A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals

In male mice, the transcription factor A-MYB initiates the transcription of pachytene piRNA genes during meiosis. Here, we report that A-MYB activates the transcription factor Tcfl5 produced in pachytene spermatocytes. Subsequently, A-MYB and TCFL5 reciprocally reinforce their own transcription to establish a positive feedback circuit that triggers pachytene piRNA production. TCFL5 regulates the expression of genes required for piRNA maturation and promotes transcription of evolutionarily young pachytene piRNA genes, whereas A-MYB activates the transcription of older pachytene piRNA genes. Intriguingly, pachytene piRNAs from TCFL5-dependent young loci initiate the production of piRNAs from A-MYB-dependent older loci, ensuring the self-propagation of pachytene piRNAs. A-MYB and TCFL5 act via a set of incoherent feedforward loops that drive regulation of gene expression by pachytene piRNAs during spermatogenesis. This regulatory architecture is conserved in rhesus macaque, suggesting that it was present in the last common ancestor of placental mammals.

[1]  K. Stamatakis,et al.  TCFL5 deficiency impairs the pachytene to diplotene transition during spermatogenesis in the mouse , 2022, Scientific Reports.

[2]  Shuiqiao Yuan,et al.  Transcription factor-like 5 is a potential DNA/RNA-binding protein essential for maintaining male fertility in mice , 2021, bioRxiv.

[3]  Z. Weng,et al.  Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes , 2021, Nature communications.

[4]  J. Dean,et al.  Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA , 2020, bioRxiv.

[5]  Z. Weng,et al.  The Evolutionarily Conserved piRNA-producing Locus pi6 Is Required for Male Mouse Fertility , 2020, Nature Genetics.

[6]  Z. Weng,et al.  Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans , 2019, Nature Ecology & Evolution.

[7]  Dan Tenenbaum,et al.  Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling , 2019, Epigenetics & Chromatin.

[8]  Deniz M. Ozata,et al.  PIWI-interacting RNAs: small RNAs with big functions , 2018, Nature Reviews Genetics.

[9]  P. Zamore,et al.  A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals , 2018, bioRxiv.

[10]  Saher Sue Hammoud,et al.  A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. , 2018, Developmental cell.

[11]  A. Barski,et al.  Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline , 2018, Proceedings of the National Academy of Sciences.

[12]  Z. Weng,et al.  Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers , 2018, BMC Genomics.

[13]  Di Zhang,et al.  Metabolic regulation of gene expression through histone acylations , 2016, Nature Reviews Molecular Cell Biology.

[14]  Steven Henikoff,et al.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites , 2016, bioRxiv.

[15]  R. Sachidanandam,et al.  PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis. , 2015, Cell reports.

[16]  Julius Brennecke,et al.  piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis , 2015, Science.

[17]  Zhiping Weng,et al.  piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production , 2015, Science.

[18]  Molly Hammell,et al.  piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis , 2015, Genes & development.

[19]  Henrik Molina,et al.  Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. , 2015, Molecular cell.

[20]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[21]  Adam P. Rosebrock,et al.  Minotaur is critical for primary piRNA biogenesis , 2013, RNA.

[22]  T. Yasunaga,et al.  GPAT2, a mitochondrial outer membrane protein, in piRNA biogenesis in germline stem cells. , 2013, RNA.

[23]  Aviv Regev,et al.  Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples , 2013, Nature Methods.

[24]  Zhiping Weng,et al.  An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. , 2013, Molecular cell.

[25]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[26]  Z. Weng,et al.  Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection , 2012, Silence.

[27]  Kunbin Qu,et al.  Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue , 2012, PloS one.

[28]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[29]  H. Tang,et al.  A-MYB (MYBL1) Stimulates Murine Testis-Specific Ldhc Expression via the cAMP-Responsive Element (CRE) Site1 , 2012, Biology of reproduction.

[30]  Lishuang Shen,et al.  A-MYB (MYBL1) transcription factor is a master regulator of male meiosis , 2011, Development.

[31]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[32]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[33]  U. Alon.  Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.

[34]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[35]  Kuniaki Saito,et al.  A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in Drosophila , 2007, Science.

[36]  N. Lau,et al.  Characterization of the piRNA Complex from Rat Testes , 2006, Science.

[37]  C. Sander,et al.  A novel class of small RNAs bind to MILI protein in mouse testes , 2006, Nature.

[38]  Ravi Sachidanandam,et al.  A germline-specific class of small RNAs binds mammalian Piwi proteins , 2006, Nature.

[39]  Haifan Lin,et al.  A novel class of small RNAs in mouse spermatogenic cells. , 2006, Genes & development.

[40]  L. Riou,et al.  Flow cytometric characterization of viable meiotic and postmeiotic cells by Hoechst 33342 in mouse spermatogenesis , 2005, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[41]  J. Goldstein,et al.  Molecular Characterization of Human Acetyl-CoA Synthetase, an Enzyme Regulated by Sterol Regulatory Element-binding Proteins* , 2000, The Journal of Biological Chemistry.

[42]  T. Katagiri,et al.  Cloning of TCFL5 encoding a novel human basic helix-loop-helix motif protein that is specifically expressed in primary spermatocytes at the pachytene stage , 1998, Cytogenetic and Genome Research.

[43]  B. R. Nebel,et al.  Calendar of Gametogenic Development in the Prepuberal Male Mouse , 1961, Science.