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Widespread RNA and DNA Sequence Differences in
the Human Transcriptome
Inamul Hasan.Madar
Gaseous Ion Laboratory,
Korea University, Korea
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http://www.nature.com/news/2011/110525/full/473432a/box/1.html
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1000 Genome Project
First project to sequence the genomes of a large number of people based on human genetic variation.
GOAL
The 1000 Genomes Project is to provide a resource ofalmost all variants, including SNPs ,structural
variants, and their haplotype contexts. This resource focus on almost all variants that exist in regions
found to be associated with disease. The genomes of over 1000 unidentified individuals from around the
world will be sequenced using next generation sequencing technologies. The results of the study was
publicly accessible to researchers worldwide.
Strategy
1)Whole-genome sequencing of 180 samples,
2) Whole-genome sequencing of 2 mother-father-adult child trios,
3)1000 gene regions in 900 samples
http://www.1000genomes.org/about
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International HapMap Project
Catalog of common genetic variants that occur in human beings.
What these variants are, where they occur in our DNA, and how they are distributed among people within
populations and among populations in different parts of the world.
Sequences will differ once in every 1,200 bases (Figure ). One person might have an A at that location,
while another person has a G, or a person might have extra bases at a given location or a missing segment
of DNA.
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B cell
B cells are lymphocytes that play a large role in the humoral immune
response .
Functions ofB cells are to make antibodies against antigens,
perform the role ofantigen-presenting cells (APCs) and eventually develop
into memory B cells after activation by antigen interaction.
B cells are an essential component of the adaptive immune system.
"B", in B cell, comes from the bursa of Fabricius in birds, where they
mature.
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ADAR- Adenosine Deaminase,
RNA-specific Double-stranded RNA-specific adenosine deaminase is an enzyme that in humans is encoded by the
ADAR gene.
RNA editing by site-specific deamination of adenosines. This enzyme destabilizes double stranded RNA
through conversion ofadenosine to inosine.
Mutations in this gene have been associated with dyschromatosis symmetrica hereditaria. Alternate
transcriptional splice variants, encoding different isoforms, have been characterized
A-to-I editing, arising from the fact that I behaves as if it is G both in translation and when forming
secondary structures. These effects include alteration of coding capacity, altered miRNA or siRNA target
populations, heterochromatin formation, nuclear sequestration, cytoplasmic sequestration,
endonucleolytic cleavage by Tudor-SN, inhibition of miRNA and siRNA processing , and altered splicing.
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APOBEC-1-C->U-editing enzyme
APOBEC1 apolipoprotein B mRNA editing
enzyme, catalytic polypeptide 1.Which is
cytidine deaminase enzyme
This holoenzyme is involved in the editing of
C-to-U nucleotide bases in apolipoprotein B
and neurofibromatosis-1 mRNAs
http://www.ncbi.nlm.nih.gov/gene/339
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RNA Editing
RNA editing is a post-transcriptional modification of RNA and markedlyincreases the complexity of the transcriptome. RNA editing occurs in thenucleus, as well as in mitochondria and plastids. To date such changeshave been observed in prokaryotes, plants, animals and virus. Thediversity of this widespread phenomenon includes nucleosidemodifications, nucleotide additions and insertions, either in coding ornon-coding sequences of RNA, which can occur concomitantly withtranscription and splicing processes.
Most of the RNA-editing processes, however, appear to be evolutionarilyrecent acquisitions that arose independently. The diversity of RNA editingmechanisms includes nucleoside modifications such as cytidine (C) touridine (U) and adenosine (A) to inosine (I) deaminations, as well as non-
templated nucleotide additions and insertions. RNA editing in mRNAseffectively alters the amino acid sequence of the encoded protein so thatit differs from that predicted by the genomic DNA sequence[1].
http://bioinfo.au.tsinghua.edu.cn/dbRES/index.php
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RNA Editing Type +---C to U RNA editing
+---A to GRNA editing
+---U to C RNA editing
+---G insertion RNA editing
+---C insertion RNA editing
+---G deletion RNA editing
+---A to C RNA editing
+---G to C RNA editing+---G to ARNA editing
+---U insertion RNA editing
+---A insertion RNA editing
+---C/U insertion RNA editing
+---AA insertion RNA editing
+---A to U RNA editing
+---GG to AARNA editing
+---AA to GGRNA editing
http://bioinfo.au.tsinghua.edu.cn/dbR ES/browse_edittype.php?edtype=NULL&geneName=NULL
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http://en.wikipedia.org/wiki/RNA_editing
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Editing by deamination
C-to-U editing is with the apolipoprotein B
gene in humans. Apo B100 express in liver &
apo B48 in intestines. B100 has a CAA seq
edited to UAA, a stop codon, in the intestines.
It is unedited in the liver.
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A funny thing happened on the way to the ribosome. That's the essence of a controversial paper
concluding that messenger RNA the molecular middleman that carries information from a cell's DNA to
its protein-making machinery is routinely and systematically altered by unknown mechanisms before its
genetic instructions can be read. The paper, published in Sciencelast week (M. Li et al. Science
doi:10.1126/science.1207018 ; 2011), is already drawing pointed reviews from computational biologists,
who cite possible flaws that could undermine the authors' claims.
If verified, the findings would require a rewrite of the 'central dogma' of molecular biology, which posits
that the RNA transcripts that carry genetic information to the ribosome, where they are used as templates
for protein assembly, are generally faithful matches to the original DNA. A revised version of the picture
would include an 'RNA editing' step along the way, which replaces individual letters in the genetic code
and changes the resulting proteins . Such a step would allow cells to generate much more diversity from
the standard DNA tool kit than previously thought. Vivian Cheung of the University of Pennsylvania in Philadelphia led the work, which involved examining
the RNA transcripts and DNA sequences of 27 people who were sequenced in the 1000 Genomes Project
and the International HapMap Project. The team found more than 10,000 sites in exons regions of
messenger RNA that have been transcribed from DNA in which the DNA and RNA sequences did not
match. The same mismatches occurred in different people, suggesting that they were not random
mistakes in transcription. Cheung's team also found proteins made from the 'mismatched' RNAs.
"Once we saw that these differences were translated into protein sequences, we were pretty certain that
they were biologically derived," Cheung says.
RNA editing a process that changes the identity of an RNA base after it has been transcribed from a
DNA sequence is not a new discovery. An enzyme called ADAR, for instance, induces mismatches in
human cells by replacing the base adenosine with another molecule that is then read as guanine when the
RNA is used to code for a protein. RNA editing also occurs in plants and human parasites.
But the extent of RNA editing posited by the Science paper is extraordinary; its authors estimate that each
person has about 1,065 mismatches sites the authors call "RNADNA differences", or RDDs. Some of
the mismatches involve base changes that are not produced by known RNA-editing mechanisms,suggesting that undiscovered mechanisms are at work.
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http://www.gene-watch.org/blog/post/Evidence-of-altered-RNA-stirs-debate.aspx
"This suggests a completely different layer of gene regulation at the RNA level," says molecular biologist
Kazuko Nishikura at the Wistar Institute in Philadelphia. "The big challenge now is to sort out the
molecular mechanism for how these RNA sequence alterations can be achieved."
Others remain skeptical. Comparative genomicist Lior Pachter at the University of California, Berkeley, has
studied how the high-throughput sequencing machines that Cheung's team used to sequence RNA make
systematic errors when sequencing DNA and RNA. He says that some of Cheung's mismatches occur at
sites that are prone to systematic RNA sequencing errors, but others do not. And in a post on the blog 'genomes unzipped' on 20 May, Joe Pickrell, a graduate student working with
human geneticist Jonathan Pritchard at the University of Chicago, Illinois, described another potential
source of error. Pickrell said that multiple regions of similar DNA in the human genome can make it
difficult to trace the origin of a short stretch of RNA to a specific DNA sequence, creating the illusion of
DNARNA differences. "If the authors are accidentally attributing RNA from two different regions of the
genome to the same DNA region, they could falsely infer RNA editing," Pickrell said. "I think many of their
results could be the result of errors in identifying the correct genomic origin of their sequencing reads."
Other researchers are combing through their own data and waiting to see the results of follow-up work
that will determine whether the concerns raised by Pachter, Pickrell and others are valid. Meanwhile,
Chueng says, "we are glad to see that our colleagues are already using our data".
If confirmed, Cheung's work has important implications for biology and for the way that researchers study
genomics. Chris Gunter, director of research affairs at the HudsonAlpha Institute for Biotechnology in
Huntsville, Alabama, says that RNA editing might have implications for the genetic origins of disease, if it
turns out that the control of how much editing occurs is inherited.
"This could make our jobs as geneticists more problematic and more interesting," she says
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DARNED RNA editing in humans. A-to-I editing, a few C-to-U
instances are also included in the DARNED dataset