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DNA Res. 2017 Apr 1;24(2):143-157. doi: 10.1093/dnares/dsw057.

An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation.

Author information

1
Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
2
Institute for Systems Biology, Seattle, WA 98109, USA.
3
G.N.R. Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
4
Sciex, Gurgaon, Haryana, India.
5
Next-Generation Sequencing Facility, National Institute of Immunology, New Delhi, India.
6
National Institute of Animal Biotechnology, Miyapur, Hyderabad, India.

Abstract

Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database. Proteomic SWATH-MS analysis provided extensive quantification of nuclear and cytoplasmic protein fractions revealing 1,670 proteins differentially located between the nucleus and cytoplasm of infant Sc and 890 proteins differentially located within those of pubertal Sc. Based on our multi-omics approach, the transcription factor YY1 was identified as one of the lead candidates regulating differentiation of Sc.YY1 was found to have abundant binding sites on promoters of genes upregulated during puberty. To determine its significance, we generated transgenic rats with Sc specific knockdown of YY1 that led to compromised spermatogenesis.

KEYWORDS:

SWATH-MS; TRANSFAC; cellular differentiation; multi-omics; sertoli cell

PMID:
28065881
PMCID:
PMC5397609
DOI:
10.1093/dnares/dsw057
[Indexed for MEDLINE]
Free PMC Article

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