complete 16/2/2015