The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation
The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate their differences, we performed strand-specific, massively-parallel sequencing of RNA from C. albicans white and opaque cells. With these data we first annotated the C. albicans transcriptome, finding hundreds of novel differentially-expressed transcripts. Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by a master regulator of the white-opaque switch (Wor1). We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation. In particular, we can now resolve the poor concordance between binding of a master regulator and the differential expression of adjacent genes, a discrepancy observed in several other studies of cell differentiation. More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome. Many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts. We also find that 5′ and 3′ UTRs of mRNAs in the circuit are unusually long and that 5′ UTRs often differ in length between cell-types, suggesting UTRs encode important regulatory information and that use of alternative promoters is widespread. Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells. Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of heritable differentiation states in eukaryotes.
Vyšlo v časopise:
The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation. PLoS Genet 6(8): e32767. doi:10.1371/journal.pgen.1001070
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1001070
Souhrn
The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate their differences, we performed strand-specific, massively-parallel sequencing of RNA from C. albicans white and opaque cells. With these data we first annotated the C. albicans transcriptome, finding hundreds of novel differentially-expressed transcripts. Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by a master regulator of the white-opaque switch (Wor1). We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation. In particular, we can now resolve the poor concordance between binding of a master regulator and the differential expression of adjacent genes, a discrepancy observed in several other studies of cell differentiation. More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome. Many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts. We also find that 5′ and 3′ UTRs of mRNAs in the circuit are unusually long and that 5′ UTRs often differ in length between cell-types, suggesting UTRs encode important regulatory information and that use of alternative promoters is widespread. Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells. Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of heritable differentiation states in eukaryotes.
Zdroje
1. JaenischR
YoungR
2008 Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132 567 582
2. TakahashiK
TanabeK
OhnukiM
NaritaM
IchisakaT
2007 Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131 861 872
3. ReikW
2007 Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447 425 432
4. DaleyGQ
ScaddenDT
2008 Prospects for stem cell-based therapy. Cell 132 544 548
5. SlutskyB
StaebellM
AndersonJ
RisenL
PfallerM
1987 “White-opaque transition”: a second high-frequency switching system in Candida albicans. J Bacteriol 169 189 197
6. MillerMG
JohnsonAD
2002 White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating. Cell 110 293 302
7. KvaalCA
SrikanthaT
SollDR
1997 Misexpression of the white-phase-specific gene WH11 in the opaque phase of Candida albicans affects switching and virulence. Infect Immun 65 4468 4475
8. LachkeSA
LockhartSR
DanielsKJ
SollDR
2003 Skin facilitates Candida albicans mating. Infect Immun 71 4970 4976
9. HuangG
YiS
SahniN
DanielsKJ
SrikanthaT
2010 N-acetylglucosamine induces white to opaque switching, a mating prerequisite in Candida albicans. PLoS Pathog 6 e1000806 doi:10.1371/journal.ppat.1000806
10. HuangG
SrikanthaT
SahniN
YiS
SollDR
2009 CO(2) regulates white-to-opaque switching in Candida albicans. Curr Biol 19 330 334
11. Ramirez-ZavalaB
ReussO
ParkYN
OhlsenK
MorschhauserJ
2008 Environmental induction of white-opaque switching in Candida albicans. PLoS Pathog 4 e1000089 doi:10.1371/journal.ppat.1000089
12. ZordanRE
GalgoczyDJ
JohnsonAD
2006 Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc Natl Acad Sci U S A 103 12807 12812
13. ZordanRE
MillerMG
GalgoczyDJ
TuchBB
JohnsonAD
2007 Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Biol 5 e256 doi:10.1371/journal.pbio.0050256
14. HuangG
WangH
ChouS
NieX
ChenJ
2006 Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc Natl Acad Sci U S A 103 12813 12818
15. SrikanthaT
BornemanAR
DanielsKJ
PujolC
WuW
2006 TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell 5 1674 1687
16. HniszD
SchwarzmullerT
KuchlerK
2009 Transcriptional loops meet chromatin: a dual-layer network controls white-opaque switching in Candida albicans. Mol Microbiol 74 1 15
17. LohseMB
JohnsonAD
2009 White-opaque switching in Candida albicans. Curr Opin Microbiol 12 650 654
18. SollDR
2009 Why does Candida albicans switch? FEMS Yeast Res 9 973 989
19. SonnebornA
TebarthB
ErnstJF
1999 Control of white-opaque phenotypic switching in Candida albicans by the Efg1p morphogenetic regulator. Infect Immun 67 4655 4660
20. LanCY
NewportG
MurilloLA
JonesT
SchererS
2002 Metabolic specialization associated with phenotypic switching in Candidaalbicans. Proc Natl Acad Sci U S A 99 14907 14912
21. TsongAE
MillerMG
RaisnerRM
JohnsonAD
2003 Evolution of a combinatorial transcriptional circuit: a case study in yeasts. Cell 115 389 399
22. StruhlK
2007 Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14 103 105
23. GeorletteD
AhnS
MacAlpineDM
CheungE
LewisPW
2007 Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. Genes Dev 21 2880 2896
24. LiXY
MacArthurS
BourgonR
NixD
PollardDA
2008 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6 e27 doi:10.1371/journal.pbio.0060027
25. ChenX
VegaVB
NgHH
2008 Transcriptional regulatory networks in embryonic stem cells. Cold Spring Harb Symp Quant Biol 73 203 209
26. MacArthurS
LiXY
LiJ
BrownJB
ChuHC
2009 Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10 R80
27. XuZ
WeiW
GagneurJ
PerocchiF
Clauder-MunsterS
2009 Bidirectional promoters generate pervasive transcription in yeast. Nature 457 1033 1037
28. NeilH
MalabatC
d'Aubenton-CarafaY
XuZ
SteinmetzLM
2009 Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457 1038 1042
29. LohYH
WuQ
ChewJL
VegaVB
ZhangW
2006 The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38 431 440
30. ChenX
XuH
YuanP
FangF
HussM
2008 Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133 1106 1117
31. MarsonA
LevineSS
ColeMF
FramptonGM
BrambrinkT
2008 Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134 521 533
32. TuchBB
LabordeRR
XuX
GuJ
ChungCB
2010 Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PLoS One 5 e9317 doi:10.1371/journal.pone.0009317
33. MitrovichQM
TuchBB
De La VegaFM
GuthrieC
JohnsonAD
2010 Evolution of yeast non-coding RNAs suggests a novel mechanism for widespread intron loss. In Preparation
34. YassourM
KaplanT
FraserHB
LevinJZ
PfiffnerJ
2009 Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A 106 3264 3269
35. DavidL
HuberW
GranovskaiaM
ToedlingJ
PalmCJ
2006 A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103 5320 5325
36. HeY
VogelsteinB
VelculescuVE
PapadopoulosN
KinzlerKW
2008 The antisense transcriptomes of human cells. Science 322 1855 1857
37. MarioniJC
MasonCE
ManeSM
StephensM
GiladY
2008 RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18 1509 1517
38. NagalakshmiU
WangZ
WaernK
ShouC
RahaD
2008 The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320 1344 1349
39. MortazaviA
WilliamsBA
McCueK
SchaefferL
WoldB
2008 Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5 621 628
40. YiS
SahniN
DanielsKJ
PujolC
SrikanthaT
2008 The same receptor, G protein, and mitogen-activated protein kinase pathway activate different downstream regulators in the alternative white and opaque pheromone responses of Candida albicans. Mol Biol Cell 19 957 970
41. DignardD
AndreD
WhitewayM
2008 Heterotrimeric G-protein subunit function in Candida albicans: both the alpha and beta subunits of the pheromone response G protein are required for mating. Eukaryot Cell 7 1591 1599
42. PuigS
Perez-OrtinJE
MatallanaE
1999 Transcriptional and structural study of a region of two convergent overlapping yeast genes. Curr Microbiol 39 369 0373
43. PrescottEM
ProudfootNJ
2002 Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci U S A 99 8796 8801
44. ShearwinKE
CallenBP
EganJB
2005 Transcriptional interference—a crash course. Trends Genet 21 339 345
45. HongayCF
GrisafiPL
GalitskiT
FinkGR
2006 Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127 735 745
46. PujolC
DanielsKJ
LockhartSR
SrikanthaT
RadkeJB
2004 The closely related species Candida albicans and Candida dubliniensis can mate. Eukaryot Cell 3 1015 1027
47. ColeC
BarberJD
BartonGJ
2008 The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36 W197 201
48. ZhangY
2009 I-TASSER: fully automated protein structure prediction in CASP8. Proteins 77 Suppl 9 100 113
49. SrikanthaT
TsaiLK
DanielsK
SollDR
2000 EFG1 null mutants of Candida albicans switch but cannot express the complete phenotype of white-phase budding cells. J Bacteriol 182 1580 1591
50. KashyapV
RezendeNC
ScotlandKB
ShafferSM
PerssonJL
2009 Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev 18 1093 1108
51. NicholsJ
ZevnikB
AnastassiadisK
NiwaH
Klewe-NebeniusD
1998 Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95 379 391
52. TakahashiK
YamanakaS
2006 Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126 663 676
53. WangZ
GersteinM
SnyderM
2009 RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10 57 63
54. DrinnenbergIA
WeinbergDE
XieKT
MowerJP
WolfeKH
2009 RNAi in budding yeast. Science 326 544 550
55. BoyerLA
LeeTI
ColeMF
JohnstoneSE
LevineSS
2005 Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 947 956
56. FraserP
BickmoreW
2007 Nuclear organization of the genome and the potential for gene regulation. Nature 447 413 417
57. LanctotC
CheutinT
CremerM
CavalliG
CremerT
2007 Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8 104 115
58. MitrovichQM
TuchBB
GuthrieC
JohnsonAD
2007 Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res 17 492 502
59. MageeBB
MageePT
2000 Induction of mating in Candida albicans by construction of MTLa and MTLalpha strains. Science 289 310 313
60. ShermanF
2002 Getting started with yeast. Methods Enzymol 350 3 41
61. HerndayAD
NobleSM
MitrovichQM
JohnsonAD
2010 Genetics and Molecular Biology in Candida albicans. Methods in Enzymology Elsevier Inc 737 758
62. van het HoogM
RastTJ
MartchenkoM
GrindleS
DignardD
2007 Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 8 R52
63. JonesT
FederspielNA
ChibanaH
DunganJ
KalmanS
2004 The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A 101 7329 7334
64. TangF
BarbacioruC
WangY
NordmanE
LeeC
2009 mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6 377 382
65. SkrzypekMS
ArnaudMB
CostanzoMC
InglisDO
ShahP
New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Nucleic Acids Res 38 D428 432
66. PepkeS
WoldB
MortazaviA
2009 Computation for ChIP-seq and RNA-seq studies. Nat Methods 6 S22 32
67. SmythGK
2004 Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3 Article3
68. HomannOR
JohnsonAD
2010 MochiView: versatile software for genome browsing and DNA motif analysis BMC Biology.
69. RheadB
KarolchikD
KuhnRM
HinrichsAS
ZweigAS
2010 The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38 D613 619
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2010 Číslo 8
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development
- Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits
- A Model for Damage Load and Its Implications for the Evolution of Bacterial Aging
- Did Genetic Drift Drive Increases in Genome Complexity?