Biology subjects

Alcaraz, N.

Publications and source records attributed to Alcaraz, N..

8 recordsLinked to original sources

bioRxiv2026

CREPAS: a reproducible nascent chromatin sequencing analysis pipeline for epigenome replication studies

Chromatin-based genomics data are essential for understanding genome regulation and the mechanisms underlying epigenetic memory. Recent methods such as ChOR-seq and SCAR-seq assess histone modifications and chromatin-associated proteins during and after replication, capturing chromatin states that contribute to memory across cell divisions. Current tools for chromatin data analysis lack scalability and reproducibility across computing infrastructures, offer limited parameters, and are applicable only to a few sequencing techniques, ignoring the information from nascent chromatin assays. To address these challenges, we developed CREPAS, a Nextflow pipeline for analyzing nascent and parental chromatin sequencing data, including ChIP-seq, ChOR-seq, SCAR-seq, OK-seq, ATAC-seq, CUT&RUN, and CUT&Tag, and derivative protocols. CREPAS provides an end-to-end solution, from quality control to advanced analyses, including downsampling, peak calling, annotation, and visualization. By harnessing quantitative assays such as qChIP-seq and qChOR-seq, the normalization methods in CREPAS allow to compare the restoration kinetics of individual marks or proteins across replication timepoints. Moreover, the pipeline includes calculations such as fork directionality and partitioning using OK-seq and SCAR-seq data, linking replication dynamics to epigenetic inheritance. CREPAS is a valuable resource that enhances the efficiency and reproducibility of nascent chromatin sequencing data analyses, enabling the study of chromatin replication and propagation of epigenetic states. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/732899v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@11634b8org.highwire.dtl.DTLVardef@df2e07org.highwire.dtl.DTLVardef@46d117org.highwire.dtl.DTLVardef@14950a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Mapping active cis-regulatory elements from transcription initiation events

Determining the activity of cis-regulatory elements (CREs) is essential for modeling gene regulation and interpreting genetic variation. Yet, current methods often lack the specificity to distinguish active regulation from permissive chromatin, the sensitivity to detect unstable enhancer RNAs, or the scalability required to profile limited input material and primary cells. Here, we introduce nucCAGE, a transcription start site (TSS) assay for profiling nuclear, capped RNAs, and PRIME, a computational framework for identifying active CREs from TSS data. Together, these methods increase sensitivity to low-abundance RNAs and enable robust detection of active regulatory elements across diverse contexts. Across multiple orthogonal functional and genetic benchmarks, including fine-mapped eQTLs, ClinVar variants, GWAS loci, and CRISPRi-tested elements, nucCAGE-derived PRIME predictions achieve superior recall compared to state-of-the-art methods while maintaining strong enrichment for phenotype-associated variation. Applying PRIME to the FANTOM5 dataset yields a comprehensive, cell-type-resolved atlas of active CREs that recapitulates known tissue-trait relationships. We demonstrate how this atlas can be used to nominate causal noncoding variants, linking immune-cell enhancer regulation of SMAD3 to asthma and NCOR2 to premature separation of placenta. Together, nucCAGE and PRIME provide a framework for high-sensitivity genome-wide discovery of active CREs and a resource for variant-to-function studies.

genomics↗

bioRxiv2026

Unified function of FACT in mammalian chromatin replication and transcription, dissolving and restoring nucleosomes to counteract genome aggregation

Nucleosomes with their associated modifications underlie genome organisation and regulation. Replication and transcription require nucleosome disassembly to access the DNA template. How this is orchestrated without jeopardizing chromatin function remains unknown. Here, we reveal a general, global requirement of the histone chaperone FACT in mammalian replication, transcription and chromatin maintenance. Upon acute FACT depletion, replisome and RNA polymerase progression is halted genome-wide and chromatin structure in their wake collapses with reduced nucleosome occupancy, irregular spacing and intermediate assemblies. Chromatin states deteriorate as modified histones are lost due to a lack of histone recycling. Chromatin fiber disorder further manifests in the 3D genome, triggering active genes to coalesce in aberrant microcompartments. This establishes a unifying mechanistic basis for mammalian chromatin replication and transcription, with FACT mediating nucleosome disruption and re-assembly and thereby guarding against spurious chromatin aggregation. Nucleosome organization can therefore dynamically regulate genome architecture.

molecular biology↗

bioRxiv2024

Retrotransposon expression is upregulated by aging and suppressed during regeneration of the limb in the axolotl (Ambystoma mexicanum)

The axolotl (Ambystoma mexicanum) has a great capacity to regenerate its tissues and whole-body parts; however, the fidelity and success of its regenerative process diminish with age. Retrotransposons make up the largest portion of the axolotl genome, and their expression may be involved in this age-related decline. Through an integrative analysis of repetitive element expression using RNA-seq, we show that Ty3 retrotransposons are highly upregulated in the axolotl as an effect of chronological aging. Other non-LTR transposons, including LINE-1, function as hubs of gene coexpression networks involved in muscle development, N-methyltransferase activity, amyloid proteolysis, and regulation of apoptosis and connective tissue replacement, which are also suppressed by the increase in age. In contrast, we find that during regeneration of the limb these pathways and the expression of Ty3 retrotransposons are distinctly downregulated. Although the blastema is able to readjust most of the transposon dysregulation caused by aging, there are still several elements that remain affected and may have an impact in the metabolic and immune responses during the regenerative process. We also report that numerous C2H2-ZFPs, especially KRAB-ZPFs, are coexpressed with hub retrotransposons, which reveals their potential as important regulators of transposable element expression during aging and regeneration. This integrative analysis provides a comprehensive profile of retrotransposon expression through chronological aging and during limb regeneration in the axolotl and indicates that transposable elements are responsive to physiological changes in a tissue-specific way and participate in the gene co-regulatory networks underlying the regenerative process. Graphical abstract.Transcriptomic analyses of adult and sub-adult axolotls offer an insight into the potential role of retrotransposons during limb regeneration and how they are affected by chronological aging. Retrotransposons of the Ty3 superfamily are usually suppressed during regeneration, but after experiencing a significant upregulation through the aging of the axolotl, their regulation during tissue repair is limited. It has been reported that the success of the axolotls regenerative process diminishes with age. Our findings show that Ty3 and other transposon families, such as LINE-1, are involved in the gene regulatory networks that suppress muscle development, apoptosis control, and tissue replacement due to aging. These results suggest that repetitive element expression may indirectly constrain the regenerative capacities of older axolotls. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/588033v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1d10844org.highwire.dtl.DTLVardef@75d566org.highwire.dtl.DTLVardef@d4af6org.highwire.dtl.DTLVardef@b47b47_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

Repair of DNA double-strand breaks leaves heritable impairment to genome function

Upon DNA breakage, a genomic locus undergoes alterations in 3-D chromatin architecture to facilitate signaling and repair. While cells possess mechanisms to repair damaged DNA, it is unknown whether the surrounding chromatin is restored to its naive state. We show that a single DNA double-strand break (DSB) within a topologically-associated domain (TAD) harboring conformation-sensitive genes causes lasting chromatin alterations, which persist after completion of DNA repair and feature structural changes, chromatin compaction and loss of local RNA species. Unexpectedly, these newly-acquired features of post-repair chromatin are transmitted to daughter cells and manifest as heritable impairments of gene expression. These findings uncover a hitherto concealed dimension of DNA breakage, which we term post-repair chromatin fatigue, and which confers heritable impairment of gene function beyond DNA repair.

cell biology↗

bioRxiv2021

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability can be largely explained by a promoters DNA sequence and its binding sites for specific transcription factors. We show that promoter expression variability reflects the biological process of a gene, demonstrating a selective trade-off between stability for metabolic genes and plasticity for responsive genes and those involved in signaling. Promoters with a rigid transcription start site architecture are more prone to have variable expression and to be associated with genetic variants with large effect sizes, while a flexible usage of transcription start sites within a promoter attenuates expression variability and limits genotypic effects. Our work provides insights into the variable nature of responsive genes and reveals a novel mechanism for supplying transcriptional and mutational robustness to essential genes through multiple transcription start site regions within a promoter.

genomics↗

bioRxiv2021

Endogenous retroviruses co-opted into divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

Transposable elements are an abundant source of transcription factor binding sites and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable elements, in particular endogenous retroviral elements, carry open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding sites, shedding light on the formation of regulatory programs and the origins of regulatory elements.

genomics↗

bioRxiv2018

The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription

H3K27ac is associated with regulatory active enhancers, but its exact role in enhancer function remains elusive. Using mass spectrometry-based interaction proteomics, we identified the Super Elongation Complex (SEC) and GBAF, a non-canonical GLTSCR1L- and BRD9-containing SWI/SNF chromatin remodeling complex, to be major interactors of H3K27ac. We systematically characterized the composition of GBAF and the conserved GLTSCR1/1L GiBAF-domain, which we found to be responsible for GBAF complex formation and GLTSCR1L nuclear localization. Inhibition of the bromodomain of BRD9 revealed interaction between GLTSCR1L and H3K27ac to be BRD9-dependent and led to GLTSCR1L dislocation from its preferred binding sites at H3K27ac-associated enhancers. GLTSCR1L disassociation from chromatin resulted in genome-wide downregulation of enhancer transcription while leaving most mRNA expression levels unchanged, except for reduced mRNA levels from loci topologically linked to affected enhancers. Our results indicate that GBAF is an enhancer-associated chromatin remodeler important for transcriptional and regulatory activity of enhancers.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=142 HEIGHT=200 SRC=\"FIGDIR/small/445148_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@10c54dborg.highwire.dtl.DTLVardef@9730dforg.highwire.dtl.DTLVardef@9985eorg.highwire.dtl.DTLVardef@1f26844_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗