Breaking Neuronal Symmetry by Chromatin Memories

The asymmetric fates of two bilaterally symmetrical neurons are determined by a two-step activation program at a miRNA locus. Very low levels of transcription ‘prime’ the locus many cell generations before the final fate determination is imposed by a bilateral ‘boost’.

Animal nervous systems are generally bilaterally symmetrical anatomically, whilst displaying many functionally important left-right asymmetries. How is asymmetry imposed on a bilaterally symmetrical ground plan? The nematode C. elegans with its invariant cell lineage and tractable genetics offers a powerful model system in which to tackle this issue. Cochella and Hobert have published an elegant new paper describing how a distinct chromatin state at a microRNA locus serves as a molecular mark encoding a memory of a cell’s ancestry in an asymmetric lineage.  After many cell generations, this mark engenders a different response to terminal differentiation from its’ bilaterally symmetric partner cell.

The bilaterally symmetrical pair of gustatory neurons ASEL(eft) and ASER(ight) express different repertoires of chemoreceptors. This functional asymmetry is underpinned by the differential expression of two transcription factors. DIE-1 is expressed in ASEL and COG-1 in ASER. Together with a microRNA, lsy-6, which represses COG-1 expression, they form a bistable feedback loop responsible for determining the asymmetric fates of ASE neurons. Loss of any of these three factors results in conversion of one ASE to the other. However, the asymmetric expression of die-1 and cog-1 only occurs within the post-mitotic neurons themselves. How then is this asymmetry established?

A schematic representation of the features of asymmetric ASE specification. Note the original asymmetry in the lineages is determined at the 4 cell stage, tbx-37/38 expression in the great-granddaughters of ABa, and lsy-6 in the loop in ASEL.

A schematic representation of the features of asymmetric ASE specification. Note the original asymmetry in the lineages is determined at the 4 cell stage, tbx-37/38 expression in the great-granddaughters of ABa, and lsy-6 in the loop in ASEL.

The two ASEs are derived from different cell lineages that diverge at the 4-cell stage. The two daughters of the 2-cell stage blastomere AB, ABa and ABp, differentiate from each other due to signalling from one of the other 4-cell stage blastomeres to ABp. This signalling event represses the expression in the ABp lineage of a pair of redundant transcription factors, TBX-37 and TBX-38, which are transiently expressed in the 8 great-granddaughter cells derived from ABa. The expression of these TBX proteins is crucial to the asymmetric fate specification of ASE neurons as in tbx-37/38 double mutants ASEL is converted into ASER. However, TBX-37 and 38 are only expressed in the lineage giving rise to ASEL six cell generations before it’s birth. This large gap between the different stages of asymmetric ASE determination lead researchers to postulate the existence of a ‘memory mark’ linking TBX-37/38 action to the expression of the asymmetry defining feedback loop.

During this hiatus between TBX-37/38 expression and terminal ASE determination, the lineages giving rise to the two neurons become symmetric. A number of left/right pairs of neuronal precursors expressing the proneural gene hlh-14 develop from the two lineages, but only the pair of ASE mother cells express the ‘terminal selector’ transcription factor CHE-1. CHE-1 drives the expression of many ASE-expressed genes and activates expression of the asymmetric loop components, lsy-6, die-1, and cog-1. It is at this point that the TBX-37/38-dependent memory mark must integrate into the bilateral activity of CHE-1 generating the asymmetric expression of the loop components.

To try to discover the nature of the memory mark Cochella and Hobert performed a detailed analysis of the expression of the loop components. lsy-6 was suggested to act upstream of die-1 and cog-1 by genetic experiments, and the researchers found that it was the first of the loop components to be expressed.  It is expressed asymmetrically from the start in the ASEL mother cell. Deletion of lsy-6 results in conversion of ASEL to ASER. A construct of lsy-6 in combination with 932 bp of upstream sequence is able to rescue this effect, but sometimes leads to the conversion of ASER to ASEL. This suggested that the ‘upstream element’ construct drove ectopic expression in ASER as well as ASEL. Indeed, the upstream element contains CHE-1 binding motifs causing expression in both the ASE neurons. Cochella and Hobert therefore assayed other lsy-6 surrounding sequence for cis-regulatory information limiting its expression to ASEL. In fact, a construct including the upstream element, lsy-6, and 300 bp of downstream sequence completely rescued lsy-6 null alleles, eliminated ectopic ASER conversion, and was expressed identically to the endogenous miRNA. Normal lsy-6 expression is therefore regulated by both the upstream and downstream elements.

When the downstream element was used alone to drive expression of a reporter gene, it produced a very different pattern. Expression started early in a few ABa-derived blastomeres, one cell division after the expression of tbx-37/38, continuing in the progenitive lineage of ASEL until its’ birth.It never drove expression in ABp derived lineages. Expression from the downstream element was completely lost in tbx-37/38 double mutants, whilst mis-expression of TBX-37/38 in ABp derived cells lead to ectopic expression of the downstream element reporter. The downstream element contains a predicted binding-site for T-box proteins, directly linking the lineage–dependent expression of tbx-37/38 with theasymmetry-defining loop.

The expression pattern driven by the downstream reporter suggested that lsy-6 may be expressed far earlier than previously observed. The researchers therefore used a very sensitive technique to image potential lsy-6 transcripts. This showed that a few lsy-6 RNAs were present in cells in the lineage giving rise to ASEL five generations before strong expression is observed in the ASEL mother cell.

Broadly therefore, lsy-6 expression occurs in two phases; a very low level of activation early, dependent on the downstream element, and a second upstream element-dependent higher level of expression in the ASEL mother cell. However, deletion of the downstream element within large genomic constructs abrogated expression at all stages, and failed to rescue lsy-6 null alleles. This contrasted with earlier observations in which the upstream element alone could drive expression and rescue. The difference between these observations suggested  that, within a normal genomic context, the upstream element can only function in combination with the downstream element.

The authors therefore posited a model in which early downstream element/tbx-37/38– dependent transcription may ‘prime’ the locus in some way, rendering it competent to respond to the later transcriptional ‘boost’ mediated by CHE-1 acting on the upstream element.

Cochella and Hobert tested their model by substituting priming via tbx-37/38/downstream element for priming via ectopic CHE-1. In worms with the downstream element deleted, they drove early expression of CHE-1 from a heat-shock promoter approximately 4 cell generations before its’ normal time of expression. This caused low levels of lsy-6 transcription, rescuing the priming phase and allowing later ASEL expression and determination. Priming is therefore not dependent on a specific transcription factor acting on the downstream element, rather as long as low levels of transcription occur at the locus, it is primed.

This suggested that the memory mark causing the different response of the lsy-6 locus may be a lineage-specific transcription-dependent chromatin state. Using a cunning technique to visualise the level of chromatin compaction on transgenic arrays containing the lsy-6 locus, they observed chromatin decompaction of thelocus in the ASEL progenitive lineage 1 cell division after tbx-37/38 expression. Chromatin decompaction is associated with active genes; in the absence of early transcription the locus becomes compacted and refractory to CHE-1 activation later. In tbx-37/38 double mutants this lineage-specific decompaction was never observed, nor was it seen when the downstream element was deleted.

The memory mark is therefore chromatin decompaction at a miRNA locus linked to very low levels of transcription imposed within a cell lineage at an early stage of development. This primed state relays asymmetric information into an otherwise bilaterally symmetrical developmental program, facilitating diversification of neuronal cell fates. The timing of the priming mechanism fits in with earlier evidence that C. elegans embryos are relatively developmentally plastic until the 64-128 cell stage when developmental genes become compacted and refractory to ectopic activation.

Although I find this paper very elegant and convincing, I do have a few qualms about the most crucial experiment: the early ectopic activation by CHE-1. It seems like a slightly dirty experiment and I think I would’ve preferred to see ectopic induction of lsy-6 transcription via an unrelated mechanism. Perhaps experiments such as these would’ve had their own problems and my doubts are unfounded. I would also have liked to see the compaction assay performed with the ectopic CHE-1 induced activation.

The demonstration of a chromatin-based lineage specific prepattern facilitating differential responses to more generic inputs later in embryogenesis has wide implications, not just for asymmetries in the worm nervous system, but for the way we understand development in many animals. Firstly a technical point; to visualise early lsy-6 transcription the authors had to use a very labour intensive and hi-tech form of in situ hybridisation. The transcription they found, of just a few individual RNA molecules per cell, had massive developmental significance. Generally the techniques used to judge expression in developmental studies is nowhere near as sensitive, implying that we may be missing a lot of important information. Secondly, a more general point; A cell or tissues’ ‘competence’ to respond to developmental signalling, a concept derived from experimental embryology, and perhaps disdained in more genetical perspectives is relevant here. Molecular memories encoded by chromatin states may be a very widespread mode for imposing pre-pattern or developmental competence during embryogenesis. It seems to me that these types of understandings can begin to blend together the two different meanings of epigenetics; namely the derivation of the word by Waddington from epigenesis (meaning the increase in complexity during development), with the more current usage of epigenetics as describing a diverse collection of non-genetic inherited information.

Cochella, L., & Hobert, O. (2012). Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans Cell, 151 (6), 1229-1242 DOI: 10.1016/j.cell.2012.10.049

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