RNA-DNA sequence difference (RDDs) occur in human cells within seconds after RNA left Polymerase II.

1. Review of
RNA-DNA Differences Are Generated in Human Cells
within Seconds after RNA Exits Polymerase II
Isabel X. Wang, Leighton J. Core, Hojoong Kwak, Lauren Brady, Alan Bruzel, Lee
McDaniel, Allison L. Richards, Ming Wu, Christopher Grunseich, John T. Lis, Vivian G.
Cheung
Cell Reports (March 2014)
DOI: 10.1016/j.celrep.2014.01.037
Presented By:
Junaed Ahmed
Reg: 2016423003

2. HIGHLIGHTS
• RNA sequences are expected to be identical to
their corresponding DNA sequences. But RNA
sequences differ from DNA sequences beyond
canonical RNA editing
• RNA-DNA sequence differences (RDDs) are
found in nascent RNAs
• RDD formation occurs soon after transcript
synthesis and before splicing

4. INTRODUCTION
• The first example of a transcript sequence that is not
encoded by DNA was reported by Benne et al. (1986),
who showed that the coxII mRNA in trypanosome has
four nucleotides that are not encoded in the DNA. They
then coined the term “RNA editing” for this “novel
mechanism of gene expression”
•
• In humans RNA editing occurs in processes mediated by
the ADAR and APOBEC families of porteins.
• In different human cells 12 types of total RDDs were
found.
• Only two types of RDD mechanisms are known.

5. EXPERIMENTAL PROCEDURES USED
• Cell Culture
• Cultured B cells from two normal individuals. GM12004 and
GM12750
• DNA Sequencing
• NGS used
• mRNA-Seq and Chromatin-Bound Nascent RNA-Seq
• GRO-Seq and PRO-Seq
• Sequence Analysis
• DNA-Seq and RNA-seq reads were aligned to the human
reference genome (hg18) using GSNAP.
• RDDs identification
• Compared an RNA seq with its corresponding DNA seq for RDDs
identification. Various filtering measure taken to improve the
quality of the result.

6. NASCENT RNA FROM GRO-SEQ AND PRO-SEQ

8. REUSLTS OF RDDS IN VERY NASCENT TRANSCRIPTS
This results were validated by
ddPCR of GRO-Seq RDDs

9. RESULT CONT’D
• Results of Genome waking Confirm that RDDs Are in
Unique Regions of the Genome
• RDD formation Occurs within Seconds after Transcription.
• RDDs in transcripts beginning at ~55 bases from the
active site or ~35 bases beyond the exit channel of
RNA Pol II.
• RDD frequency is lower in cells from a patient with
Senataxin mutation.
• Mutant SETX gene product interact with Pol II and
plays a roles in resolving R loops.
• Genes with RDDs in their Nascent RNAs are enriched for
roles in regulation and metabolism of macromolecules.

10. THE END
THANK YOU