Due to the crucial role that epigenetic mechanisms play in regulating cell identity and function, it has been a long-standing question whether and how stem cells maintain their epigenetic memory through many cell divisions. We found that during asymmetric division of Drosophila male germline stem cell (GSC), histone H3 (H3) becomes asymmetrically segregated — the “old” H3 is retained in the GSC while the “new” H3 is enriched in the differentiating daughter cell (Science, 338: 679-682). Recently, we also found that randomized H3 segregation pattern correlates with both GSC loss and progenitor germline tumor phenotypes, suggesting that asymmetric H3 inheritance is required for both GSC maintenance and proper differentiation (Cell, 163: 792–793). We propose that old and new H3 are asymmetrically deposited to sister chromatids, and mitotic machinery recognizes this asymmetry for differential segregation. To understand this question, we are using live-cell imaging to visualize spatial and temporal regulation of sister chromatids segregation. We have obtained promising data showing asymmetric microtubule activities in GSC, which first interact with the nuclear membrane at the GSC side during G2-phase, and then start “poke-in” and make a hole to interact with chromatin during G2/M phase. Interestingly, during G2 phase, centromeres cluster near the nuclear membrane at the stem cell side, with the “old” Cid (centromeric H3) enriched sister centromeres facing towards the centrosome at stem cell side, which is likely to secure attachment between old H3-enriched sister chromatids and microtubules emanating from the centrosome at the stem cell side. This occurs prior to the attachment of new H3-enriched sister chromatids to microtubules from the centrosome at the differentiating daughter cell side. Coincidentally, we also observed that sister chromatids enriched with old versus new H3 are condensed in a temporally separable manner: the old H3-enriched sister chromatids condense prior to new H3-enriched sister chromatids. We hypothesize that asymmetric microtubule activity, asymmetric centromere and differential condensation of sister chromatids act together to ensure their proper attachment followed by asymmetric segregation. By contrast, such an asymmetry in either the microtubule activity or sister chromatid condensation is not observed in symmetrically dividing progenitor germ cells. Together, we propose that the GSC microtubule has a novel function— it directs the orientation of sister chromatids. This proposed function provides an unappreciated role of the microtubule, namely, in selectively recognizing and segregating sister chromatids based on their differential epigenetic information.