The testis cell type enriched transcriptome

The main function of the testis is the production of sperm, the male gamete cells that are essential for reproduction, as well as synthesis of hormones that are important for male sex characteristics. The majority of cells in the testis reside in the seminiferous duct, where spermatogenesis takes place. Additional testis-specific cell types are the hormone producing Leydig cells that are located outside the seminiferous ducts.

7048 genes were predicted to have cell type specificity in the testis.

  • 9 cell types profiled
  • 5387 very highly enriched genes
  • 688 highly enriched genes
  • 1128 moderately enriched genes

Testis cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within testis are detailed in Table 1. Identified genes are subdivided into 3 specificity categories, based on the difference between the enrichment score in the corresponding cell type, compared to the other cell types profiled in the tissue (see Methods Summary page for details):

  • Predicted specificity: ´Very high´ - Differential score vs. other profiled cell types within the tissue >0.35
  • Predicted specificity: ´High´ - Differential score vs. other profiled cell types within the tissue >0.25
  • Predicted specificity: ´Moderate´ - Differential score vs. other profiled cell types within the tissue >0.15

Table 1. Number of genes in each specificity category in the testis cell types.

Cell type Very highHighModerate Total enriched
Spermatogonia 249 336 438 1023
Spermatocytes 947 192 167 1306
Early spermatids 3675 3 0 3678
Late spermatids 2376 0 0 2376
Sertoli cells 50 188 376 614
Leydig cells 0 4 16 20
Peritubular cells 0 4 38 42
Endothelial cells 0 12 97 109
Macrophages 1 5 54 60
All cell types 53876881128 7048

NB: Co-enriched genes can appear in 2 or more germ cell types.

Figure 1. Bar plot of the number of enriched genes in the cell types of the testis, divided by specificity category

Testis cell type enriched transcriptome: Illustrative examples


Spermatogonia are diploid cells that form the basal layer of the seminiferous duct and present the initial phase of spermatogenesis. The spermatogonia undergo asymmetric mitotic cell division resulting in two subtypes, type A cells that have stem cell like properties and maintain the spermatogonia population, and type B spermatogonia that will continue to evolve into preleptotene spermatocytes. Rhox Homeobox Family Member 1 (RHOXF1) is a transcription factor regulated by androgens, which is implicated in human reproduction. MAGE Family Member A4 (MAGEA4) and DDB1 And CUL4 Associated Factor 4 Like 1 (DCAF4L1) are both also predicted to have specificity in spermatogonia, but the function of these proteins is currently unknown.

MAGEA4 - Testis


RHOXF1 - Testis


DCAF4L1 - Testis



Spermatocytes are derived from type B spermatogonia and can be subdivided into primary spermatocytes, which are diploid cells that enter the first meiosis, and secondary spermatocytes, which are haploid cells that and enter the second meiosis, to produce spermatids. Several of the testis-specific proteins localized to spermatocytes are involved in testicular differentiation, proliferation and meiosis. Pachytene spermatocytes are meiotic cells at the very end of prophase I. Synaptonemal Complex Protein 3 (SYCP3) is an essential structural component of the synaptonemal complex involved in synapsis, recombination and segregation of meiotic chromosomes. BEN Domain Containing 2 (BEND2) is thought to participate in protein and DNA interactions which occur during chromatin restructuring or transcription. Helicase, Lymphoid Specific (HELLS) is also likely involved in processes involving DNA strand separation, including replication, repair, recombination, and transcription.

SYCP3 - Testis


BEND2 - Testis


HELLS - Testis


Early Spermatids

Early spermatids (also called round spermatids) are transcriptionally active haploid cells that have been derived from secondary spermatocytes. These cells begin to develop cell polarity and undergo a complex process of metamorphosis called spermatogenesis. Zona Pellucida Binding Protein (ZPBP) plays a role in acrosome compaction and sperm morphogenesis. Calmegin (CLGN) is a testis-specific endoplasmic reticulum chaperone protein, which is important for normal sperm migration and adhesion and penetration into the egg zona pellucida. Ly-1 antibody reactive clone (LYAR) has numerous functions, including rRNA processing and a role in transcriptional regulation.

ZPBP - Testis


CLGN - Testis


LYAR - Testis


Late Spermatids

Late spermatids, or elongated spermatids, are transcriptionally inert, and are almost fully developed into mature spermatozoa, with a digestive acrosome covering the head of the spermatid, a long tail, and thickened mid section containing many mitochondria. However the spermatids are still atatched to the walls of the seminiferous duct until fully mature when they are released into the epididymis. Armadillo Repeat Containing 12 (ARMC12) was recently described as having a role in mitochondrial sheath formation, the absence of which causes abnormal mitochondrial coiling along the flagellum, resulting in reduced sperm motility and male sterility. Actin Like 7A (ACTL7A) is a member of a family of actin-related proteins that are involved in diverse cellular processes, including vesicular transport, spindle orientation, nuclear migration and chromatin remodeling, however, its exact function is not known. BPI Fold Containing Family A Member 3 (BPIFA3) was also predicted to be have specificity in late spermatids, but its function is currently unknown.

ARMC12 - Testis


ACTL7A - Testis


BPIFA3 - Testis


Germ cell co-enriched genes

A large number of genes were found to be co-enriched in adjacent cell types along the spermatogenesis developmental trajectory i.e., Spermatogonia and spermatocytes, spermatocytes and early spermatids, and early and late spermatids. No genes were predicted to be enriched in non-adjacent developmental stages however, and only one gene, Meiosis Specific With Coiled-Coil Domain (MEIOC), which is required for germ cell transition to the meiotic cell cycle, was predicted to be enriched in three stages.
MEIOC - Testis

Spermatogonia and Spermatocytes

Genes co-enriched within both the mitotic spermatogonia and meiotic spermatocytes include SPT16 homolog, or SUPT16H, which is a component of the FACT complex, required for the disassembly and reassembly of the histone H2A/H2B structure during transcription, and WD repeat and HMG-box DNA binding protein 1 (WDHD1), which is thought to be important in DNA replication.

SUPT16H - Testis


WDHD1 - Testis


Spermatocytes and Early Spermatids

Genes co-enriched within both meiotic spermatocytes and early spermatids include Rac GTPase activating protein 1 (RACGAP1), a Rho GTPase binding protein with a role in stabilisation of the centralspindlin complex during cell division and cytokinesis, and Shugoshin 2 (SGO2), which is essential for the protection and correct regulation of the cohesin complex during meiosis.

RACGAP1 - Testis


SGO2 - Testis


Early Spermatids and Late Spermatids

Genes co-enriched within both early and late spermatids include Chromosome 17 open reading frame 97 (C17orf97), also known as Ligand of Ate1 (LIAT1), which codes for a protein with little currently known function, although is believed to be involved in liquid–liquid phase separation within the nucleolus in some cell types, and Myeloid leukemia factor 1 (MLF1), thought to play a role in hemopoetic cell determination

C17orf97 - Testis


MLF1 - Testis


Sertoli cells

Sertoli cells are interspersed between the developing germ cells, and are sometimes referred to as nurse cells as they function to protect and nurture the developing sperm cells throughout the various stages of spermatogenesis. They also play a role in spermatogenesis itself by transducing hormonal signals, as well as phagocytosing waste portions of spermatids as they condense and shrink in size during development. Fetal And Adult Testis Expressed 1 (FATE1) is involved in the regulation of endoplasmic reticulum (ER)-mitochondria coupling and Prion Like Protein Doppel (PRND) is a membrane glycosylphosphatidylinositol-anchored glycoprotein that is found predominantly in testis, but it function is not well understood. The function of (KIAA1210) is not currently known.

FATE1 - Testis


KIAA1210 - Testis


PRND - Testis


Peritubular cells

Peritubular cells, or peritubular myoid cells, are thin cells that surround the seminiferous tubule in several layers, and contain smooth-muscle contractile proteins which assist in transport of spermatozoa within the tubules. Peritubular cells also produce connective tissue related proteins that help maintain the structure of the tubule. Collagen Type XV Alpha 1 Chain (KIAA1210), microfibril Associated Protein 4 (MFAP4) and versican (VCAN) are all extracellular matrix proteins involved in cell adhesion and other functions, such as tissue morphogenesis and maintenance.

COL15A1 - Testis


VCAN - Testis


Leydig cells

Leydig cells, also known as interstitial cells, are hormone producing cells located outside the seminiferous tubule, and are the primary source of the hormone testosterone in men. Cytochrome B5 Type A (CYB5A) is a membrane bound hemoprotein which functions as an electron carrier for several membrane bound oxygenases. Cytochrome P450 Family 11 Subfamily A Member 1 (CYP11A1) is a member of the cytochrome P450 superfamily of enzymes, which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids.

CYB5A - Testis


CYP11A1 - Testis