Computational identification of transcription frameworks of early committed spermatogenic cells

Lalancette, Claudia; Platts, Adrian E.; Lu, Yi; Lu, Shiyong; Krawetz, Stephen A.

doi:10.1007/s00438-008-0361-2

Cited by 13 publications

(6 citation statements)

References 48 publications

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“…The overlap of RNA‐Seq and qPCR assay results validated LHS‐dependent testicular gene expressions in buntings. In LD states, we found an increased HOOK1 expression, consistent with its role in spermatid differentiation (Chen et al, ), and a decreased RGS2 expression, consistent with its downregulation with the transition from spermatogonia to spermatocyte stage in murine spermatogenesis (Lalancette, Platts, Lu, Lu, & Krawetz, ). We also found high CYFIP2 mRNA expression in both LDES and LDLS, although the levels were still significantly lower in former than the latter state.…”

Section: Discussionsupporting

confidence: 83%

Transcriptome‐wide changes in testes reveal molecular differences in photoperiod‐induced seasonal reproductive life‐history states in migratory songbirds

Sharma

Das

Kumar

2019

Molecular Reproduction Devel

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We investigated the molecular basis of seasonal testicular states in black‐headed buntings (Emberiza melanocephala), in which seasonal migrations limit reproduction to a narrow time‐window during the year. We examined testicular gene expressions in buntings during short day‐induced photosensitive nonreproductive state (SDSE), and during long day‐induced early (LDES) and late (LDLS) gonadal maturation and regressed photorefractory (LDRF) seasonal states. Using Kallisto, we pseudoaligned the RNA‐Seq transcripts and calculated the transcript abundance. We found 1,799 differentially expressed genes (DEGs) between the four photoperiod‐induced seasonal states. Further pairwise comparison with SDSE revealed 1,187, 1,224, and 1,238 DEGs in LDES, LDLS, and LDRF, respectively; 852 genes were common to three comparisons. We then identified genetic pathways putatively involved in seasonal testicular cycle. DEGs that enriched calcium ion binding were highly expressed in testicular maturation states. Similarly, DEGs that enriched glycolytic pathway were highly expressed in LDES and LDRF states. More specifically, quantitative polymerase chain reaction showed significant differences between the photoperiod‐induced states in testicular expression of genes (HOOK1, RGS2, PRDX4, BCL6, CYFIP2, PDCD4, P2RX4, and GABRA1) involved in gametogenesis and associated pathways. Overall, these results show significant transcriptional differences, and provide insights into the molecular basis of seasonal changes in the reproductive life‐history states in a photoperiodic species.

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Section: Discussionsupporting

confidence: 83%

Transcriptome‐wide changes in testes reveal molecular differences in photoperiod‐induced seasonal reproductive life‐history states in migratory songbirds

Sharma

Das

Kumar

2019

Molecular Reproduction Devel

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“…Several zinc finger domain encoding RNAs have been observed that include a range of binding domains, e.g., C2H2 and GATA DNA binding, CCHC single strand RNA binding, and PHD and RING protein binding domains. Binding sites for their interactions as part of transcriptional frameworks have been identified in genes that are active during spermatogenesis (Lalancette et al 2008). Other transcripts retained specifically in sperm with known roles in embryogenesis encode for protein components of the centrosome (CEP85L and KIAA0101), extraembryonic structures (SLC38A7) or those regulating events during early embryogenesis (NNAT and PTK7).…”

Section: Spermatozoal Retained Rnasmentioning

confidence: 99%

The protein and transcript profiles of human semen

2015

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The increasing use of "-omics" (genomic, transcriptomic, proteomic, epigenomic, and metabolomic) high-throughput measurement technologies over the past decade is beginning to reveal the complexity of human biology and physiology through the interactions of DNA, RNA, related proteins and small molecules. In reproductive medicine, the majority of this work, has thus far focused on the female factors, e.g., the oocyte, since they provide both the environment and the majority of elements required for embryogenesis. State-of-the-art sequencing and computational analyses have enabled a deeper understanding of the underlying components. Contrary to being simply a silent delivery vehicle to the oocyte of the packaged male DNA, sperm provide both a specific epigenetically marked genome together with a complex population of RNAs and proteins that are crucial for early embryogenesis. In addition to the sperm, seminal fluid appears to serve multiple roles providing a supplementary series of components that allow the sperm to successfully reach and fertilize the oocyte and prepare the female immune system to tolerate the semiallosteric embryo. A global analysis and review of what is presently known regarding the unique role of each component of the male factor and their associated interactions begins to shed light on this emergent field.

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“…Therefore, whereas spermatozoa are produced asynchronously during postpubertal life, germ cells differentiate synchronously during the first wave of spermatogenesis. Hence, prepubertal testes of a given age have homogeneous contents, and comparing the transcriptome contents of gonads at different ages allowed the identification of stage-specific transcripts [5] , [6] , and putative transcriptional networks were proposed from these data [7] .…”

Section: Introductionmentioning

confidence: 99%

Inactivation of the Celf1 Gene that Encodes an RNA-Binding Protein Delays the First Wave of Spermatogenesis in Mice

et al. 2012

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BackgroundThe first wave of spermatogenesis in mammals is characterized by a sequential and synchronous appearance of germ cells in the prepubertal testis. Post-transcriptional controls of gene expression play important roles in this process but the molecular actors that underlie them are poorly known.Methodology/principal findingsWe evaluated the requirement for the RNA-binding protein CELF1 during the first wave of spermatogenesis in mice. Mice inactivated for Celf1 gene were not viable on pure genetic backgrounds. On a mixed background, we observed by histology and gene profiling by RT-qPCR that the testes of inactivated prepubertal mice were characterized by several features. (i) Spermiogenesis (differentiation of post-meiotic cells) was blocked in a subset of prepubertal inactivated mice. (ii) The appearance of the different stages of germ cell development was delayed by several days. (iii) The expression of markers of Leydig cells functions was similarly delayed.Conclusions/significance Celf1 disruption is responsible for a blockage of spermiogenesis both in adults and in prepubertal males. Hence, the spermiogenesis defects found in Celf1-inactivated adults appear from the first wave of spermiogenesis. The disruption of Celf1 gene is also responsible for a fully penetrant delayed first wave of spermatogenesis, and a delay of steroidogenesis may be the cause for the delay of germ cells differentiation.

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Computational identification of transcription frameworks of early committed spermatogenic cells

Cited by 13 publications

References 48 publications

Transcriptome‐wide changes in testes reveal molecular differences in photoperiod‐induced seasonal reproductive life‐history states in migratory songbirds

Transcriptome‐wide changes in testes reveal molecular differences in photoperiod‐induced seasonal reproductive life‐history states in migratory songbirds

The protein and transcript profiles of human semen

Inactivation of the Celf1 Gene that Encodes an RNA-Binding Protein Delays the First Wave of Spermatogenesis in Mice

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