Gene-microorganism interaction and microbiome and endogenous retroviruses and genome integrity"

1. Gene-microorganism interaction and microbiome
By Andrea ZamoraSuárez,ID 00391126
Microbiota
Host epigenome and
responses
Composition and
function of gut bacteria
change
During the day
Non-codingRNA
Responseof intestinal
epithelial cellsto
bacteria
Participate in the
Regulate gene
expression by binding
to itstargets3´UTRs
Set of microorganismspresent in a
defined environment
Isthe
Microbiome
Isthe
Entire habitat,including
microorganisms,their genesand
environmental conditions.
Generate signalsthat modify
Isassociated with
active gene
transcription
Iscatalyzed by HAT
M.tuberculosis
downregulared
miR-let-7f in
macrophages
Regulate TLR4 and
MYD88 by decreasing
miR-18aand
miR-4802
miRNA can
Infection altersmiRNA F.nucleatum
Deposition of acetyl groups
Define the
microbiota
Microorganisms
References
1.Jin,B.,Li,Y.,& Robertson,K.D.(2011).DNA methylation: superior or subordinate in the epigenetichierarchy?.Genes& cancer, 2(6),
607?617.https://doi.org/10.1177/1947601910393957
2.Ruthenburg,A.J.,Li,H.,Patel,D.J.,& Allis,C.D.(2007).Multivalent engagement of chromatin modificationsby linked bindingmodules.
Nature reviews.Molecular cell biology,8(12),983?994.https://doi.org/10.1038/nrm2298
3. Zhang,P.,Wu,W.,Chen,Q.,& Chen,M.(2019).Non-Coding RNAsand their Integrated Networks.Journal of integrativebioinformatics,
16(3),20190027.https://doi.org/10.1515/jib-2019-0027
L.reuteri,Bacteroides
acidifaciens,R.gnavus
and M.schaedleri
OTUs affected include
Serotonin,xylose,
cytidine,proline and
biotin
Fluctuations influence
ESAT-6
By secreting
Histone Modification
Acetylation
Iscatalyzed by HDAC
Are responsive to metabolic changes
Deacetylation
Removesacetyl groups
from histone tails
Which
Transfer an acetyl
group from
acetyl-coenzyme A
Which
SCFAs,acetate,
propionate and
butyrate
Generate
Methyl Donors
DNA
Methylation/Demethylation
Signalsthat balance
inflamatory responses
against stress
Bifidobacterium and
Lactobacillus
Folate that supportsthe
generation of SAM
TETdioxygenasa
family can reverse
this through
oxidation of 5hmC
DNATsadd amethyl
group from SAM to
5mC
Methylation
Influence expression
While Regulated by
Folate can be produced by
Generate
M. tuberculosis
inducesDNA
demethylation
Methylation in the
TLR4 gene
Innate immune
system
TLR4 recognizes LPS
Activates
Through the
oxidation of 5mC to
5hmC
Demethylation
Microbes increase Is catalyzed by TET proteins
Bacteria,archaea,
eukaryotesand
viruses
Including
There are asmany as1014 micro-organismslivingsymbiotically with an individual human
in theskin, mouth,gut and other mucosal surfaces.
Resideson the
intestinal mucosal
surfaces
Gut microbiota
Digesting food,
harvesting energy,and
immune development
Plays an integral role in
Short chain fatty acids,
choline metabolitesand
lipids
Can generate
The gut,liver,heart and
CNS
Induces effects in
Obesity,diabetes,
metabolicsyndrome
and colorectal cancer
Dysbiosis is associated with
Dietary supplement,
antibiotictreatment,
infectionsand diurnal
oscillations
Can be affect by
Microbiota and dietary
components
Can change because of
ButyrateisaHDAC
inhibitor
By suppressing NF-kB
and STAT1 activation
Exerts anti-inflammatory activity
SAM,Fe2+/Fe3+ and
?-KG
Is modulated by

2. "Endogenousretrovirusesand
genome integrity"
By AndreaZamoraSuárez,ID 00391126
HERV role in the evolution and
shaping of human genome
Ensemble of TEs
widespread in DNA
Parallel regulatory
network
Constituting a sort of
Multiple host genesand
shape pathways
involved in cellular
processes
Transcription factor bindingsites
and regulatory signals
Are important for
HERVsasActivatorsof Antiviral Innate
Immunity
Is the first line of defense
Thepresence of PAMPsallowsPRRsand
DAMPs
Defense systemsto
downregulate
Developed strategiesto
control geneexpression
Have been dispersed
by class1 HERV
sequences
Influence human
genome plasticity and
cellular networking
Influence
One third of p53 HERV insertions And
Activation of PRRson
APCs
PRRs
References
1. Grandi,N.,& Tramontano,E.(2018).Human EndogenousRetrovirusesAre Ancient Acquired ElementsStill ShapingInnate
Immune Responses.Frontiersin immunology,9,2039.https://doi.org/10.3389/fimmu.2018.02039
2.Ruthenburg,A.J.,Li,H.,Patel,D.J.,& Allis,C.D.(2007).Multivalent engagement of chromatin modificationsby linked binding
modules.Nature reviews.Molecular cell biology,8(12),983?994.https://doi.org/10.1038/nrm2298
A adaptation of the
harboning organism
Involves
Syncytins
For example
An ensembleof Env
proteinsencodend
that are
The production of
codingor non-coding
RNA transcripts
HERV sequences leads to
Syncytin 2 isinvolved in
maternal immune
tolerance to the fetus
ERVWE1 and ERVWE2
Silencing of TEs
Evolution of the
primates genome
Represent
HERV derived ncRNAs
Provide cis-regulatory
elements
Disruption or insertion
of genesor homologous
recombination
Genomic
modificationsand
insertions
Regulatehost genes
activity
Prodiding regulatory
elements
By
That are able to
Is found in Can be produced through
HERV derived ncRNAs
Hasaimportant
role in the
development and
plasticity of NS
Post-transcriptional
regulation of gene
expression
RNA spongesbinding
and dampening
microRNA families
Can act as
Involved in
1.HERV DNA
2.HERV ncRNAs
3.HERV proteins
HERV levels
For example Arc Gag-like
tm and cytPRRs
Include five classes of receptors
Are represented
by TLRsthat
detecsPAMPs
tmPRRs
IncludesRLRs,
NLRs and CLRs
cytPRRs
Long-lasting adaptive
immunity
Evokes the development of
Production of
antibodiesby B
lymphocytes
Expansion of naive
cytotoxicT cells
Onset of specific
cellular and humoral
defenses
Leading to
And can
Macrophagesand B
lymphocytes
Improves
T-cells
Activates
HERVsare highly
transcribed during
embryonicdevelopment and
expressed at variable levels
in several adult tissues.
HERVsare DNA sequencesof retroviral origen
Multiple integrationsby now-extinct exogenous
retroviruses(germ linecells)
Have been acquired through
Two LTRs that flank the internal portion of gag, pro-pol, env
Structure composed of
Class1:
Gammaretrovirus
like
Class2:
Betaretrovirus
like
Class 3:
Spumaretrovirus
like
HERVs are dividen into classes
PBSand PPT are located between 5´LTRand gag
Development of
immune systems,for
example,MHCloci
PRRstimulation by PAMPsactivatesa
cascade of signaling of proinflammatory
molecules: IFN-1,cytokines