The role of repetitive DNA in the centromeric organization of Saccharum spp

• Grant number: 13/00714-3
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date until: May 01, 2013
• End date until: January 31, 2016
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Marie-Anne van Sluys
• Grantee: Sárah Gomes de Oliveira
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function, AP.BIOEN.TEM
• Associated scholarship(s): 14/23828-7 - Evolutionary dynamics and chromosomal distribution of telomeric repeats on chromosomes of Saccharum spp, BE.EP.PD

Abstract

The sugarcane (Poaceae: Saccharum spp) is a tropical crop, economically important. Modern sugarcane cultivars (2n = 100-130) are complex polyploids derived from interspecific hybridization between S. officinarum and S. spontaneum, with unequal contributions of the parental genomes. In plants, the typical centromeres are often associated with heterochromatic regions consisting of large arrays of repetitive DNA sequences. In sugarcane, the hybridization of a centromeric BAC showed some signals larger and brighter than others, which may indicate differences between the centromeres of S. officinarium and S. spontaneum. The centromeric chromatin, in general, is distinguished by the presence of a centromere specific histone H3 variant (CENH3). The centromeric in tandem repeats SCEN and the centromeric retrotransposons were significantly precipitated with anti-CENH3 in sugarcane, showing that these repeats interact directly with the centromere. ChIP experiments allow the recognition of DNA regions associated with histones variants, and has been used together with immunofluorescence using anti-CENH3 to identify the centromeric DNA. Additionally, the transcription of centromeric repeats, sRNAs and processing of siRNA seem to be essential components of centromeres. In sugarcane, the in silico mapping identified distinct patterns of sRNA concentration in different lineages and families of LTR-RT. GISH, FISH and fiber-FISH using repetitive DNA probes, and in silico mapping of sRNAs, combined with ChIP experiments and immunofluorescence with anti-CENH3 can clarify the organization of repetitive elements in sugarcane cultivars, and establish which sequences compose the functional centromere and determine the origin of the centromere sequences.