Biology subjects

Lettice, L. A.

Publications and source records attributed to Lettice, L. A..

5 recordsLinked to original sources

bioRxiv2026

Loop extrusion dynamics and cooperative activation independently regulate enhancer-driven transcription

How enhancers transmit their activation signals to target promoters is a fundamental unanswered question. Gene activation by distal enhancers is affected by the three-dimensional organisation of chromatin driven by cohesin-mediated loop extrusion, but how the dynamic loop extrusion cycle shapes transcriptional outcomes is not fully understood. In addition, genes are typically regulated by multiple enhancers and cases of cooperativity between enhancers have been observed that depend on the relative position of enhancers and gene. The reason for such context-dependent cooperativity is unknown, and whether it is linked to loop extrusion has not been explored. Here, we use synthetic gene activation to show that NIPBL depletion, which decreases loop extrusion rate, reduces long-range activation in a dose-dependent manner. In contrast, WAPL depletion, which reduces cohesin turnover, can both increase and decrease distal gene activation depending on the presence of adjacent CTCF binding sites. These effects on gene activation correlate with the impact on chromatin contacts. Depletion of the co-activator BRD4 also affects long-range activation, but not by changing chromatin contacts. Synthetic activation from two locations results in super-additive responses, which can be predicted by an independently determined response model. These predictions hold for dual activation from proximal and/or distal sites, and with perturbed NIPBL, WAPL, or BRD4. Distal activation therefore appears to be equivalent in nature to proximal activation, and context-dependent cooperativity can arise simply from different level of activation inputs operating on a non-linear response function.

molecular biology↗

bioRxiv2024

Bystander activation across a TAD boundary supports a cohesin-dependent hub-model for enhancer function

Enhancers in the mammalian genome are able to control their target genes over very large genomic distances, often across intervening genes. Yet the spatial and temporal specificity of developmental gene regulation would seem to demand that enhancers are constrained so that they only activate the correct target gene. The sculpting of three-dimensional chromosome organization, especially that brought about through cohesin-dependent loop extrusion, is thought to be important for facilitating and constraining the action of enhancers. In particular, the boundaries of topologically associating domains (TADs) are thought to delimit regulatory landscapes and prevent enhancers acting on genes close in the linear genome, but located in adjacent TADs. However, there are some examples where enhancers appear to act across TAD boundaries. In these cases it was not determined whether an enhancer can simultaneously activate transcription at genes in its own TAD and in an adjacent TAD. Here, using a combination of mouse developmental genetics, and synthetic activators in stem cells, we show that some Shh enhancers can activate transcription simultaneously, not only of Shh but also at a gene Mnx1 located in an adjacent TAD. This occurs in the context of a chromatin configuration that maintains both genes and the enhancers close together and is influenced by cohesin. To the best of our knowledge this is the first report of two endogenous mammalian genes transcribed simultanously under the control of the same enhancer, and across a TAD boundary. Our data have implications for understanding the design rules of gene regulatory landscapes, and are most consistent with a transcription hub model of enhancer-promoter communication.

genetics↗

bioRxiv2023

Insights into Digit Evolution from a Fate Map Study of the Forearm

The cellular and genetic networks which contribute to the development of the zeugopod, (radius and ulna of the forearm, tibia and fibula of the leg) are not well understood, although these bones are susceptible to loss in congenital human syndromes and to the action of teratogens such as thalidomide. Using a new fate mapping approach in transgenic chickens, we show that there is a small contribution of SHH expressing cells to the posterior ulna, posterior carpals and digit 3. We establish that while the majority of the ulna develops in response to paracrine SHH signaling in both the chicken and mouse, there are differences in the contribution of SHH expressing cells to other tissues of the zeugopod between these two species as well as between the chicken ulna and fibula. This is evidence that although zeugopod bones are clearly homologous according to the fossil record, the zeugopod bones of the wing and leg are formed by subtly different signalling and patterning events during embryonic development, which can be used to understand the shaping of the bird wing skeleton during the evolution of powered flight.

developmental biology↗

bioRxiv2021

Cohesin is required for long-range enhancer action

The mammalian genome is organised into topologically associating domains (TADs) that are formed through the process of cohesin-driven loop extrusion1-3 and whose extent is constrained at TAD boundaries by orientation-dependent CTCF binding4-7. The large regulatory landscapes of developmental genes frequently correspond to TADs, leading to the hypothesis that TADs and/or loop extrusion are important for enhancers to act on their cognate gene8,9. However, it has proven hard to interpret the consequences of experimental disruption of TADs or loop-extrusion on gene regulation3,6,10, in part because of the difficulty in distinguishing direct from indirect effects on enhancer-driven gene expression. By coupling acute protein degradation with synthetic activation by targeted transcription factor recruitment in mouse embryonic stem cells, here we show that cohesin, but not CTCF, is required for activation of a target gene by distant distal regulatory elements. Cohesin is not required for activation directly at the promoter or activation from an enhancer located closer to the gene. Our findings support the hypothesis that chromatin compaction mediated by cohesin-mediated loop extrusion allows for genes to be activated by regulatory elements that are located many hundreds of kilobases away in the linear genome but suggests that cohesin is dispensable for more genomically close enhancers.

genetics↗

bioRxiv2019

A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development

Enhancers that are conserved deep in evolutionary time regulate characteristics held in common across taxonomic classes. Here, deletion of the highly conserved Shh enhancer SBE2 (Shh brain enhancer 2) markedly reduced Shh expression within the embryonic brain specifically in the rostral diencephalon; however, no abnormal anatomical phenotype was observed due to compensatory low levels of expression mediated by a second enhancer. In contrast, a further reduction of Shh levels, achieved by crossing the SBE2 deletion with the Shh null allele, disrupted brain and craniofacial tissue; thus, linking SBE2 regulated Shh expression to multiple defects and further enabling the study of the effects of differing levels of Shh on embryogenesis. Development of the hypothalamus, derived from the rostral diencephalon, was disrupted along both the anterior-posterior (AP) and the dorsal-ventral (DV) axes. Expression of DV patterning genes and subsequent neuronal population induction were particularly sensitive to Shh expression levels, demonstrating a novel morphogenic context for Shh. The role of SBE2, which is highlighted by DV gene expression, is to step-up expression of Shh above the minimal activity of the second enhancer, ensuring the necessary levels of Shh in a regional-specific manner. We also show that low Shh levels in the diencephalon disrupted neighbouring craniofacial development, including mediolateral patterning of the bones along the cranial floor and viscerocranium. Thus, SBE2 contributes to hypothalamic morphogenesis and ensures there is coordination with the formation of the adjacent midline cranial bones that subsequently protects the neural tissue.

developmental biology↗