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Organización y Regulación del genoma de plantas Paris japonica
Amborella trichopoda
Picea abies
Arabidopsis thaliana
Zea mays
Blog: hKp://www.traduccionbm.wordpress.com Dra. Tzvetanka D. Dinkova Depto. Bioquímica, Facultad de Química Conjunto E, Lab. 103 [email protected]; [email protected] Es7mación del tamaño de genomas mamíferos plantas hongos bacterias mitocondriales virus 1e1
1e2 1e3
Tamaño en nucleóPdos. 1e4
1e5
1e6
1e7 1e8
1e9 1e10 1e11 1e12
Tamaño del genoma nuclear de algunas plantas (Mbp) Paris japonica
Picea abies
150,000 20,000 Genoma nuclear en plantas Se localiza en cromosomas
Baja densidad de genes
27,206 genes para proteínas en Arabidopsis
Secuencias repetidas
Número de cromosomas variable (algunas especies
tienen más de 200)
•  Frecuentes Aneuploidías y Poliploidías
(Angiospermas)
• 
• 
• 
• 
• 
Organización del genoma nuclear Telómero
Centrómero
Telómero
Centrómero:
•  Secuencia de DNA que recluta a proteínas del cinetocoro y a los microtúbulos
durante la mitosis.
•  Secuencias y extensión variable entre especies
•  Contiene repetidas, en tandem o aisladas, retrotransposones, DNA satélite
•  En plantas, esta región se puede transcribir por la presencia de
retrotransposones
Telomeros:
•  Extremos del cromosoma; estabilización
•  Extensión 2 – 75 kb (heptanucleótido repetido)
•  Telomerasa ausente en tejidos vegetativos, se expresa en meristemos,
floración y en cultivo de tejidos in vitro
Cromosomas Short arm
Organ
Long arm
Chromatid
Chromatid
Telomere
NOR
secondary
constriction
Chromosome regions:
Centromere
primary
constriction
Pericentric
(pericentromeric)
paracentric
(paracentromeric)
Telomere
Intercalary
interstitial
Subtelomeric
terminal
Cambios cromosómicos Relocalización de material genéPco Pérdida de material genéPco Ganancia de material genéPco Evolution of the A. thaliana (n = 5) karyotype based on comparative
chromosome painting in A. lyrata (n = 8).
Martin A. Lysak et al. PNAS 2006;103:5224-5229
Alteraciones numéricas cromosomales Fenotipos en plantas de maíz
con trisomía en el brazo corto
del cromosoma 5
Makarevitch et al., 2008
Autopoliploidía Alopoliploidía Duplicaciones en la evolución de plantas Plant Genome Duplica0on Database Diploid: 2!7
Diploid: 2!7
Triticum monococcum (2n =14)
AA
Triticum searsii (2n =14)
BB
Generación del trigo
hexaploide moderno
Sterile hybrid (1n =14)
AB
Chromosome doubling
Tetraploid: 4!7
Triticum turgidum (2n =28)
AABB
Diploid: 2!7
Triticum tauschii (2n =14)
CC
Sterile hybrid(1n =21)
ABC
Chromosome doubling
Hexaploid: 6!7
Triticum aestivum (2n =42)
AABBCC
Plant Genomics
Vigor de genomas híbridos Genoma mitocondrial en plantas Cromosomas circulares
Genomas multipartitas
Tamaño 200 a 2,500 kb
Codifica rRNA, tRNA, proteínas cadena
respiratoria.
•  La mayor parte de proteínas mitocondriales
codificada en núcleo.
•  Flujo de DNA entre Mt, Cp y Nu
•  Muchos ORFs de función desconocida
• 
• 
• 
• 
Transferencia de secuencias entre los genomas celulares Tamaños de genoma mitocondrial en plantas trends in plant science
Clasificación de secuencias en el genoma reviews
mitocondrial Other
repeats
Intron
sequences 3.9%
8.8%
Plastid
origin
1.2%
Nuclear nuc — mt Recombinative
origin homologies repeats
2.2%
2.9%
4.0%
Protein coding
genes
16.1%
rRNAs
1.3%
orfs >100 aa
tRNAs 10.2%
0.4%
49% unaccounted for
Trends in Plant Science
Fig. 1. Genome sequences in Arabidopsis. To date, half of the mitochondrial genome sequences in
Arabidopsis are accounted for. Some of the nuclear–mitochondrial homologies are probably sequence
transfers from the mitochondrial genome to the nucleus. Duplications of sequences listed in two categories of repeats might cover parts of genes or total genes. Intron sequences exclusively belonging to
ge
to
an
fro
of
Co
tra
re
th
its
pl
tra
as
m
in
In
ge
th
m
ge
du
Dramá7ca expansión del genoma mitocondrial en el género Silene Enormous Fast-Evolving Plant Mitochondrial Genomes
Figure 8. Silene mitochondrial genome sizes relative to all sequenced mitochondrial and eubacterial genomes from the National
Center for Biotechnology Information (NCBI) Genome database.
doi:10.1371/journal.pbio.1001241.g008
do not include chromosomes in S. noctiflora and S. conica that only
contain partial gene fragments that require trans-splicing with
transcripts originating from other chromosomes to generate
Sloan et athe
l., 2functional
012 PloS Biology complete coding sequences).
Therefore,
significance
(if any) of these ‘‘empty’’ chromosomes and the evolutionary forces
that maintain their presence and abundance within the mito-
efficacy of selection against the proliferation of noncoding
elements even if the intensity of that selection has increased with
higher mutation rates. There is some evidence to support this
possibility, particularly in S. noctiflora, which appears to have a very
low Ne based on the striking lack of polymorphism in genes from
all three genomes (Table S3) [49]. However, the finding of high
Genoma de cloroplasto Múltiples moléculas circulares
Tamaño 120 – 160 kb
Similar al DNA mitocondrial
Codifica rRNA, proteínas involucradas en
transcripción/traducción, fotosíntesis y
transporte de electrones
•  Intrones, repetidas invertidas
•  Asociación con proteínas remodeladoras
• 
• 
• 
• 
Organización del genoma de cloroplasto wikrowska et al.
Plastid nucleoids
•  El DNA se asocia con la membrana
•  Aumenta el número de nucleoides durante
el desarrollo y se unen proteínas que
ayudan a compactar el DNA
•  Papel de las proteínas asociadas en
replicación, transcripción y reparación
Powikrowska et al.
Plastid nucleoids
FIGURE 1 | Visualization of plastid nucleoids by using different
chloroplasts. (C) Specimen prepared by high pressure freezing and freeze
microscopic techniques. (A) Nucleoids visualized by fluorescence
substitution (HPF-FS). (D) Immunogold labeling of nucleoids in leaf sections
microscopy of SYBR Green in leaf sections, bar: 10 µm. (B) Conventional
obtained from specimen prepared by high pressure freezing and freeze
Powikrowska et al., 2014 Fron0ers in Plant Science electron micrographs showing nucleoids with DNA filaments in mesophyll
substitution (HPF-FS) using a DNA specific antibody, bar: 500 nm.
possess thylakoids but lack grana stacks and are devoid
photosynthetic complexes resulting in compromised
thesis (Luo et al., 2013). Taken together, these studies
state of the photosynthetic apparatus (Pfannschmidt et
Thereby the composition of the photosynthetic appa
continuously be adjusted to the ever changing envir
3 | Nucleoid organization during chloroplast development.
besides
a green
containing
chloroplasts.
Chloroplasts wer
Powikrowska et apart
l., 2014 Fron0ers in Plant Science Reestructuración del genoma del cloroplasto Clasificación de genes Genes que codifican
proteínas
RNA mensajero
Genes nocodificantes
RNA estructural y otro
Proteínas
Proteínas
estructurales
Región
intergénica
RNA de
transferencia
Enzimas
RNA
ribosomal
Otro
RNA
Genes duplicados •  Codifican proteínas relacionadas •  Familias mulPgénicas frecuentes en plantas •  Neo-­‐ o sub-­‐funcionalización, silenciamiento Pseudogenes •  Son copias no funcionales de genes •  No se expresan por mutaciones sin senPdo, falta de secuencias reguladoras o problemas en procesamiento de RNA DNA repe77vo •  Secuencias moderadamente repePdas –  Función conocida (proteínas, tRNA, rRNA) –  Función desconocida •  SINEs (short interspersed elements) –  200-­‐300 bp –  100,000 copias •  LINEs (long interspersed elements) –  1-­‐5 kb –  10-­‐10,000 copias •  Secuencias altamente repePdas –  Transposones –  Pericentroméricas y Centroméricas –  Telómeros ant
Organización de secuencias repe7das Simple tandem array
Transposable
element
h-
antities of
heir needs
function.
ll percentlly encode
uction of
e genome
ranscribed
low-copyDNA segenes are
umbers of
on with so
into the
st of these
noncoding
Repeat/single-copy interspersion
Single-copy gene
Inverted repeats
Compound tandem array
Repeat/repeat interspersion
(a) Different arrangements of repeated and
inverted DNA sequences
(b) Transposable element excision and
reinsertion
FIGURE 43.4
Organization of repeated DNA sequences and the mechanism of transposable
criteria,
equire a
can be
at the
oteins
ack the
plicative
Type I — Retrotransposons
LTR
Non-LTR
LTR
gag
pol
5′ UTR
orf1
orf2
LTR
Transposones (TE) AAAAAAA
,
step to
sposase
out of
te. The
nt
on by
ently,
Type II — DNA transposons
Autonomous
TIR
Transposase
TIR
Non-autonomous
Mutation derivative
Transposase
TIR
TIR
Barbara Mc Clintock, 1951
A-
ers, but
ts. Nonnsposon
nally,
n.
e
he Alu
on-LTR
TIRs conserved
TIR
MITE
TIR
TIR
TIR
Autonomous helitron
Replicase
Helicase
Slotkin & Mar7enssen, 2007 Contribución de los TE al tamaño de los genomas s: Biology and Evolution
27
.
),
a
28
E. Kejnovsky et al.
a Relative contribution of main groups of TEs to genome coverge in various plants (species arrayed according to genome size)
Arabidopsis thaliana
Fragaria vesca
Cucumis sativus
Oryza sativa
Lotus japonicus
Populus trichocarpa
Vitis vinifera
Brassica oleracea
)
omes, while copia-like elements
n species with smaller genomes
timescales (Bennetzen 2005). One of the best-known
examples in plants comes from maize, where repeated bursts
of retrotransposon amplification over the past 6 million years
g closely related species or even have been responsible for generating approximately half of
mily may also differ substantially, the modern maize genome (SanMiguel et al.
1998; Walbot
Sorghum
bicolor
Glycine max
Zea mays
Gossypium raimondii
e is often a direct reflection of a and Petrov 2001). Similarly, a three-fold increase in the
TE families that have undergone genome size of diploid members of Gossypium is due to the
n are usually absent among closely accumulation of LTR retrotransposons over the past
es that have undergone amplifica- 5–10 Myr (Hawkins et al. 2006). In Oryza australiensis,
ints can be shared among closely three LTR retrotransposon families proliferated during the
duct of their shared evolutionary last 3 million years leading to a two-fold increase in genome
e former was demonstrated via size compared to that of Oryza sativa (Piegu et al. 2006). The
Kejnowski t al., 2012 higher copy number of TEs in Arabidopsis
among wheat and barley,
where etwoto threefold
undant in one species were virtu- lyrata compared to A. thaliana correlate and may be attributed
Relative coby numbers of main groups of TEs in various plant genomes (species arrayed according to genome size)
b
tive (Wicker et al. 2009). The rate to the higher expression of TEs in A. lyrata, apparently caused
Arabidopsis
Cucumis sativus
Oryza sativa
Fragaria vesca
ar (through either vertical or hori- by less efficient TE silencing in this species (Hollisterthaliana
et al.
LTR
non-LTR
DNA TE
Helitrons
Ac7vidad de Transposones Retrotransposones
Transposones de ADN
Los transposones pueden causar reordenamientos y cambios en los genomas Dinámica de los genomas
Transposones Transferencia de DNA
Duplicación de DNA
Los Virus
Evolución de genomas
Regulación Epigenética
EUCROMATINA • 
• 
• 
• 
• 
Poco condensada Distribuida a lo largo del cromosoma Rica en genes Rápida replicación Recombinación en Meiosis HETEROCROMATINA • 
• 
• 
• 
• 
• 
Altamente condensada Centrómeros y telómeros Rica en secuencias repePdas Pobre en genes Se replica tardíamente No sufre recombinación meióPca Epigenética: cambios reversibles y heredables
en la expresión genética que no implican
cambios en la secuencia de DNA!
!
Herencia Epigenética: transferencia de
información diferente a la secuencia de DNA
desde una célula progenitora a células hijas!
!
Información Epigenética: se almacena como
metilación de DNA y marcas de histonas. !
!
!
Relevancia de algunas modificaciones de H3
La tri-metilación de K9 y K27 son marcas de silenciamiento asociadas a metilación del DNA
La tri-metilación de K4 es una marca asociada a genes transcripcionalmente activos
La metilación de K36 parece tener rol represivo o de activación dependiendo del contexto
nloaded from www.annualreviews.org
9/23/11. For personal use only.
ANRV410-PP61-17
ARI
4 May 2010
15:12
Función de las marcas de Histonas
Lys9 Impresión
(K9), Lys27 (K27),
Lys36 (K36) of
de la and
marca:
histone
These
modifications
written (específicas)
-  H3.
Metil
transferasas
de are
Histonas
by different
histone lysine
methyltransferases
-  Acetlilasas
de Histonas
Writer: an enz
(HKMTs)
(Table 1). In contrast to mammals that is responsib
-  Otros
and yeast, in which Lys20 (K20) of histone adding a
Writer
Eraser
Reversible H4 (H4K20) is methylated, H4K20 is acety- posttranslationa
lated in Arabidopsis, though mono-methylated modification(s)
given protein (e
H4K20 (H4K20me1) has been reported to be
HKMT)
detected by immunostaining (94). Another difReader: a prot
ference is the lack of an Arabidopsis homolog
protein comple
of DOT1, an H3 lysine 79 (H3K79) methyl- recognizes and
transferase required for telomeric silencing in specifically to a
mammals and yeast; nor is any H3K79 methy- particular
lationLectura
detected de
(147).
addition, Arabidopsis posttranslationa
la In
marca:
modified substr
and rice were shown to have much higher lev-  Remodeladores de cromatina
els of H3K4 di-methylation (H3K4me2) than Eraser: an enz
-  Factores de transcripción
that removes a
mouse and human, and Arabidopsis has much
posttranslationa
-  Metilasas de DNA
lower H3K9me2 and H3K9me3 levels (42, 47). modification(s)
Reader
These results indicate that global histone mod- given protein (e
ification levels and patterns in Arabidopsis and HDM)
Figure 1
rice are quite different from those in mam- HKMT: histon
Schematic representation of the processes of
mals, possibly reflecting differences in genome lysine
writing, reading, and erasing the histone
Liu et amethyltransfera
l., 2010 composition.
posttranslational modifications. Writer enzymes add
Control epigenético de floración
FLC – represor floral
Tritorax
Polycomb
Metilación del DNA
Metilación*DNA
A.#thaliana
Simétrica*/*
de*mantenimiento
% Aproximado de TEs en Genomas de
plantas
Asimétrica*/*
de#novo
90
80
CHG
70
CHH
60
% CG
24.0*%
**6.7*%
1.7*%
MET1
CMT3
DRM2
RdDM
Law & Jacobsen, 2010
50
40
30
20
10
0
Arabidopsis
thaliana
Oriza sativa
Lockton & Gaut, 2009
Zea mays
s (DCL2 and
d into ARGOArabidopsis),
se complexes
ever, compelalso be loaded
AGO proteins
ues) [26–28],
nuclear tranads to methycontexts by
ases through
e methylated
nscription, or
en transcripshut off [31].
hylation and
RNA-directed
Metilación del DNA dependiente de RNA
Trends in Plant Science May 2014, Vol. 19, No. 5
Inicio
(A)
AGO1/AGO2
AGO
AAAAAA
DCL2/DCL4
RDR6
AAAAAA
DCL
21/22 nt
DCL3
DCL
Cytosol
Nucleus
24 nt
DRM1/DRM2
AGO4/AGO6
DRM
TSS
Pol II
AGO
AAAAAA
AGO
AGO
n and
ected
nerand the
AGO
s own
oblem
RNA
ction,
s [32]
ted to
close
h are
se are
nsposcriposons
th 218], as
9–41].
AAAAAA
Metilación del DNA dependiente de RNA
Mantenimiento
(B)
Nucleus
DCL3
RDR2
24 nt
AGO4/AGO6
VIM1-MET1
TSS
Pol IV
SHH1
CG
DRM1/DRM2
CG
Non-CG
Non-CG
H3K9me2
AGO
DRM
Pol V
AGO
KYP-CMT3/CMT2
(C)
Kim & Zilberman, 2014
Nucleus
hich are
hese are
transporanscripnsposons
with 21[28], as
[39–41].
is likely
t exhibit
hermore,
stranded
ssed by
RNA can
dicating
egrated.
e desired
by Pol IV
ng DNA
ces with
ANT IN
tebrates)
SHH1
AGO
Metilación del DNA dependiente de RNA
Non-CG
H3K9me2
KYP-CMT3/CMT2
Reforzamiento
(C)
DDM1
VIM1-MET1
VIM
Nucleus
KYP-CMT3/CMT2
KYP
Non-CG
MET1
CG
H3K9me2
CMT
TSS
H1 H1 H1
H1
H1
H1
H1
H1
TRENDS in Plant Science
Figure 1. Progression of transposon DNA methylation and silencing from Pol IIand RDR6- mediated RdDM (A) to self-reinforcing Pol IV- and Pol V-mediated
Paisaje epigenético de A. thaliana
The epigenetic landscape of A. thaliana
The epigenetic landscape of A. thaliana
The relative abundance of genes, repeats, cytosine methylation and siRNAs is
shown for the length of A. thaliana chromosome 1, which is ~30 Mb long.
The relative abundance of genes, repeats, cytosine methylation and siRNAs is
Bottom right: diagram of chromosome, with white bars indicating euchromatic
shown for the length of A. thaliana chromosome 1, which is ~30 Mb long.
arms, grey bars indicating pericentromeric heterochromatin and the black bar
Bottom right: diagram of chromosome, with white bars indicating euchromatic
indicating the centromeric core.
arms, grey bars indicating pericentromeric heterochromatin and the black bar
Henderson & Jacobson, Nature 447, 418 (2007)
indicating the centromeric core.
Distribución de actividad transcripcional
Distribution
patterns
and
transcription
activity
Distribution
patterns
and
transcription
activity
detailed distribution
detailed distribution
patterns and
patterns and
transcription activity
transcription activity
(vertical blue bars) in a
(vertical
blue
bars)
inenes a
a) R
egión r
ica e
n g
gene-rich region (top)
gene-rich region (top)
and a repeat-rich region
and a repeat-rich region
(bottom).
(bottom).
Red boxes: genes;
Red boxes: genes;
Arrows indicate the
Arrows indicate the
direction of transcription.
direction of transcription.
b) Región rica en repe7das Zhang, Science 320, 489 (2008)
Zhang, Science 320, 489 (2008)
Reprogramación epigenética en reproducción
REVIEWS
A
Ba Male gametophyte
Tricellular
pollen grain
St
Ov
SCs
(Silenced
transposons)
?
21-nt
siRNAs
VN
(Reactivated
transposons)
C
?
Double
fertilization
Bb Female gametophyte
AC AC AC
Endosperm
(Hypomethylated)
Embryo
(Hypermethylated)
2n
CCN
(Demethylation)
Transposon
reactivation?
siRNAs?
?
Reinforced silencing?
Syn
EC
Syn
Nature Reviews | Genetics
Law & Jacobsen, 2010