Biology subjects

Marco-Ferreres, R.

Publications and source records attributed to Marco-Ferreres, R..

4 recordsLinked to original sources

bioRxiv2025

Reducing the environmental footprint of laboratory research using visual communications: A pilot study in Spain

Addressing the environmental impact of laboratory research provides a meaningful opportunity for workplace-level mitigation. However, in Spain, the importance of sustainability in research is only starting to be recognised at a national level. We developed a scalable, visual-oriented communications strategy that was designed with input from scientific staff and included a live seminar and a coherent set of graphic materials. Five pillars were targeted: three key areas of consumption (energy, water, and plastic use), procurement, and colleague engagement. The scheme was piloted in two of the largest biomedical research centres in Spain: the Severo Ochoa Molecular Biology Centre (CBM) and the Spanish National Centre for Biotechnology (CNB). The pilot engaged 50 laboratories and services across both centres, of which 34 were followed up for 5 months. The results indicate engagement with sustainability measures and shifts toward best practice across metrics, including equipment switch-off, water use, plastic item reuse, and purchasing decisions. During the follow-up period, 23% of participants adopted new measures related to freezer maintenance, decluttering, or sample organization, 55% removed old data from storage to save energy, 100% reduced their use of lifts, and 94% discussed research sustainability with their laboratory/group. The findings also revealed key areas for improvement, including the management of shared resources and resistance to change protocols. These results offer a wide range of quantitative and qualitative insights to guide further efforts and scaling at regional and national levels. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/675379v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@b50baeorg.highwire.dtl.DTLVardef@11ccdeorg.highwire.dtl.DTLVardef@a13b46org.highwire.dtl.DTLVardef@13a9b0b_HPS_FORMAT_FIGEXP M_FIG C_FIG Sustainability spotlightThis paper describes a scalable, visual-oriented communications strategy that can be used to promote sustainable behaviours in research laboratories. We present pilot results indicating engagement in sustainability and shifts toward best practice across metrics. Our work contributes to UN Sustainable Development Goal (SDG) 9 (industry and infrastructure) and SDG 12 (responsible consumption and production).

scientific communication and education↗

bioRxiv2025

Chip (Ldb1) is a new cofactor of Zelda forming a functional bridge to CBP during zygotic genome activation

The cofactor Ldb1 (Chip) is linked to many processes in gene regulation, including enhancer-promoter communication, inter-chromosomal interactions and enhanceosome-cofactor-like activity. However, its functional requirement and molecular role during embryogenesis has not been assessed to date. Here, we used optogenetics (iLEXY), to rapidly deplete Drosophila Ldb1 (Chip) from the nucleus at precise time windows. Remarkably, this pinpointed the essential window of Chips function in just one-hour of embryogenesis, overlapping zygotic genome activation (ZGA). We show that Zelda, a pioneer factor essential for ZGA, recruits Chip to chromatin, and both factors regulate concordant changes in gene expression, suggesting that Chip is a cofactor of Zelda. Surprisingly, Chip is not required for chromatin architecture at these stages, instead it recruits CBP, and is essential for the placement of H3K27ac. Taken together, our results identify Chip (Ldb1) as a functional bridge between Zelda and the coactivator CBP to regulate gene expression in early embryogenesis.

genomics↗

bioRxiv2022

New enhancer-promoter interactions are gained during tissue differentiation and reflect changes in E/P activity

To regulate gene expression, enhancers must come into proximity with their target gene. At some loci the timing of enhancer-promoter proximity is uncoupled from gene activation, while at others it is tightly linked. Here, we assessed this more globally for 600 characterized enhancers or promoters (E/P) with tissue-specific activity in Drosophila embryos, by performing Capture-C and insulator ChIP in FACS-purified myogenic or neurogenic cells at different stages of embryogenesis. This high-resolution view enabled direct comparison between E/P interactions and activity across 5 developmental conditions. This revealed largely invariant E/P contacts between the blastoderm and cell fate specification stages, despite changes in activity. However, E/P interactions diverge during terminal tissue differentiation when many tissue-specific interactions are gained on top of a pre-existing topology. Changes in E/P proximity reflect changes in enhancer activity and gene activation, and are generally not accompanied by changes in insulator binding. Using transgenes and deletions, we show that many tissue-specific interactions represent functional E-P pairs. Our results reveal a shift in E-P landscapes as embryogenesis proceeds, from largely pre-formed topologies at early stages to more distal tissue-specific loops during differentiation, when E/P proximity appears coupled to activation.

developmental biology↗

bioRxiv2017

The cis-regulatory dynamics of embryonic development at single cell resolution

Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types.

genomics↗