title: An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation.
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.
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
authors.forename: Kamal
authors.initials: K
authors.lastname: Mandal
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Samuel L
authors.initials: SL
authors.lastname: Bader
authors.affiliation: G.N.R. Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Sciex, Gurgaon, Haryana, India.
authors.forename: Dipankar
authors.initials: D
authors.lastname: Malakar
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
authors.forename: Bhola Shankar
authors.initials: BS
authors.lastname: Pradhan
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
authors.forename: Rajesh K
authors.initials: RK
authors.lastname: Sarkar
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
authors.forename: Neerja
authors.initials: N
authors.lastname: Wadhwa
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.
authors.forename: Souvik
authors.initials: S
authors.lastname: Sensharma
authors.affiliation: Next-Generation Sequencing Facility, National Institute of Immunology, New Delhi, India.
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Jain
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: Cellular Endocrinology Laboratory, National Institute of Immunology, New Delhi, India.|National Institute of Animal Biotechnology, Miyapur, Hyderabad, India.
authors.forename: Subeer S
authors.initials: SS
authors.lastname: Majumdar
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D008297:Male; D011401:Promoter Regions, Genetic; D040901:Proteomics; D051381:Rats; D017208:Rats, Wistar; D012708:Sertoli Cells / Q000378:metabolism / Q000502:physiology*; D013091:Spermatogenesis; D013737:Testis / Q000378:metabolism / Q000502:physiology*; D050986:YY1 Transcription Factor / Q000378:metabolism* / Q000502:physiology
chemical_list: D050986:YY1 Transcription Factor
keywords: SWATH-MS; TRANSFAC; cellular differentiation; multi-omics; sertoli cell