Supplementary Materials

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

Upasna Sharma, Colin C. Conine, Jeremy M. Shea, Ana Boskovic, Alan G. Derr, Xin Y. Bing, Clemence Belleannee, Alper Kucukural, Ryan W. Serra, Fengyun Sun, Lina Song, Benjamin R. Carone, Emiliano P. Ricci, Xin Z. Li, Lucas Fauquier, Melissa J. Moore, Robert Sullivan, Craig C. Mello, Manuel Garber, Oliver J. Rando*

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

Download Supplement
  • Materials and Methods
  • Figs. S1 to S13
  • Captions for Tables S1 to S8
  • Full Reference List
Table S1
Additional Data table S1 (separate file) Complete small RNA dataset. All murine small RNA-Seq datasets. Rows give read counts mapping to rRNAs, tRNAs, repeatmasker consensus sequences, unique piRNA clusters, and microRNAs are all provided here. Reads mapping to Refseq are excluded in the interest of space, but are provided for tissue averages in Table S2.
Table S2
Additional Data table S2 (separate file) Small RNA abundance for all tissues. Small RNA data for all tissues are shown here normalized to ppm (excluding rRNAs). For each tissue, total reads were obtained by summing reads from each relevant library.
Table S3
Additional Data table S3 (separate file) Small RNA-Seq of B. taurus caput sperm reconstitutions. Data for four replicate sperm reconstitutions are shown, with counts of RNAs mapping to rRNAs, tRNAs, or microRNAs shown as indicated. Samples include purified caput sperm, mock-treated caput sperm (incubated at 37 °C), caput sperm incubated with cauda epididymosomes, cauda epididymosomes alone, and a single sample of cauda sperm.
Table S4
Additional Data table S4 (separate file) ES cell mRNA abundance. Affymetrix microarray data are shown for ES cells transfected with GFP knockdown siRNAs, or with an LNA antisense targeting the 5’ end of tRNA-Gly-GCC.
Table S5
Additional Data table S5 (separate file) tRF-Gly-GCC effects on translation in ES cells. RNA-Seq data and ribosome footprinting for ES cells subject to mock tranfection, GFP knockdown, or tRF-Gly-GCC inhibition (4 replicates each).
Table S6
Additional Data table S6 (separate file) tRF-Gly-GCC effects on 4-cell stage gene expression. Single embryo RNA-Seq data for 4-cell stage embryos. Zygotes generated via IVF were microinjected with H3.3-GFP mRNA, with or without an antisense oligo targeting tRF-Gly-GCC, then allowed to develop to the 4-cell stage and subject to single embryo RNA-Seq.
Table S7
Additional Data table S7 (separate file) Dietary effects on preimplantation gene regulation. Single-embryo RNA-Seq data for embryos at varying stages of development, generated using IVF with sperm obtained from male mice consuming the indicated diets.
Table S8
Additional Data table S8 (separate file) RNA effects on preimplantation gene regulation. Single-embryo RNA-Seq data for ICSI experiments, sperm small RNA injections, and tRF-Gly-GCC injections. All data are for late 2-cell stage embryos, and data are only shown for transcripts expressed at greater than 5 parts per million in a given experiment.