Xmas ESC A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation, bioRxiv, 2019-09-14
SummaryAlthough female pluripotency significantly differs to male, complications with in vitro culture of female embryonic stem cells (ESC) have severely limited the use and study of these cells. We report a replenishable female ESC system, Xmas, that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. We utilised our Xmas ESC system to screen for regulators of the female-specific process of X chromosome inactivation, revealing chromatin remodellers Smarcc1 and Smarca4 as key regulators of establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation.
biorxiv cell-biology 0-100-users 2019Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing, bioRxiv, 2019-09-13
ABSTRACTThe human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts for Human Leukocyte Antigen (HLA) class I and II receptors which are essential for selfnon-self discrimination by the immune system as well as transcripts encoding B cell and T cell receptors (BCR and TCR) which recognize, bind, and help eliminate foreign antigens.HLA genes are highly diverse within the human population with each individual possessing two of thousands of different alleles in each of the 9 major HLA genes. Determining which combination of alleles an individual possesses for each HLA gene (high-resolution HLA-typing) is essential to establish donor-recipient compatibility in organ and bone-marrow transplantations. BCR and TCR genes in turn are generated by recombining a diverse set of gene segments on the DNA level in each maturing B and T cell, respectively. This process generates adaptive immune receptor repertoires (AIRR) of composed of unique transcripts expressed by each B and T cells. These repertoires carry a vast amount of health relevant information. Both short-read RNA-seq based HLA-typing1 and adaptive immune receptor repertoire sequencing2–5 currently rely heavily on our incomplete knowledge of the genetic diversity at HLA6 and BCRTCR loci7,8.Here we used our nanopore sequencing based Rolling Circle toConcatemeric Consensus (R2C2) protocol9 to generate over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9%. We used this dataset to demonstrate that deep and accurate full-length cDNA sequencing can - in addition to providing isoform-level transcriptome analysis for over 9,000 loci - be used to generate accurate sequences of HLA alleles for HLA allele typing and discovery as well as detailed AIRR data for the analysis of the adaptive immune system without requiring specific knowledge of the diversity at HLA and BCRTCR loci.
biorxiv genomics 0-100-users 2019Peptide-based quorum sensing systems in Paenibacillus polymyxa, bioRxiv, 2019-09-13
AbstractPaenibacillus polymyxa is an agriculturally important plant growth-promoting rhizobacterium. Many Paenibacillus species are known to be engaged in complex bacteria-bacteria and bacteria-host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date no quorum sensing systems have been described in Paenibacillus. Here we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
biorxiv microbiology 0-100-users 2019Dynamic arousal signals construct memories of time and events, bioRxiv, 2019-09-11
AbstractEveryday life unfolds continuously, yet we tend to remember past experiences as discrete event sequences or episodes. Although this phenomenon has been well documented, the brain mechanisms that support the transformation of continuous experience into memorable episodes remain unknown. Here we show that a sudden change in context, or ‘event boundary’, elicits a burst of autonomic arousal, as indexed by pupil dilation. These boundaries during dynamic experience also led to the segmentation of adjacent episodes in later memory, evidenced by changes in memory for the timing, order, and perceptual details of recent event sequences. Critically, we find that distinct cognitive components of this pupil response were associated with both subjective (temporal distance judgements) and objective (temporal order discrimination) measures of episodic memory, suggesting that multiple arousal-mediated cognitive processes help construct meaningful mnemonic events. Together, these findings reveal that arousal processes may play a fundamental role in everyday memory organization.
biorxiv neuroscience 0-100-users 2019Hormonal and neural correlates of care in active versus observing poison frog parents, bioRxiv, 2019-09-11
The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental care in a typically male uniparental species, the Dyeing Poison Frog (Dendrobates tinctorius). We first characterized hormone levels and whole brain gene expression across parental care stages during sex-typical care. Surprisingly, hormonal changes and brain gene expression differences associated with active parental behavior in males were mirrored in their non-caregiving female partners. To further explore the disconnect between neuroendocrine patterns and behavior, we characterized hormone levels and neural activity patterns in females performing sex-reversed parental care. In contrast to hormone and gene expression patterns, we found that patterns of neural activity were linked to the active performance of parental behavior, with sex-reversed tadpole transporting females exhibiting neural activity patterns more similar to those of transporting males than non-caregiving females. We suggest that parallels in hormones and brain gene expression in active and observing parents are related to females ability to flexibly take over parental care in the absence of their male partners.
biorxiv neuroscience 0-100-users 2019Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains, bioRxiv, 2019-09-11
ABSTRACTIdentification of gene expression traits unique to the human brain sheds light on the mechanisms of human cognition. Here we searched for gene expression traits separating humans from other primates by analyzing 88,047 cell nuclei and 422 tissue samples representing 33 brain regions of humans, chimpanzees, bonobos, and macaques. We show that gene expression evolves rapidly within cell types, with more than two-thirds of cell type-specific differences not detected using conventional RNA sequencing of tissue samples. Neurons tend to evolve faster in all hominids, but non-neuronal cell types, such as astrocytes and oligodendrocyte progenitors, show more differences on the human lineage, including alterations of spatial distribution across neocortical layers.
biorxiv evolutionary-biology 0-100-users 2019