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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Implication of transposons distribution on chromatin state and genome architecture in human

We categorized human genome 100kb non-overlapping segments by their DNAse Hypersensitive Sites (DHS) counts based on data in (Sheffield et al., 2011). They fit a Weibull long tail distribution with a peak at around 14 DHSs per bin. The few (around 50) bins maintaining less than 14 DHSs were mostly gene deserts, long introns, or some quite distinct gene clusters like ubiquitin peptidase family.

Then we performed linear regression analysis between categorized by families transposons counts and #DHS. We revealed two major classes of transposons families: those that prefer -silent- chromatin and those tending to reside in -open- chromatin bins with high confidence. Further on, we discovered that number of Alu retroposons strongly correlates with the number of genes in the bin. Based on this observation, we worked out a method based on a non-linear Alu-gene correlation to infer some non-linear evolution events like the emergence of tandem repeated gene clusters. It was shown previously, that monomer length in tandem repeats relates to nucleosome positioning in plants (Levitsky et al., 2014). Effect of tandem repeats cluster goes beyond local repeats density. Symmetrical appearance of Alu sequences in genome bins varying by GC contents was suggested recently in (Rapoport and Trifonov, 2013). Discussion of Alu counts in opposite strands in DHS bins is provided.

We also crossed the family - categorized transposons with Txn table (transcription factor binding sites verified by ChIP-Seq; genome.ucsc.edu) to elucidate their transposon specific propagation similar to (Jjingo et al., 2014). Further on, we assessed chromosome wise bias of repeat families and found that most chromosome - specific repeat families expansions (LINEs in majority) are maintained at X chromosome. Some CTCF-related open chromatin LTR expansions were observed specifically at chromosome 19 in a way similar to B2 Sine in mouse (Lunyak et al., 2007).

Overall we report that the properties of transposons distribution and density within a genomic segment can disclose its specific evolutionary history and features.

The work has been supported by ICG SB RAS budget project VI.61.1.2.

References
    Jjingo, D., Conley, A. B., Wang, J., Mario-Rami­rez, L., Lunyak, V. V., Jordan, I. K. (2014) Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob DNA. 5, 14.

    Levitsky, V. G., Babenko, V. N., Vershinin, A. V. (2014) The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning. J Biomol Struct Dyn. 32(1), 115-26.

    Lunyak, V. V., Prefontaine, G. G., Nunez, E. et al. (2007) Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science. 317(5835), 248-251. Rapoport, A. E., Trifonov, E. N. (2013) Compensatory nature of Chargaff's second parity rule. J Biomol Struct Dyn. 31(11), 1324-36.

    Sheffield, N. C., Thurman, R. E., Song, L. et al. (2013) Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 23(5), 777-788.


Vladimir N. Babenko1, 2*
Vladimir F. Matvienko 2
Nataly S. Safronova2

1Institute of Cytology and Genetics SB RAS,
2Novosibirsk State University, Novosibirsk, 630090, Russia

Phone: +7(383)3634974
Fax: +7(383)3331278
bob@bionet.nsc.ru