+; p6õ4 4g Ê 6õ m %Ê'2c ' _ [ ' _ ^ ~
TRANSCRIPT
2013 2015
(Stroke 2012)
RNF213 c.14576G A (rs112735431) 2011 11 2014 4
64991 19
185 74 11025 normal control 145
RNF213 c.14576G A 84.6% 77/91
63.1% 12/1924.3%
45/185 11 control 2
c.14576G A
(Stroke 2013)
2013
RNF213
c.14576G>A
c.14576G>A RNF213RNF213
c.14576G>ARNF213
271141 RNF213 resequence
c.14576G>ARNF213 exon 68
target resequence
RNF213 185
82 Noncoding103 Coding Coding
Synonymous 42 Missense61 Nonsense 0 Frameshift 0 Coding
Missense 61 MissenseCase-control study
casec.14576G
A (rs112735431)
rare variant 8c.14576G A (rs112735431)
RNF213 c.14576G>ARNF213 c.14576G>A
validation
2014, 2015 RNF213 c.14576G>A
RNF213c.14576G>A 2%
1000 10.1% RNF213 c.14576G A
2%RNF213 c.14576G A
2014, 2015
2014
RNF213 c.14576G A15 30 whole exome
2015 RNF213 c.14576G A2 whole exome
100 whole exome76
RNF213 c.14576G A
2%
MRI
- 353 -
2011
nod
niffix
nod, nif fix
Mesorhizobium loti
Roche 454
6.7 Mbp 7.3 Mbp 17.0 x 44.7 x 2 8 scaffold
HiSeq 3kbp 4kbp 1015 MiSeq
400 bp 150
454Phe-tRNA
415615kbp 400 600 ORF
HiSeq MiSeq
165nod
niffix
trb
16S-23S rRNAPhe-
tRNA rRNA
NaCl
Mesorhizobioum Aminobacter
Phylobacteriaceae
400kbp
P4Phe-tRNA
Kasai-Maita H et al. Microbes and Environ-ments 28(2): 275-278 (2013)
- 354 -
2010 2015
4.8
(
)
/
Chara braunii, S2768 RNA
Illumina RNA-seq2010
/ RNA12 3
Illumina RNA-seq2015
RNA-seq
35,883 36,887
/
6,300
RT-PCR in situ/
Sato, M. et al. Phycol. Res. 62, 214–221 (2014)Hackenberg, D. et al. Plant Physiol. 163, 1510–1517 (2013)Hoepflinger, M. et al. J. Exp. Bot. 64, 5553–5568 (2013)Yang, Y. et al. BMC Res. Notes 4, 330 (2011)Kato, S. et al. J. Phycol. 47, 999–1008 (2011)
- 355 -
2013
- 356 -
2010
RNA
KDKD
BAC
PCR
BAC
BAC
ES
DNA ES(384 well plate, 220
BACBLAT
BACBAC
BAC
BAC
BAC
ES iPS
BAC
Sato K et al., Scientific Reports, 5, 2015, DOI: 16894-16901
- 357 -
2014
HHippo
2015
Hippo
NIH3T3Hippo Tead
TeadTead
( )
NIH3T3
CRISPR/Cas9 gRNA
Cas9 NIH3T3NIH3T3
gRNA4 10gRNA
gRNA 4
10 DNAgRNAgRNA
2014 Koike-YusagRNA (Nat Biotech 32, 267-273, 2014) 2 2015
Zhang gRNA(Nat Methods 11, 783-784, 2014)
2
<2014
2014 Koike-Yusa gRNA(Nat Biotech 32, 267-273, 2014) NIH3T3
Hippo
Nf2, Sav1, Amotl2 HippogRNA
- 358 -
2gRNA
16
106
6
<2015 >
2015gRNA
gRNAnon-target gRNA 1000
Zhang gRNA (Nat Methods 11, 783-784, 2014) 4
gRNAgRNA
non-target gRNA2
( )2
gRNAgRNA
- 359 -
2013
500Mb EST(16537 )
360 Mb N50 1.7 Kb
342bp, 545bp PE( 300, PE500, 2820bp, 4,545bp, 7,926bp,
8,945bp, 13,158bp, 15,125bp MP( )3k, MP5k, MP8k, MP10k, MP15k, MP20k
150bp2,2 2.5 1.2 3.6 1.31.7 Platanus
43,738419 Mb 340 Kb N50; 21,362 bp
15,668 scaffold 467 Mb, 4.25 Mb, N50; 796 kb
500 Mb9 NCBI
EST 9 90%Phytometasyn RNA
9 50
scaffold
P450P450
P450 CYP82
scaffoldCYP82
CYP82
CYP82 P450
CYP82CYP82
P450
RNA
50(2), 93-93 (2015)
- 360 -
2013
( )
2
2F1
DNA
Gy
F1
F1 F1
C57BL/6 C3H
C57BL/6 C3H F1
C57BL/6 4 GyF1 C57BL/6
C3HF1
3 F13 F1
DNA
DNA Illumina Hiseq 2000 500bp DNA
100bp
bwa-mem (mm10)samtools GATK
8
90 Gb F1500
1 F1 F1
15 0.350.65 de novo
6 F1 72
47 3 F1
16 4GyF1 31
F1
4 GyF1 F1
2
- 361 -
2014
RNA (dsRNA)
RNA
dsRNA
dsRNA
dsRNA
dsRNA
RNA siRNA
DICER
dsRNA
dsRNA
dsRNA
dsRNA
dsRNA
RNA
trans kingdom interfering RNA
(tkiRNA)
RNA
RNA-seq
RNA
mRNA-seq
tkiRNA tkiRNA
mRNA-seq
RNA
24hr
RNA
- 362 -
2014
- 363 -
2010 2012
- 364 -
Yasuka, Y. et al. (2016) J. Exp. Bot. In press. Motomitsu, A. st al., (2015) Essays in Biochem. In press. Shimizu, N., et al., (2015) New Phytologists 208.1104-1113 Kinoshita, A., et al., (2015) Plant Signaling & Behavior. 10:6, e1028707 Kinoshita, A, et al., (2015) Development 142., 444-453.
Ishida, T.,et al., (2014) EMBO rep. In Press. Tabata, R. and Sawa, S. (2014) Frontiers in Plant Science 04 July; doi:
10.3389/fpls.2014.00311. Miyawaki, et al., (2013) Curr. Opin. Plant Biol. 16.598- 606. Yamada, M., and Sawa, S. (2013). Curr. Opin. Plant Biol. 16. 1-6. Tabata, R., et al., (2013) Plant Signaling & Behavior. 8. e22534
- 365 -
2010 2012 2013
2
Vibrio tritonius AM2
V. harveyi S20fosmid
112
V. halioticoli V. tritoniusRNA-Seq
I.
V. tritonius AM2
3 L 10 L
FHL24 kb
8 9
hyfV.
tritonius FHL
II.
V. halioticoli
V. halioticoli
V. tritonius 24 kb FHL
3 4
III.
78 9
14
V. aerogenes, V. gazogenes, V. rhizosphaerae
H21 3
Vibrio
- 366 -
Factory
update
140
Sawabe, T. et al., Front. Microbiol. 4, 414 (2013) Matsumura, Y. et al., Int. J. Hydrogen Energy 40, 9137-9146 (2015).
- 367 -
2010
Macaca fascicularis iPS
MHC
MHCMHC
MHC MafaMHC
Roche GS FLXMafa
MafaMHC
MHC (Mafa) I
RT-PCR (400 bp 500 bp) 300 Roche GS FLX
Mafa 112
Mafa I58
17 2312 Mafa-A Mafa-B/I Mafa-E
HpF/A/E/B-Hp1 F/A/E/B-Hp1 10.5%, 10.2%
Mafa
NGS Mafa
Mafa-A, -B, -I, -E, -F, -DRB, -DQA1, -DQB1, -DPA1, -DPB1
188
PCR127
PCR GS Junior Ion PGM
MHC
5,000 47MHC
5 A-Hp8.1 E-Hp2 B/I-Hp1 #7
iPS
iPS
MHC
DNA
Shiina T. et al., Immunogenetics 63, 485-499 (2011) Arikata M. et al., PLoS One 7, e37220 (2012) Blancher A. et al., Immunogenetics 64, 605-614 (2012) de Groot NG. et al., Immunogenetics 64, 615-631 (2012) Shiina T. et al., Tissue Antigens 80, 305-316 (2012) Morizane A. et al., Stem Cell Reports 1, 1-10 (2013) Blancher A. et al., Immunogenetics 66, 219-230 (2014) Kisu I. et al., J Obst Gynaecol Res. 40, 907-918 (2014) Kono A. et al., J Immunol. 192, 3239-3246 (2014) Kisu I. et al., Int J Pharmacol. 40, 907-918 (2014) Shiina T. et al., Immunogenetics 67, 563-578 (2015) Morita D. et al., Nature Communications In press. Kawamura T. et al., Stem Cell Reports In press.
- 368 -
2012 ~ 2013
- 369 -
2014
Allium cepa15 Gbp DNA , ,
,
DNA Allium Transcriptome Database Allium TDB
DB
DNA
DNAFF+1A-FF+8A
RNA-Sequencingunigene
RNA-seq 302,000
20M 30 = 600M 6 600M
HiSeq1 1-2 8 1-2
100PE
3 , 20Mreads . ,
unigeneRPKM reads
per kilobase of exon per million mapped sequence reads,
AlliumTDB ,
RPKM ,
RNA-Sequencing
RPKM 0 unigene10,197
RPKM unigene5,308
1A 803, 2A 830, 3A 799, 4A 594, 5A 603, 6A 622, 7A 568, 8A 489.
unigeneunigene
DH DHF2
SNP
QTL
F2
SNP
30RNA-seq
unigene
5,000 unigene
QTL
- 370 -
2011 2012
DNA/RNA
DNA
- 371 -
2014
3Protobothrops flavoviridis P.
tokarensis P. elegansDNA
3 3
WGS
WGS
RNA
6 45 4
1Ovophis okinavensis 1
44,
, , ,
21 ,
.
529
150
3
RNA-seq
329
Shibata et al. Genetic divergence of mitochondria genome sequence of the Habu viper, Protobothrops among Japanese subtropical islands.
- 372 -
2011 2012
DNA
2 SNP SNP
SNP 2F1 poly A RNA
SNPF1
F1F1
small RNARNA
F1DNA
DNA
F1 DNA
- 373 -
2012
HSP
HSP
SPG175
60AD
AR
(AR)(HSP) 2
1AR
HSP
1 5 23 5,6,13,17
lod 1
12
1F****
208AR HSP 89 F****
F****f**** Transcription
activator-like effector nuclease (TALEN)
1 1(AD) HSP
SPG3A ATL1(p.F413L)
2 ATL1(p.Y459Y)
ARAD-HSP
2 1 11,2,3,6,8,10,11,14,15,19,22 lod
2
16
V*****326 AR
HSP 89 13 HSPV*****
V***** v*****TALEN
2 4 22 1,2,10,11
lod 1
1 SPG3A
- 374 -
F****2 V*****
25
2014 1 8
- 375 -
2010 2011 2013
1-deoxynojirimycin DNJ 1,4-dideoxy -1,4-imino-D-arabinitol D-AB1
DNJ D-AB1
-FFaseDaimon et
al., 2008, JBC -FFase BmSuc1
Suc1
[ 1]
Trilocha varians Ernolatia moorei Rondotia menciana
Bombyx mandarinaSamia cynthia ricini Antheraea pernyi
Mamestra brassicaeHyphantria cuneaGlyphodes pyloalis
RNA RNA GA IIx HiSeq2000
HiSeq2500 RNA-seq [ 2]
p50T
"spli" "p50T"
RNA RNAGA IIX RNA-seq
- 376 -
Suc1
Mal1 Suh -
1. Wang, H., Kiuchi, T., Katsuma, S., and Shimada, T., A novel sucrose hydrolase from the bombycoid silkworms Bombyx mori, Trilocha varians, and Samia cynthia ricini with a substrate specificity for sucrose. Insect Biochemistry and Molecular Biology 61:46-52
1 1 1,2 1,3
1,4 1 1 5 5
1. 2. 3. 4. 5.
- 377 -
2015
A
W
2014 WRNA Z
Masc mRNA
Kiuchi et al., Nature, 2014 Masc
Masc
Masc
DNA MascChIP
MascRNA-seq
(1) BmN4 Masc ChIP-seq 9
Masc
BmNMasc
ChIP
(2) RNA-seq 9
BmN Masc
(1)RNA RNA-seq
(3) RNA-seq 8
RNA-seq
Masc
(1) Masc
MascCCCH
2
Masc -GFPBmN4
ChIP-seq MascMasc
Masc
piRNA
- 378 -
2014
RT multicopy single-stranded DNA msDNARNA-DNAVibrio cholerae RT retmsDNA msr -msd 2
ORF orf540 orf205-Vc95
-Vc95V. cholerae O1/O139
-Vc95
-Vc95 ret
TSC-11 MDO-6TSC-11/pBNR-1
VC0176 transcriptional regulator, putative VC0177
transcriptional regulator, VspRVC0176
VC0177 VSP-1 Vibrio seventh pandemic island pathogenicity island
2msDNA
VC0176 VC0177
msDNA DNA
msDNAVC0176
VC0177
VC0176VC0177
msDNA DNA
in vitroDNA VC0176
in vivo VC0176DNA
VC0176ChIP-Seq
V. cholerae O1 El Tor P1418 FLAG
VC0176VC0176
pBAD33
ChIP-seq
VC0176
VC0176 1 kb
transcriptional start site, TSS55
33% hypothetical protein 27%9% 4%
2% 18% DNA-directed RNA
polymerase subunit VC0328msDNA
msDNA VC0176RNA polymerase
msDNA
ChIP-Seq msDNA
VC0176
VC0176msDNA-Vc95
- 379 -
2011
2000
1.5 Gbp 245 Gbp
BAC fosmid
(TSS)
1. (Symbiodinium minutum) DNA
BAC 38482 31,104
2. DNA fosmid
384 20619,200
3. mRNA (TSS)RNAseq
29.1 Gbp TSS
1.
(Shoguchi et al., 2013) BAC fosmid
TSS
2. DNA
TSSTSS
12(Mungpakdee et al., 2014)
3.
fosmid TSS
(Shoguchi et al., 2015) 4.
S. minutum
(Beedessee et al, 2015) TSS
Symbiodinium
Symbiodinium
1. Shoguchi, E. et al., Curr. Biol. 23, 1399-1408 (2013)2. Mungpakdee, S. et al., Genome Biol. Evol. 6,
1408-1422 (2014)3. Shoguchi, E. et al., Genome Biol. Evol. 7, 2237-2244
(2015)4. Beedessee, G. et al., BMC Genomics 16, 941 (2015)
- 380 -
2013
DNA
(1) 1
PacBio RS CLR
(2) 1
(3) 768
DNA
500 bp2 kb 5 kb 10 kb 15 kb
IlluminaHiSeqPacBio RS 2
80%
90%
80%
Illumina MiSeq
8
12 RAD-Seq
5 1 SNP
- 381 -
2012
Shh
Shh 1 Mb
10
KbShh
(1) ChIP-seq
CTCF CohesinShh
ChIP-Seq 11.52 CTCF
Cohesin Smc1a Cohesin Mau2 3
2DNA DNA 8
HiSeq (2) 4C-seq
Chromosome Conformation Capture (3C)4C Shh
11.5 Shh
DNA PCR
Shh7 Shh
Shh CTCFShh CTCF
Achieropodia Shh Lmbr1 7
PCR HiSeq
ChIP-Seq CTCF Cohesin
ShhCTCF Shh
3.5 Kb 6.5 Kb
20 KbShh 800 Kb
CTCF MFCS1Shh CTCF
ChIP-seq ShhCTCF
4C-Seq Shh
MFCS1 1 Mb
Shh MFCS1
Shh
Shh Lmbr1Shh
ShhShh Lmbr1
ChIP-seq CTCF
ShhCRISPR/Cas9
Shh Lmbr1
CRISPR/Cas9 Shh
Lmbr1 60 Kb
- 382 -
2015
(cSNP)F1 (
)
Mus musculus domesticus C57BL/6JMus musculus molossinus
MSM/Ms F1
RNA-seqC57BL/6J MSM/Ms
2 F15
610
Transposase-Accessible Chromatin (ATAC)-seq
ATAC-seq
(201512 ) 2
ATAC-seqC57BL/6J MSM/Ms
2 F1 5
C57BL/6J MSM/Ms2 F1
5 610
RNA-seq 36pb3,000
2
F1
C57BL/6J MSM/Ms2 F1
ATAC-seq
DDBJ
- 383 -
2015
IgA
IgApoly-reactive
IgA
IgA W27W27
W27
W27
IgA
W27 IgA
Lactobacillus casei Bifidobacterium bifidum
W27
IgA
16S rRNA
W27 DNA16S rRNA W27
W278
IgAIgA IgA
W27 IgAIgA
AIDW27
W27 W27DNA 16S rRNA
AID
16S rRNA
16S rRNA
- 384 -
2010 2011
2005India
202010
16 201120 IM India-Mishima
IM
2010
2011
14IM 2
2
IMIM IM
IM
2IM
14 2 0.14
IM 0.14
1
IM
TALEN Transcription Activator-Like Effector Nucleases CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
IM 10
IM
IM
IM 2
IM
- 385 -
2012
- 386 -
2015
IlluminaNextera
Kmer
Nextera transposome DNAadaptor ligation
Illumina TruSeq KAPA BiosystemKmer
transposomeNextera
182
high-throughput KAPA Biosystem HyperPlus kit MiSeq
2016/1/20HDD
PacBioHiSeq PacBio
HiSeq
2016/1/4
AD
MRSA-ST8
200
CGH
MRSA Clade
2016/1/20
- 387 -
2015
Amoebidium parasiticumSphaeroforma arctica
PacBio
2015
- 388 -
2015
- 389 -
2013
- 390 -
2012
334
243
31
1144
5 20
112
PCR
5000 PCR
FLX junior
80
PCR
PCRPCR
PCR
PCR
5000 PCRFLX junior
- 391 -
2015
RRNA
RNARNA
RNA tRNArRNA RNA
mRNA non-coding RNA
RNARNA
3A-to-I RNA
tRNAX
N4
RNA
mRNAnon-coding RNA (I) N6-
(m6A)
RNA
I RNAADAR RNA
(A)I I
(G)A G
A-to-I RNAI
RNA 30,000 I
ADAR1RNA (RNA 1, 2 )
3’ (UTR)Alu I
RNARNA RNA
deep-seq RNARNA
8 A172 (Mock, Luc
siRNA, ADAR1 siRNA 2 , RNA 1
siRNA 2 , RNA 2 siRNA 2 )polyA+ RNA Illumina
strand-specific RNA-seq cDNA
Hiseq2500150bp Rapid
3
(hg38)RNA ADAR1
Alu
90% strand
RNA 1%30,000 I
20I RNA
II
2 RNAI
I
RNA
IRNA 3’UTRmRNA
RNA RNA
RNAI I
Okada, S. et al., Methods in Enzymology, 560, 331-353(2015) Suzuki, T. et al., Nature Protocols, 10, 715-732(2015) Sakurai, M. et al., Genome Research, 24, 522-534(2014)
- 392 -
2015
(IBD)IBD
(DNA Res., 21:15-25, 2014.)
IBD
T( )
DNA 16S rRNA V1-2 Miseq
( )10,000~20,000
/ 16S
150 DNA
Miseq( ) 100~200 Mbase(x30~50 )
- 393 -
2013
anammoxanammox
DNA
anammox
anammox Candidatus BrocadiaBrocadia
1) Anammox total community DNA
total community DNA 1DNA 4 3MiSep 1,300 ~ 3,500
paired end 300~400 bp
R1, R2 400bp
MAPLE (Metabolic And Physiological potentiaL Evaluator)
16S rDNA
2) Anammox total community DNA DNAPacBio anammox
1) Anammox total community DNA16S rDNA
anammoxFirmicutes,
Proteobacteria, Chloroflexi 3Anammox
anammox Planctomycetes
16S rDNA
MAPLE
anammox
anammox0.3 0.08%
anammoxanammox
2) anammoxPacBio anammox CandidatusBrocadia
contig 2
Armatimonadetes
3) Anammox
MAPLE
Anammox
abundanceanammox
abundanceanammox
Betaproteobacteria Gammaproteobacteria2
Deltaproteobacteria
1) Anammox total community DNA
anammoxanammox
anammoxanammox
2) anammoxanammox Brocadia
Armarimonadetes
anammox
anammox anammox
- 394 -
2012 2013
72
72
DNAphi29
DNAAncient Illumina sequencing library
DNA
HiseqMiseq
,
DNA
16S rRNA
DNA
DNA
- 395 -
2010 2012 2015
- 396 -
- 397 -
2013~15
Pathway
ISS
- 398 -
2013
1000
Damaster blaptoides
QTL
D.
b. fortuneiNextera Matepair Kit
fosmid 40kb
fosmidNextera Matepair Kit
20kb
180 bp 500 bp
20 kb
2.5 kb, 3.5 kb, 4.5 kb, 7 kb, 11 kbPlatanus 1.2.1
180 Mb scaffold N50 3.5 MbPacBioRS
1,654bp40
PBjelly 13.10.22contig N50
RADQTL
RAD-seq
QTL
QTL
QTL
- 399 -
2010 2012
ChIP-seq
ChIP-seq
Xenopus/Silurana tropicalisChIP-seq RNA-seqmassive parallel sequencingChIP-seq 6Otx2 Lim1 (Lhx1) Gsc (Goosecoid) Mix1 VegTSia (Siamois) p300
TLE/GrouchoH3K4me1 H3K27ac RNA-seq
RNA ChIP-seqX. tropicalis
ver. 4 2012 ver. 7
MACS
Otx2 Lim1 Gsc ChIP-seq
RNA-seq Otx2 Lim1 Gsc
19903
Otx2 Lim1Gsc ChIP-seq
p300 TLE/H3K4me1 H3K27ac
ChIP-seqH3K27me3
cis-regulatory module: CRMChIP-seq
CRM2
CRMCRM
RNA-seq
p300 TLE
p300 TLETLE CRM
TLEChIP-seq
CRM p300 TLEOtx2
Otx2CRM TLE Otx2/TLE
CRM Otx2/TLE CRM 13,443
Otx2
Lim1Gsc
Otx2 Lim1 Otx2Gsc
Otx2/TLE/Lim1CRM Otx2/TLE/Gsc CRM 2
MIMELim1
Otx2/GscOtx2/TLE/Lim1 CRM Lim1
type I 1250Otx2/TLE/Gsc CRM Otx2/Gsc
type II 1039
- 400 -
type I CRMtype II CRM
type I CRM Otx2 Lim1 Gsc 3
type II CRM
Otx2CRM Otx2
OtxOtx
CRM type I type II
Mix1 VegT Sia ChIP-seq
enhancerdevelopmentally poised enhancer
Mix1 VegT
developmentally poised enhancer
CRM Mix1 VegTCRM
developmentally poised enhancer
Sia Wnt
Sia
SiaSia Otx2 Mix1 TLE
p300 CRM type A CRM
type A CRM
Sia type A CRM Otx2 Mix1
ChIP-seq RNA-seqX. tropicalis
Yuuri Yasuoka, Yutaka Suzuki, Shuji Takahashi, Haruka Someya, Norihiro Sudou, Yoshikazu Haramoto, Ken Cho, Makoto Asashima, Sumio Sugano, Masanori Taira (2014). Occupancy of Tissue-Specific cis-Regulatory Modules by Otx2 and TLE/Groucho for Embryonic Head Specification. Nat. Commun. 5, 4322 (article number).
Yuuri Yasuoka, Yutaka Suzuki, Shuji Takahashi, Haruka Someya, Norihiro Sudou, Yoshikazu Haramoto, Ken Cho, Makoto Asashima, Sumio Sugano, Masanori Taira "Genomics Study of the Spemann-Mangold Organizer: Occupancy of Tissue-Specific cis-Regulatory Modules by Otx2 and TLE/Groucho for Embryonic Head Specification." PD
15th International Xenopus ConferenceAsilomar (California, USA) 2014 8 24 30
Yuki Honda, Yoshiaki Kirigaya, Yuuri Yasuoka, Saya Imai, Yutaka Suzuki, Shuji Takahashi, Makoto Asashima, Sumio Sugano, Masanori Taira
ChIP-Seq analysis of Transcription factor Siamois for mechanisms of head organizer formation 36 2013
12 3 6 Yuuri Yasuoka, Yutaka Suzuki, Shuji Takahashi, Norihiro Sudou, Yoshikazu Haramoto, Yukiko Tando, Kaoru Kubokawa, Ken W. Cho, Makoto Asashima, Sumio Sugano and Masanori Taira "Otx2 and TLE/Groucho occupancy marks tissue-specific cis-regulatory modules for head specification" 35 2012
12 11 14 Yuuri Yasuoka, Yutaka Suzuki, Shuji Takahashi, Norihiro Sudou, Yoshikazu Haramoto, Yukiko Tando, Kaoru Kubokawa, Ken W. Cho, Makoto Asashima, Sumio Sugano and Masanori Taira "Massively parallel regulation of head and non-head genes by Otx2, Lim1 and Gsc is based on evolution of the head organizer in the chordate"
45 2012 5 2831
- 401 -
2013
RRNA
NGS
RNAB
RNALi et al. Science 2011
RNA Ader
15 RNARNA
Danecek et al. Genome Biology, 2012
RNA
ApoB mRNA Apobec1
Chen et al. Science, 1987; Powell et al. Cell, 1987 Apobec1
Hirano et al. JBC, 1996; Morrison et al. PNAS, 1996 Apobec1 ApoB
RNA
C57BL/6J (B6; Mus musculus domesticus)
MSM/Ms (MSM; Mus musculus molossinus)
B6MSM
Takada et al. Genome Res. 2008; Takada & Shiroishi, Exp. Anim. 2012
B6
(Takada et al. Genome Res. 2008)MSM
Takada et al. Genome Res. 2013; Takada et al. Mammal. Genome 2015 B6-MSM
RNA
RNA
RNA
B6 MSMNGS
B6MSM 2 4
3 24 RNAHiSeq
100bp 30-70M QV30: >93.26%)DDBJ DRA
2
RNA SNPRNAB6
MSM RNADEG
non-DEG 2GO Term
B6MSM
RNA
- 402 -
2014
Mus musculus
C57BL/6J (B6; Mus musculus domesticus) MSM/Ms(MSM; Mus musculus molossinus)
Takada et al. Genome Res. 2008
2 bp
B6
MSM
PacBioRS llDNA
cDNA
PacBio
cDNA MSM B68
10RNA cDNA
2-3kb1-3kb 3-6kb cDNA 2
60
cDNA
MSM
cDNAMSM
RNA
- 403 -
2013
RNA II Pol II
Pol IIPol II RNA
Pol IIMed26
Super elongation complex SECc-Myc Hsp70
Takahashi H, et al. Cell 2011Med26Little elongation complex LEC
Med26 SEC LEC
SEC
ELL AF4 AFF4 AF9 ENL MLLMixed Lineage Leukemia
MLLSEC Hox
1
Pol IIMed26 SEC
Med26 Pol II
HEK293T Med26 AFF4 SEC
KIAA0947 LECChIP
MLL REH
MLL-SECRS4-11 MLL-AF4
Med26 ChIP
HEK293T Med26 AFF4 SECKIAA0947 LEC
TAF7 ChIP
1 Med26 ChIP-seq Med26
SEC small nuclear RNAsnRNA non-coding RNA LEC
2 LEC KIAA0947 ChIP-seqKIAA0947
LECsnRNA non-coding RNA
3 TFIID TAF7 ChIP-seqTAF7
TAF7 Med26KIAA0947 LEC snRNA
HEK293T TAF7snRNA LEC
TAF7 Med26LEC
Med26 TAF7
Med26 TAF7SEC LEC
Med26 SEC LEC
TAF7 Med26SEC LEC
Takahashi H., Takigawa I., Watanabe M., Anwar D., Shibata M., Tomomori-Sato C., Sato S., Ranjan A., Seidel CW., Tsukiyama T., Mizushima W., Hayashi M., Ohkawa Y., Conaway JW., Conaway RC., Hatakeyama S.: MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Nature Commun., 6, 5941, 2015.
- 404 -
2014
MMed26 LEC
RNA IIPol II
Pol IIRNA
Med26 N NTD2 Super
elongation complex SEC Little elongation complex LEC
Med26 SEC LEC
Med26
Control siRNAMed26 siRNA
HEK293 RNA-seq
Med26Med26-/-Med26-/- RNA-seq
Med26 NTD 1-113 61 R Arg62 K Lys A Ala
Med26-mut SEC LECMed26-/-
Med26 Med26Med26-/- + Med26-wt
Med26-/- + Med26-mutRNA-seq Med26-/- + Med26-mut
Med26 HEK293
c-Myc Hsp70 c-Jun
Med26
HistoneMed26
Med26-/- + Med26-wt
Med26-/- + Med26-mut
RASGRP2 RAS guanyl-releasing protein 2Wnt6 Wingless-type MMTV integration site family, member 6Med26 Med26
Med26 SECLEC
Pol II
Histone mRNAPolyA
Med26Histone mRNA
Med26RNA-seq Histone
Med26Histone
Takahashi H., Takigawa I., Watanabe M., Anwar D., Shibata M., Tomomori-Sato C., Sato S., Ranjan A., Seidel CW., Tsukiyama T., Mizushima W., Hayashi M., Ohkawa Y., Conaway JW., Conaway RC., Hatakeyama S.: MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Nature Commun., 6, 5941, 2015.
- 405 -
2015
PPol2
30RNA II Pol II
20 50
Pol IIc-Myc
Hsp70
Pol II Pol IIRNA
Med26 2 Super elongation complex SEC Little
elongation complex LEC
Med26 SEC c-Myc Hsp70
LEC small nuclear RNAnon-coding RNA
Takahashi H, et al. Cell 2011 Takahashi H, et al. Nature Communications 2015
Med26 SEC LEC
Med26SEC LEC
Med26 SEC LEC
Med26 AFF4SEC KIAA0947 LEC
HEK293RNA-seq
LEC
Micrococcal nucleaseChIP LEC
KIAA0947 NARG2 ChIP-seq
LEC NARG2 RNA
LEC
RNA non-coding RNA
LECKIAA0947 NARG2 RIP RNA
immunoprecipitation CLIP cross-linking immunoprecipitationLEC RNA
Med26 SEC
Med26 LEC
LEC RNA Med26LEC
Med26 SEC LEC
Med26mRNA
Med26 SEC LEC
1
- 406 -
2014
1930
()
( )
( >
) (Oryza sativa)
( >)
(Lotus japonicas)
(< )
(Cucumis sativus)
() ( )
RNA
RNA RNA Oligo-dT
poly(A) RNA poly(A)-RNA cDNA
Illumina HiseqTM 2500 FASTAQ
TophHat 2.1.10cuffdiff
38 19
19
(q < 0.05)
42 (q < 0.05) 3RNA
29 (q < 0.05) 15 RNA
RNA-Seq mRNA
RNA-Seq
RNA-Seq
- 407 -
2014
2007
AUREOCHROME
DictyopterisSargassum
RNAseq
mRNA
1000 MbmRNA
4
4
http://bioinfo.med.niigata-u.ac.jp/takahashi2/8
5 24
myb-like
c6-typereal time PCR
RT-PCR
PacBio
RNA-seq
2016 3 19 20
- 408 -
2015
HP1 FACT
RNA lncRNARNAi
FACT
FACT
HP1 FACTlncRNA
HP1 FACTH3K9
H3K9me
HP1FACT
RNAi
RNA-seq
HP1
Swi6 ChIP seq HP1
Chp2 ChIP seq FACT
Spt16 ChIP seq
RNA-seq
FACTHP1/Swi6 ChIP seq
HP1/Swi6
H3K9meH3K9me
HP1/Swi6
HP1/Swi6TTS: Transcriptional
Termination SiteHP1/Swi6 TTS
HP1/Swi6H3K9me
HP1/Swi6 DNA TTS
FACT ChIP seq FACTH2A/H2B
HP1/Swi6 Spt16Spt16 swi6+
HP1/Swi6FACT
HP1/Swi6TTS FACT
swi6+HP1/Swi6 Spt16
TTSgene body
RNA-seqswi6+ FACT
HP1/Swi6 FACTTTS
H3K9me
H3K9me
HP1/Swi6 H3K9meTTS
FACT TTS
TTS
Suzuki S. et al., Nucleic Acids Research, in press
- 409 -
2010 2011
T TCR
CD8T
CD8T
TCR
CD8T
CD8
RNA DNA
TCR V N
CD8T
CD8T RNA
Illumina
Genome Analyzer RNA-seq
TCR CDR3
RNA-seq TCRV
33 N
T CDR3
CDR3
CDR3N
CDR3
ASRT ASSY
TCR
1000
CDR3
TCR
TCR
TCR
TCR
T
Takada K, et al. Nature Immunology. 16, 1069-1076,
2015.
- 410 -
2014 2015
RNA 2014
2015
3
HA
1 5M2
5
- -RNA -RNA ligationMiSeq
RNAMiSeq
RNA - RNA-
RNA
RNA
- -RNA-RNA ligation HiSeq
RNA
- 411 -
2012 2013
90NaCl
1, 3 1, 7
5 PolyA RNA
120 RNA-seq
5String Analyses
21
2
2
in situ hybridization
2-3
DNA microarraySubtractive Differential Display
Osmotic Transcription Factor 1 (Ostf-1)
2
1
(early response gene)
Wong, M., et al., BMC Genomics 15:1134 (2014) Ando, M., et al., Am. J. Physiol. 307:R653-R663 (2014)
- 412 -
2012
- 413 -
2013
2009
172 19
RAD-tag
GeneDBKa4C1 line
http://www.genedb.org/Homepage/Bxylophilus
GO
3 2011Kikuchi et al., PLOS
Pathogens, 2011
RAD-seq
3
3
CYP
daf-1
Caenorhabditis elegans
DNAAFLP amplified fragment length
polymorphismSSR; simple sequence repeat
SNPsingle nucleotide polymorphism
- 414 -
2014
BLM
F (B6×129) ES
Loss of Heterozygosity: LOH
DNA
Aprt LOH
DNA
Aprt
Aprt
Yamanishi A et al. Genome Res 23:
1462-1473, 2013
DNA
DNA
illumina HiSeq 2500 paired-end sequencing
(500-bp size range, 100-bp read length, 30 depth)
COSMOS (Control
sample based detection of structural variation)
(Yamagata K et al. in press)
Chromothripsis(Stephens PJ et al., Cell.2011)
arrayCGH (Comparative genomic hybridization)
Chromothripsis
arrayCGH
Yamagata K. et al., Nucleic Acids Res., in press
- 415 -
2013
(Lotus japonicus)
AMAM
RNA-Seq
gain of function CCaMK
NSP1 RAMI1 c-myc tagDNA
Chip-Seq
AMcerberus
cerberusXyloglucan endotrans
-glucosylase / hydrolases (XTHs) cerberus
XTHXTH
AM
XyloglucanXyloglucan
cerberusXyloglucan
Xylose cerberus
AMCERBERUS
AM
AMSbtM1
rami1RAMI1
rami1
AM
rami1
RAMI1
Chip-Seq
Chip
- 416 -
2010 2011 2013
Zic1( Zic4)
Zic1
Zic1
Bisulfite seq
Da /
ChIP-seq
H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K27Ac
H3K4me3 H3K27me3 H3K4me2 H3K27me3
RNA seq
Zic1 DNAH3K27me3
Zic1
DNA
H3K27me323kb DNA
DNA
DNADNA
Zic1
DNA16%
H3K27me3
DNADNA
DNAZic1
DNA
HMD
HMD
Nakamura, R. et al., Development 141, 2568-2580 (2014)
- 417 -
2013
NFATc1
B
(1)
RAGEAGEs
RAGE-AGEs
(JCB, 2009)
(Cell. 2007)
NFATc1NFATc1 (nuclear factor of activated T cells
c1) RANKL (receptor activator of NF-
(Takayanagi H, et al. 2002 Dev Cell)
(De la pompa JL,
et al. 1998 Nature; Ranger AM, et al. 1998 Nature)
Osteopetrosis ( )(Asagiri M, et al. 2005 J Exp Med;
Winslow MM, et al. 2006 Dev Cell)NFATc1
(1)(2)
(3)HClK (4)-
( 1)NFATc1
TRAP (tartrate-resistance acid phosphatase), - integrin
(2)
conditioned medium
RAGEparacrine signaling
-
NFATc1
RNA-sequence
- 418 -
(Monocyte/ Macrophage )
Dcstamp Ocstamp
Sealing zone
K
Receptor activator
of NF-
stimulating factor (M-CSF)
RAW264.7 RANKL
RNA-seq
1 Micro-array RNA-seq
non-coding RNA
1 Micro-RNA (Mir1902, Mir762,
Mir2861) non-coding RNA
RANKL
RANKL
RANKL
signal
non-coding RNA
RANKL 3 protein
coding genes
protein-coding, non-coding genes
30
Myc TNF receptor
TRAF1 small nucleolar RNA, small nuclear
RNA, micro RNA, transfer RNA
non-coding RNA
master regulator
Nuclear factor of activated T-cells, cytoplasmic 1
(Nfatc1) Mmp9, Nhedc2, Ctsk,
Atp6v0d2
protein-coding genes
30 protein-coding genes
Ocstamp
Acp5
- 419 -
RANKL RAW264.7
RANKL
NFATc1
conditional
knockout mice
NFATc1-dependent genes (Aliprantis AO, et al. J
Clin Invest 2008; Charles JF, et al. Bone 2012)
Calcr, Ctsk,
Mmp9 Nfatc1
Oscar, Clcn7, Serpind1
Car2, Acp5
Nfatc1
Nfatc1
Nfatc1
NFATc1
RANKL dynamic
NFATc1
Tandem affinity purification
LC-MS/MS NFATc1
- 420 -
2010 2012
p53 p53
ES
ES/iPS
ES/iPS p53Dual SMAD inhibition
PAX6p53
CRISPR/Cas9p53 ES/iPS
p53ES/iPS PAX6
p53 ES/iPSsingle SMAD inhibition PAX6
p53 ES/iPSPAX6
PAX6p53H3K4
SCID ES/iPSp53
p53 ESPAX6 repressive
ES/iPS p53 linc RNA
p53 ES/iPS
p53
ES/iPS
Suzuki, S. et al., PNAS 107, 7461-7466 (2010) Horiuchi, S. et al., J Immunol 186, 6378-6389 (2011) Hosokawa, H. et al., PNAS 110, 4691-4696 (2013) Hosokawa, H. et al., PNAS 110, 18626-18631 (2013)
- 421 -
2010
p53
p53
p53
ChIP-seqp53
Glutaminase2(GLS2)DPYSL4
GLS2
GLS2TCA
ATP
NASH p53-GLS2
NASH- GLS2
GLS2 In vitro p53
migration, invasionGLS2
SCID
GLS2
NASH GLS2
GLS2
GLS2
GLS2
GLSWT
GLS2NASH
NASH-STAM
STAMGLS2 WT
NAH-GLS2
NAC
p53
GLS2-NASH-
NASHNASH
NASH
E NASH
GLS2 NASH-
- 422 -
2010
ALS
3-4ALS
ALSDNA
200630
Japanese Consortium for Amyotrophic Lateral Sclerosis Research (JaCALS)DNA
1000 JaCALS
ALS
ALS
5-10%ALS TAR DNA
binding protein 43 kDa(TDP-43) ALS
ALSALS
ALS
ALS 611 DNA
22
11 SNV450,000
rare 30,000
400 indel35,000
rare 2,50035
SNV indel
ALS
ALS heterogeneous
4ALS
22
ALS
ALS600
HGVD
ALSALS
ALS
Nakamura, R. et al., Neurobiol Aging. 2015 Dec 7. [Epub ahead of print]
- 423 -
2013
Methylobacterium10-20%
MDH
M. aquaticum 22A
22A
22ARNA
22A
contig500
454 Illumina 47xPCR
7.56 Mb
PGAP, MiGAP6944 CDS
RNA 11 tRNA 95MDH
PQQt-zeatinACC deaminase ,
Type VIType III, IV
22A RNA-Seq
RNA3 RNA-Seq
RNA riboZero RNA
MaserBWA rRNA
CDS FPKM (Ca) MDH
MxaF (La) XoxF
XoxF
MDH
MxaF CaCaLa
22A
RNA-Seq
Ca,La
GC 69.1% LaCDS GC (<60%)CDS
GCLa
RNA-Seq
La
transcript
RNA-Seqgenome, transcriptome
Tani A., et al., Genome Announc 3(2) e00266-15
(2015)
- 424 -
2010
cAMP
long-term-olfactory-aversive-memory
Total RNAPCR cDNA
cDNA
spaced trainingmassed training
CREBspaced sample massed sample
spaced samplespaced sample massed sample
12
spaced sample
massed sample
in situ hybridization Q-PCR
cAMP
cAMP
Adenylyl Cyclase (rutabaga ) PKA
cAMPcAMPPhosphodiesterase PDE
dunce cAMP
6 PDEDunce
PDE
pde1cin situ hybridization pde1c
pde1c
spaced training
cAMPpde1c
RNA
pde1c
- 425 -
2013 2014
chromatin immunoprecipitation sequencing, ChIP-seq
ChIP-seq
ChIP-seqChIP-seq
ChIP-seq
2013ChIP-seq IRF8
ChIPChIP DNA
1010 1
ChIP-seqChIP-seq
2014
ChIP DNA
IRF8 PU.1ChIP-seq
ChIP-seq
ChIP-seq
ChIP-seq
- 426 -
2015
RNA-seqB
RNA-seqcDNA NGS
DNA400
cDNA NGS
DNA
RNA-seq
RNA-seq
- 427 -
2014 2015
mRNA
Illumina
RNA
RNA3’ Takara 3’ RNaseT1
15 5’ PCR
UU
5’ 6
5’ 3’
U 2
RNA-seq contig
700-2000 contigU mRNA
URNA-contig ID
U U mRNA
A
RNA
Ochi H, Saki A, Tachibana K, Hara M., and Chiba K.
Block of Cdk1-dependent poly(A) elongation of cyclin
B mRNA in MI-arrested starfish oocytes is released by
intracellular pH elevation upon spawning.
Mol Reprod Dev 83 79-87 (2016)
- 428 -
2013
Cynops pyrrhogaster
Japan Newt Research Community (JNRC)
TG
TG
16mRNA-seq
reference transcriptome
JNRCreference transcriptome 2013
mRNA-seq
20 25
30 50
mRNA-seq Illumina HiSeq200-2500; 100bp paired-end read
reference transcriptome
JNRC16
0-1413.620 25 30 50
8.7
reference transcriptome
n=12 20Gbp
Non-coding RNA 2014-2015
2014
14
20Tsonis
Endo, Y. et al. Proceeding of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2014), ISBN 978-989-758-012-3, 215-220 (2014).
- 429 -
2014
Cynops pyrrhogaster
Japan Newt Research Community (JNRC)
TG
TG
mRNA reference transcriptome2013 mRNA-seq
Illumina HiSeq 2000-2500 100bp paired-end read JNRC
160-14
13.620 25
30 508.7
de novo assemblytranscriptome transcriptome
mRNA-seq/transcriptome
mRNA-SeqRPE
RPE RPE stem cell cDNAIllumina HiSeq
2000-2500 100bp paired-end read
read Trinity version
20131110 de novo assembly697,670 N50: 2,380 b
transcriptomemRNA-seqtranscriptome
transcriptome
transcriptome Reference transcriptome
mRNA-seqRPE 100
REPLI-g SensiPhi PolymerasecDNA RPE
4 RPE stem cell 6 5.6
readDDBJ/NCBI 2013transcriptome JNRC
IMORI (http://antler.is.utsunomiya-u.ac.jp/imori/)transcriptome 2015
3
TALEN/CRISPR
220
Yokoe, M. et al., Int. J. Mol. Sci. 15, 15210-15224 (2014) Nakamura, K., et al., PLoS ONE 9, e109831 (2014) Islam, M.R. et al., Sci. Rep. 4, 6043 (2014)
- 430 -
2015
Cynops pyrrhogaster
Japan Newt Research Community (JNRC)
TG
TG
2013-2014transcriptome
RPE mRNA
transcriptome
3 7 mRNA
cDNA mRNA Pax6RPE
RPE cDNA Illumina HiSeq 2000-2500 100bp paired-end read
2013-2015
transcriptome 211 transcriptome 694,138
N50: 2,294 b GC: 45.52%transcriptome de novo assembly
697,670
JNRC ‘MORI’ http://antler.is.utsunomiya-u.ac.jp/imori/)
2015
TTX de novo
assemble 2014
RPE
4,433 6,871
5,407 -
8,372 RPE
2014
in vitro in vivo
transcriptome
200cDNA
transcriptomen=12, ~20 Gbp
Inami, W. et al., Zool. Sci. (2016) in press Sousounis, K. et al., eLife 2015;10.7554/eLife.09594. (2015) Kudo, Y. et al., Toxicon 101, 101-105 (2015) Endo, Y. et al., IPSJ Transactions on Bioinformatics 8, 2-8 (2015) Casco-Robles, M.M. et al., Transgenic Res. 24, 463-473 (2015)
- 431 -
2012
DNAHypomethylated domain; HMD
ES
H3K27me3H3K4me2 HMD K27HMD
K27HMDK27HMD 4kb
large K27HMD 4kb small K27HMD
K27HMDH3K27me3 large
K27HMD
K27HMDHMD
K27HMD
DNA 5hmC
K27HMD5hmC
RNA-seq ChIP-seq DNA
RNA-seq 1
ChIP-seq H3K4me2
H3K27me3
1
RNA-seq large K27HMD small K27HMD1
large K27HMD
RNA
RNA-seqzygotic gene
activationRNA-seq
K27HMDRNA-seq
K27HMD H3K27me3
K27HMD
K27HMDlarge
K27HMD
K27HMD
hydroxymethyl collector5hmC
DNA 5hmC
DNA K27HMD
5hmCK27HMD DNA
K27HMD
DNA H3K27me3K27HMD
DNA
DNA H3K27me3
K27HMDK27HMD
Nakamura, R. et al., Development, 141, 2568-1580 (2014)
- 432 -
2013
IM294
MITE (miniature inverted-repeat transposable element) mPing
mPingmPing
mPing
mPingmPing
mPing
mPing
mPing 1,000
mPing1,000
DNAmPing 4
Post-bisulfite Adaptor Tagging (PBAT) mPing
HiSeq
Bismark mPing
146,467,644Bismark
mPing46,180 (0.03%) mPing
5,652 (0.004%)mPing
mPing 1,000106
mPing 21mPing
mPing CGCHG CHH 95%
58% 31%
16 mPingmPing(
)mPing (
)
mPingmPing
mPing DNA
mPing
mPing
2013
PBAT mPing
- 433 -
2010
/ /
ALS/PDCtau
ALS/PDC
phenocopy
2ALS/PDC
1 21
rare variants2 10
rare variants MSA
14 7
/2
21
/ HiSeq2000
BWA hg19 alignment62.8X 72.9X
SAMtools3604450 3576323
587322 585433
dbSNP347 326 52 46
5
MSA 14 7
1 10,000 12,00021 42
29,359 42 113,345 45.5
1 18,850 64.2%1
dbNSFPver1.1Polyphen2, SIFT, MutationTaster, LRT, Phylop
54 18,850
4,028MSA 14 7
/
ALS/PDCphenocopy
short indel
- 434 -
ALS/PDC
COQ2 2013 GBA2015
The Multiple-System Atrophy Research Collaboration (Mitsui J et al.,) N Engl J Med. 2013; 369: 233-44.
Mitsui J, Tsuji S. Biochem Biophys Res Commun. 2014; 452: 221-5.
Mitsui J et al., Ann Clin Transl Neurol. 2015; 2: 417-426
- 435 -
2010
4 [3-(3CB) (Phn) 3
(PAHs)] ()
3CB Phn
3CB
3CB
Burkholderia 6 PhnMycobacterium Paenibacillus
(Roche 454) (2)3CB
16S rRNA (Roche 454)
(Illumina HiSeq 2000)
1 3CB 3 PAHs
3-Proteobacteria Burkholderia
1 3CB-Proteobacteria Phn-Proteobacteria Actinobacteria
Burkholderia3 Mycobacterium sp. EPa45
(1-1)3CB Burkholderia Phn
MycobacteriumBurkholderia(1-2) Mycobacterium EPa45
Phn
PhnPhn
Mycobacterium (1-3)
Burkholderia
4 3CB 12
3CB 3
(2-1)Burkholderia
( 4) (2-2) 3CB
BurkholderiaBurkholderia
3CBBurkholderia 3CB
Phn
Mycobacterium Burkholderia
Mycobacterium 1Burkholderia Mycobacterium Phn
PhnMycobacterium EPa45Burkholderia
Phn Burkholderia
, J. Environ. Biotechnol. 10: 63-71 (2010)
J. Environ. Biotechnol. 13: 51-56 (2013) Mori, H. et al., DNA Res. 21: 217-227 (2014)Nagayama, H. et al., Appl. Microbiol. Biotechnol. 99:
4453-4470 (2015)Kato, H. et al., Genome Announc. 3: e00782-15 (2015)
. 30: 57-64 (2015)Kato, H. et al., DNA Res. 22: 413-424 (2015)
- 436 -
2011~2012
Onoda, A.et al., Nucleic Acids Res. 42, 9005-9020 (2014)Miyaji, M. et al., J. Cell. Biochem. 116, 677-685 (2015)
- 437 -
2015
10-6
1940
RNA-seq
RNA-seq (Escherichia coli K12 derivative strain)
18 (6 samples, 3 biological replicates) 6
RNA 1) 2) 3)
4) 5) 6)
1 231 RNA-sequencing
RNA-sequencing
- 438 -
2014 2015
siRNA RNA
RNARNA TRBP
RNARNA
TNRC6A RIP-SeqmiRNA siRNA
mRNA
RNARNA
- 439 -
2014 2015
GGVHD
(allogeneic
hematopoietic stem cell transplantation: allo-HSCT) ,
, (graft-versus-host disease: GVHD)
GVHD T ,,
, ,GVHD ,
,,
allo-HSCT , GVHD, GVHD
, Paneth GVHD(Eriguchi et al, Blood
2012) Paneth , -defensin,
, GVHD, Paneth
,(dysbiosis) Dysbiosis ,
GVHDGVHD,
GVHD
, X
PanethPaneth ,
,
, X ,GVHD , dysbiosis
GVHD,
,X
, GVHD ,
,X ,
16S rRNA
, ,
,
, ,16S rRNA ,
,(Kim et al, Cell Host Microbe.
2014) ,
,,
GVHD(Uryu et al, Blood 2015) ,
GVHD, 18S ITS
1.DNA , 16S rRNA PCR
MiSeq,
2.
DNA , 18S ITS PCRMiSeq
,
1. X Paneth ,-defensin :
X naïve 6 ,
Paneth Paneth-defensin
-defensin ,X
, Xnaïve
Naïve -denfensin
2. X , GVHD-defensin :
, 5 T, GVHD
GVHD Paneth, X
4 7 PanethGVHD
GVHD Paneth, -defensin
X Paneth, 7 -defensin
- 440 -
3. X , GVHDdysbiosis GVHD :
7 DNA ,PCR 16S rRNA ,
MiSeq, GVHD
, (Syngeneic), GVHD
Syngeneic dysbiosis(diversity)
, Shannon Simpsondiversity
, GVHD SyngeneicFirmicutes
, Escherichia/Shigella
GVHD dysbiosis ,X
,PERMANOVA , GVHD
naïve syngeneic,
X naïvesyngeneic
dysbiosis , donor T, GVHD
4. dysbiosis: ,
dysbiosis
5. :,
,, ,
,,
DNA , 16S rRNA
6. :,
, , GVHD
, GVHD ,
T,
, ,
, , X Paneth
-defensin ,-defensin , GVHD
-defensin ,,
(Masuda et al. J Innate Immun 2011) , ,
, GVHD,
, ,
[ ]
[ ] 1. Teshima T. Protection of the tissue stem cell
and niche system as a novel approach to control GVHD, 2nd Australia-Japan Haematology Consortium, Sep 11-12 2015, Brisbane, Australia.
2. Hayase E, et al. R-Spondin1 promotes Paneth cell growth, maintains intestinal microbial ecology, and ameliorates graft-versus-host disease, 57th ASH Annual Meeting, Dec 6th 2015, Orlando, FL, USA.
3. Teshima T. Emerging concepts on tissue injury in GVHD. BMT Tandem Meeting 2016, Feb 18th 2016, Honolulu, HI, USA. (
)
- 441 -
2010
Transcription Activator Like Effector Nuclease (TALEN) Clustered Regularly Interspaced Short Palindromic Repeat)/Cas9 (CRISPR)
deletion
deletion
- 442 -
2014 2015
RNA-seq
RNA-seq
3
17,20 -DHP 4RNA 1 RNA-seq
RNA 2014, 2015
22
RNA 2 6
RNA-seq
4 6
RNA-seq
6
22015
RNA-seq
CRISR/Cas9
RNA-seq
RNA-seq
q-PCRRNA-seq
- 443 -
2010
(PD)
PD
gIQ 70
3
6
6 coverage x423, x204, x461, x224,
x200, x220 Mapping rate 86%, 86%, 86%, 85%, 84%, 84% PCR duplicate10.5%, 5.6%, 12.8%, 7,1%, 7.5%, 8.4%Insert size 213(SD 64), 230 (67), 205 (60), 229 (70), 209 (63), 213 (65) DB
rare SNV 37918, 23455, 57363, 25195, 32372, 40746 Indelrare coding 71, 45, 57, 51, 50, 51
SNV
- 444 -
2011
(PD)
PD
gIQ 70
3
IQ
IQ 2 4IQ 1 45 1 30 1
SD = 15 2 61 1
11
- 445 -
2014
Tonoki and Davis.,JNeurosci.,2015
- 446 -
2015
2015
- 447 -
2015
(MV)MV
MV
MV
MV
1) DNA2) 3) ,
MV 4
MV DNA
MV DNAMV
Burkholderia
cenocepacia H111 Paracoccus denitrificans Pd1222 Bacillus subtilis 168
Clostridium perfringens 13 MVDNA( mvDNA)mvDNA MV
B. cenocepacia H111 B. subtilis 168 MVmvDNA 6
MV, FPKM
6P. denitrificans Pd1222 B.
subtilis 168
Pseudomonas aeruginosa MV
(Nature communications ) P. denitrificans Pd1222 MV
P. aeruginosa MV
MV B. subtilis 168
DNA MVB. subtilis 168 MV
MV
MV DNA
MV DNA
MV
MV DNA
MV DNA
MV
DNA
MV MV
mvDNA , MV
MVMV
MV
MVMV
MVMV MV
- 448 -
2014
DNA
Schizosaccharomyces pombe
Factors of Centromere rearrangement (FOC) FOC
FOC
S. pombeDNA
DNA Positive pool Negative pool
DNADNA MiSeq Illumina
DNA Pooled Linkage Analysis (PLA) PLA
DNA100x
coverage
Positive pool Negative pool
FOC1FOC1
FOC1 DNARad51
foc1DNA
MMSDNA rad51
DNA Rad51 Foc1
BRCA2
FOC
FOC1
- 449 -
2012
-hexachlorocyclohexane ( -HCH)-HCH
(B) 22~24
-HCHHCH
-HCH
-HCHSphingobium sp. TKS -HCH
Pseudomonas sp. TKPHCH
t-HCH ( -, -, -, -HCH )
-HCHSphingomonas sp. MM-1 -HCH
Pseudomonas aeruginosa MTB-1
-HCH
454illumina
HCH-HCHtotal read 454 1 Gb
illumina 5.5 GbPseudomonas sp. TKP total read
454 240 Mb illumina 50 MbPseudomonas aeruginosa MTB-1
total read 454 200 Mbillumina 500 Mb
TKP MTB-1
MTB-1 Pseudomonas aeruginosa
P. aeruginosaMTB-1
phage/island TKPP. fluorescens SWB P. poae RE*1-1-14
Pseudomonas2 JCM
MTB-1 TKP -HCHlin -HCH
-HCHTKS TKP
Cupriavidus ( -proteobacteria) Sphingobium ( -proteobacteria)
Pseudomonas ( -proteobacteria)
-HCH
Cupriavidus sp. TKCAchromobacter sp. TKA Hyphomicrobium sp. TKH
-HCH-HCH
TKS-HCH
-HCH
Ohtsubo Y et al. 2014. Complete genome sequence of Pseudomonas aeruginosa MTB-1, isolated from a microbial community enriched by the technical formulation of hexachlorocyclohexane. Genome Announcements 2:e01130-13.Ohtsubo Y et al.. 2014. Complete genome sequence of Pseudomonas sp. strain TKP, isolated from a -hexachlorocyclohexane-degrading mixed culture.
Genome Announcements 2:e01241-13.
Pseudomonas aeruginosa MTB-1 (JCM 19686) Acc No CP006853
Pseudomonas sp. TKP (JCM 19688) Acc No CP006852
- 450 -
2011
Mycobacterium ulcerans
WHO17 Neglected Tropical Diseases
1980 M. ulcerans M. ulcerans subsp. shinshuense (M. shinshuense)
M. ulcerans
mycolactone
mycolactone170kbp plasmid code
1-2 M. ulcerans
(1999 ) Agy99
M. shinshuense
2015 12 57M. shinshuense
Mycobacterium
ulcerans subsp. shinshuense ATCC 33728( mycolactoneShT-P ATCC 33728
ShT-N 225
23 27 ShT-P
ShT-N 2 Roche454GS FLXShT-P
250Illumina
25 Illumina
ShT-P PacBio
”Mycobacterium
ulcerans subsp. shinshuense” ATCC 33728
( mycolactoneShT-P Roche 454 GS FLX
250 gap close
PacBioM. shinshuense ATCC33728
(5,899,681 bps) re-arrangement5027 CDS, 46
tRNA, 451 pseudogene, 245 PE/PPE family ( 96 pseudogene), 221 insertion sequence ( 37 )
M. marinum 6.6MbpsM.
ulcerans Agy99 5.6MbpsCDS M. marinum 5424 Agy99 4160
M. shinshuense5027 pseudogeneM. marinum 65 Agy99 771
M. shinshuense 245 M. shinshuenseM. marinum Agy99
25 (ATCC37728 26 )
M. ulcerans plasmid
GCPacBio
plasmid 1-2plasmid plasmid
26
M. ulcerans
mycolactone code plasmid(mycolactone producing
mycobacteria MPM)
M. ulceransMPM
Yotsu, RR. et al.,J. Dermatol. 39, 587-593(2012) Nakanaga, K. et al., J.Dermatol. 40,151-159(2013) Nakanaga, K. et al., JJID 66,83-88(2013) Ohtsuka,M.et al.,JAMA Dermatol.150,64-67(2014) Yotsu, RR. et al.,J. Dermatol. 42,1-9(2015) Sugawara, M.et al., J. Dermatol. 42,588-595(2015)
- 451 -
2012 2013
Streptococcus mitis SM
SMS. pneumoniae
-MGS
MGSSM
CDC-
SMSM
SM
SM
2012 9 SM 1 SMillumina MiSeq Roche 454 GS
FLX Newbler2013 36 SM
4 SM 40 illumina MiSeq
2014 CDCSM 10
2 PacBio
2012 SM SM10 coverage
59.9 152.1 contig 30 68 scaffold2 5Average nucleotide index ANI
SM
SM SMSM
SM
-PBP
SM PBP
-PBP
SM -3 PBP PBP1A PBP2B PBP2X
2013 36 SM
coverage 73.1209.4 scaffold 25 119
MLST4 ddl, gdh,
rpoB, sodAClustalW MEGA
SMSM
S. pseudopneumoniae SPpn
SM
2014 CDCSM 10
20bp bp
10 2PacBio 2
1
SM 3 CDC
CDC pneumolysinmitilysin MLY SM Nm-65
SMSm-hPAF 5CDC ExD-CDC
CDCCDC
CDCSm-hPAF
2SPpn
Sm-hPAFSM
ExD-CDCSm-hPAF
- 452 -
2MLY
scaffold
SMSM
SMCDC
SMCDC
SM CDC
SM CDC
SM
MGSSM
MGSSM
- 453 -
2010
- 454 -
2013
500 1000
10Asian Microbiome Project
(AMP)
AMP Phase I study
16S rRNAB
303Phase I study
36
DNA
Illumina Nextera KitDNA Illumina HiSeq 150 bp
10Gb
hg38Bowtie BMTagger
170 base11.1 8,5 M
Bowtie2 Platanus-UD40 671
bp contig MetaGeneMark55
KEGG Gene Blast70 KEGG
B AMP Phase I
303 16S rRNA
PBB
MtetaHIT
P BB
BB
PBB
P BB
(Yatsunenko et al., Nature 2012)
16S rRNA
, , 29, 135-144
(2015).
- 455 -
2015
21
1000
NIH
Human Microbiome Project(HMP)Metagenomics of Human Intestinal Tract (MetaHIT)
2009
Asian Microbiome Project (AMP)Phase I study
5 10Nakayama et al., 2015. Sci.
Rep 303 16S rRNA
P
BB 2013
30336
BBP
P
BB
2014 P
BB
P
P
P BB
AMP
BB
PP BB
500 1000 100
- 456 -
2012 2013
IgA
- 457 -
2014
IgA
- 458 -
2014
- 459 -
2014 2015
2015
3RNAi
3
- 460 -
2015
B
37
Ultrabithorax Ubx
Ubx RNAi
1
RNA-seq2
RNAi
RNAi
larval RNAi
loss-of-functiongain-of-function
- 461 -
2013~2014
Haplochromis chilotes H. sauvagei 2
QTL
22013 2
GP RNA-seq2
H. chilotes RNA x 4H. sauvagei RNA x 4
Tag Hiseq2000 2
2014
2 L. rufus 6
1GP
H. chilotes H. sauvagei QTL
22 LOD 10MAGP4
7
2013 RNAseqBroad Institute
Pundamilia nyerereiMAGP4 H. chilotes BAC
clones 4 clonesMAGP4
7 MAGP4MAGP4-CD H. chilotes
qPCR MAGP4
Smith-Magenis Syndrome
SMS 1H. chilotes
MAGP4
H. chilotes
MAGP4-CD cis
3 6
MAGP4-CD
MAGP4
QTL
RNAseqcis
Kudo, Y. et al., GENE 560, 156-164 (2015)
Brawand, D. et al., Nature 513, 375-381 (2014)
Nikaido, M. et al., Genome Biol. Evol. 6, 1135-1144
(2014)
- 462 -
2015
ancV1R
5
ancV1R
ancV1R
ancV1R
ancV1R
ancV1R
ancV1R
ancV1R
PCR ancV1R
1 1total RNA Hiseq2500
1 PETRINITY
de novoGP
. V1R
total RNA
ancV1R
OR, V1R, V2R, TAAR
- 463 -
2013
Enteroaggregative Escherichia coli, EAEC HEp-2
biofilm
EAEC PCRAggR aggR
aggR atypical EAECEAEC
EAEC 0422 EAEC
EAEC
aggR
138 atypical EAEC 22aggR 31
Atypical EAEC biofilm assayHEp-2
ESBL blaCTX-M MLSA (multilocus sequence analysis
MiSeq 25blast
MLSA aggRA B1 B2 D 4
1 ST200 (O126:H7 ) ST40 (O111:H21 ) ST3570 (O86a:H27 )
1990
EAEC aggR B2 O25:H4:ST131
20031 EAEC
EAEC pic shET1 aaiC(UPEC)
afaB 2UPEC O25:H4:ST131 EAEC
blaCTX-M-14ESBL
Atypical EAEC A B2 OUT (untypable)
EAECEAEC
aggRaggR EAEC
PCR
EAEC
10
UPEC EAEC ESBL (CTX-M)
EAEC
EAECaggR EAEC
Phylogenetic analysis of EAEC isolated in Kagoshima and Osaka, Japan, revealed emergence of CTX-M-14-producing EAEC O25:H4:ST131. Imuta N. et al (in submission)
- 464 -
2014
Basidiomycota
Saccharomycotina
Pezizomycotina
Ascomycota
TaphrinomycotinaSchizosaccharomyces
GC
Saitoella complicata DNARNA DNA
S. complicataSchizosaccharomyces pombe
S. complicata
enteroblastic
S. complicata DNA
A TSA 1S. complicata
RNATSA 0
S. complicataDNA
S. complicata DNA104 N50, 239 Kbp 14.1 Mbp
SchizosaccharomycesRNA 6933
7119
n = 20524GC 52.4% n = 13591
GC 48.0%
DNA2
S. complicata Sch. pombeS. complicata
Mixia osmundae 2
S. complicataGC 52.6% Sch. pombe 36.0%
M. osmundae 55.5%
TSA 3 TSA
25%154 131
TSA 3 2
S. complicata
S. complicataRNA
DNA
DNA
DNADNA
Yamauchi K et al. (2015) Genome Announcements 3:e00220-15
- 465 -
2010
Sall1
Sall1 (Nishinakamura et al., Development 2001; Osafune et al., Development 2006)
WntSix2
Sall1
Sall1 Six2
Sall1
Six2Sall1 Six2
(ChIP-seq) 16.5 ChIP
DNA
Sall1
Sall1
Sall1
Sall1
ChIP-seq Sall1Six2
(500bp )
Sall1 Six2 (Osr1, Robo2, Eya1 )
Sall1Sall1 Six2
Six2Sall1 Mi2/NuRD
(Nkx6.1 ) Six2 (Wnt4,Fgf8 )
Sall1 Six2
iPS (Taguchi et al., Cell
Stem Cell 2014)
ChIP-seq
ChIP-seq
Kanda, S. et al., J. Am. Soc. Nephrol. 25, 2584-2595 (2014)
- 466 -
2015
(Hynobius retardatus)
RAD
(restriction-site-associated DNA)-seq
RAD-seq
mtDNA
RAD-seq
mtDNA
20100 DNADNA EcoRI, BglII
Hiseq 4
366,238,834
3662388 /sample
RAD-seq
1)
RAD-seq
RAD-seq
)
PCR
- 467 -
2012 2013
2.3Gb
S276 250bp
PE 150(PE150) 5
PE100 2 PE150 S277 ( ) 250bp
PE PE150
S276Scaffold_N50 2Mb
S277
map scaffoldS276
DNA
11,808 scaffold 1.75Gb, N50 2.26Mb 90% 550kb scaffold
RNA-seq
Augustus35883
36877
CEGMA 248
57%complete, 76% partial87.5% complete, 91.9% partial
CEGMA
S277 S276
BamHI
PCR
S276 S277
scaffold
- 468 -
2011
“ ”“OTOKOGI”(PlestMID)
Nozaki et al. 2006, Cur. Biol.
“ ”(Ferris et al. 1997, PNAS 94: 8634-8639)
2011
Gonium pectorale
23Hamaji et al. 2013, PLoS
ONE Hanschen et al.
(Smith and Lee 2010, MBE; Smith et al. 2013, MBE)
mutational-hazard hypothesis (Lynch 2007. The origins of genome architecture. Sinauer Assoc.)
GCS1(HAP2) GpGCS1
GpGCS1 G+C
(Kawai-Toyooka et al. 2014, Eukaryotic Cell)
Hamaji et al.
Ferris et al. 2010, Science
2
GCS1 GpGCS1GpGCS1 cDNA
GC 72% PCR
Hamaji, T. et al., PLoS ONE 8, e57177 (2013) Kawai-Toyooka, H. et al., Eukaryotic Cell 13,
648-656 (2014)
- 469 -
2012 2014
“OTOKOGI”
Nozaki et al. 2006, Curr. Biol.16: R1018
(MT)MT
(Ferris et al. 2010, Science 328: 351) MT
13MT
Charlesworth & Charlesworth 2010, Curr. Biol. 20:R519
MT
2011
YamagishiellaEudorina
Eudorina sp. Yamagishiella unicocca
Eudorina sp. Yamagishiella unicocca
MIDEudorina sp. Yamagishiella
unicocca
FUS1 Eudorina sp. Yamagishiella unicocca
Hamaji et al.
FUS1Ferris et al. 2010,
Science Eudorina sp.
2014
MIDHamaji et al. 2009, J. Phycol.
Ferris et al. 2010 MTD1 Eudorina sp. Yamagishiella unicocca
Yamagishiella unicocca2 Eudorina sp.
Eudorina sp. Yamagishiella unicocca
Eudorina sp.
Eudorina sp. Yamagishiella unicocca
- 470 -
2015
YY
3Y
YY
3
2 Drosophila albomicans D. americana PacBio100
2 Illumina50
PacBio
D. albomicans DNA
PacBio
N50 22Mbp8 9
Illumina
IlluminaPacBio
Illumina
D. americana
DNA 11DNA
12 DNA PacBioD. albomicans
IlluminaDNA PacBio
D. albomicans
PacBio
RNA-seq
Y
- 471 -