decoding of exon splicing patterns in the human runx1-runx1t1 fusion gene vasily v. grinev associate...
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DECODING OF EXON SPLICING
PATTERNS IN THE HUMAN RUNX1-RUNX1T1 FUSION GENE
Vasily V. GrinevAssociate ProfessorDepartment of Genetics
Faculty of Biology
Belarusian State University
Minsk, Republic of Belarus
MOLECULAR ANATOMY OF THE TRANSLOCATION t(8;21)(q22;q22)
RUNX1T1 gene structure
chromosome 8
chromosome 21
RUNX1 gene structure
Chromosome 8 and chromosome 21 are partnersin non-homological reciprocal translocation t(8;21)(q22;q22)
MOLECULAR ANATOMY OF THE TRANSLOCATION t(8;21)(q22;q22)der 8
der 21
RUNX1-RUNX1T1 fusion gene structure
The main outcome of the translocation t(8;21)(q22;q22)is fusion gene RUNX1-RUNX1T1
Domains and key interaction partners of the fusion protein RUNX1-RUNX1T1
DIVERSITY OF RNA PRODUCTSOF THE FUSION GENE RUNX1-RUNX1T1
Exon graph-based model of organization of the fusion gene RUNX1-RUNX1T1
For fusion gene RUNX1-RUNX1T1,there is a lot of identified transcripts:135 full-length RNA products63 expressed sequence tags
POWER-LAW BEHAVIOR OF THE LOCAL COMBINATORICS OF THE RUNX1–RUNX1T1 EXONS
ECI (exon combinatorial index) is a quantitative measure of local exon combinatorics and it means a number of unique splicing events that involve an exon.
List of competitive statistical models:1) power-law distribution;2) truncated power-law distribution with an exponential cut-off;3) exponential distribution;4) log-normal distribution;5) Yule-Simon distribution;6) stretched exponential distribution (complementary cumulative Weibull distribution);7) Poison distribution.
Set of exonsof the fusion gene RUNX1-RUNX1T1
empirical data― power-law― truncated power-law― exponential― log-normal― Yule-Simon― stretched exponential― Poison
Set of exonsof the whole human transcriptome
SEQUENCE FEATURES OF THE EXONS AND FLANKING INTRONS
Some example of sequence features of flanking introns
Genomic elements for extraction of sequence features
SEQUENCE FEATURES OF THE EXONS AND FLANKING INTRONS
Some example of sequence features of exons
DIFFERENT “ATTRACTIVENESS” OF EXONS FOR ALTERNATIVE SPLICING IS ASSOCIATED WITH SEQUENCE-RELATED FEATURES
Sequence features are not equalin importance for the prediction
of the ECI value
Compendium of the sequence features permits to predict the values of the ECI
by regression random forestswith a high accuracy
A complex relationship betweenthe sequence features
and the ECI value
GENES OF SPLICING FACTORS DIFFERENTIALLY EXPRESSED IN t(8;21)-POSITIVE AML BLASTS
The RBFOX3 gene is not expressedor expressed under the threshold of detection by RT-PCR in normal hematopoietic cells but
this gene is expressed in leukemia cells
There is a significant (according to Mann–Whitney U test) differential expression of the splicing factors
genes in leukemia cells in comparison with normal hematopoietic cells
The lanes on the upper electrophoregram: Fermentas GeneRulerTM 100 bp DNA Ladder Plus (1), amplification of cDNA of the TBP gene from Kasumi-1 cells (2), amplification of cDNA of the RBFOX3 gene from normal PBMNC (3, 5), BMMNC (7, 9), CD34+HPSC(11, 13) and from Kasumi-1 cells (15) and amplification of cDNA of the RBFOX3 gene from respective RT−negative controls (4, 6, 8, 10, 12, 14, 16).The lanes on the bottom electrophoregram: Fermentas GeneRulerTM 100 bp DNA Ladder Plus (1), amplification of cDNA of the RBFOX3 gene from the bone marrow samples of nine children with t(8;21)-positive AML (2, 4, 6, 8, 10, 12, 14, 16, 18) and respective RT−negative controls (3, 5, 7, 9, 11, 13, 15, 17, 19).
ACTIVITY OF THE NMD SYSTEM IN CHILDREN t(8;21)-POSITIVE AML CELLS IS DEREGULATED
Expression of NMD genes is significantly increased or decreased in leukemia cells in comparison with normal hematopoietic cells
EXONS WITH HIGH ECI VALUES ARE “HOT POINTS” OF THE RUNX1–RUNX1T1 MRNA SPLICING
In silico modeling supports a strong sensitivityof splicing of RUNX1–RUNX1T1 transcripts to
skipping of exons with high ECI values
(A) Skipping of exons that were listed in the descending order of their ECI values: experimentally verified transcripts (on the top), predicted transcripts (on the bottom).(B) This picture is similar to (A), but exons were excluded from splicing process in the ascending order of values of their ECI.
Legend:— diversity of transcripts— average size (in number of exons) of transcripts— average length (in number of nucleotides) of transcripts— average length of ORF— portion of transcripts containing PTC
MORE DETAILS IN:
Tatiana V. RamanouskayaAlina V. VaitsiankovaIlia M. Ilyushonak
Alexandr A. MigasOlga A. MishkovaOlga V. Aleinikova
Petr V. NazarovLaurent Vallar
Aksana D. Kirsanava
Natalia Jr. Siomava
MANY THANKS TO THE MEMBERS OF OUR TEAM:
THANK YOU FOR ATTENTION!
HETEROZYGOATSJust allele uneven