Biology subjects

Maass, P. G.

Publications and source records attributed to Maass, P. G..

7 recordsLinked to original sources

bioRxiv2026

A Distributed Architectural Code Governs DNA Repair

Repair of DNA double-strand breaks (DSBs) depends on large-scale changes in nuclear shape and genome organization. How damage signaling coordinates such remodeling remains unclear. We find that the human DNA damage response (DDR) couples interdependent, temporally ordered tubulin modifications to nuclear membrane and lipid regulation, driving nuclear reshaping (nucleomorphosis) through DSB-capturing nuclear envelope tubules (dsbNETs). Tubulin detyrosination by vasohibins 1/2 (VASH1/2) and acetylation by -tubulin acetyltransferase 1 (ATAT1) promote dsbNET formation and support both homologous recombination and non-homologous end joining. Microtubule-dependent processes also promote the phosphorylation-dependent inactivation of the membrane stress-sensing lipid regulator CTP cytidylyltransferase- (CCT), which typically restrains baseline nuclear lipid droplets (nLDs) and dsbNETs while supporting ATR signaling. Damage-induced nLD formation requires diacylglycerol acyltransferases 1/2 (DGAT1/2) and supports dsbNETs. Our findings reveal a distributed architectural code spanning interconnected cytoskeletal, membrane, and lipid regulators. This code governs nucleomorphosis and its role in DNA repair and genome stability.

molecular biology↗

bioRxiv2023

DNA double-strand break-capturing nuclear envelope tubules drive DNA repair

The nuclear envelope is a membrane separating nuclear from cytoplasmic processes. Existing models suggest that damaged DNA moves to the envelope at the edge of the nucleus for repair. Yet, most damaged human DNA does not reposition to the nuclear periphery during repair. Here we show that human cells relocate the nuclear envelope to non-peripheral damaged DNA, providing solid support promoting the reconnection of DNA break ends. Upon DNA double-strand break (DSB) induction, cytoplasmic microtubules poke the nuclear envelope inwards, inducing an extensive network of DSB-capturing nuclear envelope tubules (dsbNETs). The formation of dsbNETs, which encompass the nuclear lamina and the inner and outer nuclear membranes, depends on DNA damage response kinases, dynamic microtubules, the linker of the nucleoskeleton and cytoskeleton (LINC) proteins SUN1 and SUN2, nuclear pore protein NUP153, and kinesin KIF5B. Repressing dsbNETs compromises the reassociation of DSB ends. The timely reversal of dsbNETs by the kinesin KIFC3 also promotes repair. DSB ends reconnection is restored in dsbNETs-deficient cells by enlarging the 53BP1 DNA repair center. The lamina-binding domain of SUN1 mediates its entry into the tubules and DSB capture by the envelope. Fusing truncated SUN1 to the NHEJ repair protein KU70 fails to localize SUN1 to the tubules but rescues DSB targeting only to the boundary envelope. Although dsbNETs typically promote accurate DSB repair and cell survival, they are co-opted by the PARP inhibitor olaparib to induce aberrant chromosomes restraining BRCA1-deficient breast cancer cells. We uncover dsbNETs, which bring the nuclear envelope to DSBs for repair and potentiate the efficacy of anti-cancer agents. Our findings revise theories of the structure-function relationship of the nuclear envelope and identify dsbNETs as a critical factor in DNA repair and nuclear organization, with implications for health and disease.

molecular biology↗

bioRxiv2021

Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.

molecular biology↗

bioRxiv2021

Environmental enrichment induces epigenomic and genome organization changes relevant for cognitive function

In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization. Highlights- Environmental enrichment (EE) alters chromatin conformation, CTCF binding, and spatially 3D genome changes, thereby regulating cognitive function during the first steps of life after birth. - Transcription-associated gene body marks H3K79me2 and H3K36me3 are differently influenced by EE in cortical brain cells and binding is exacerbated upon stimulation in an age-dependent manner. - EE-induced changes of 3D genome organization increase inter-chromosomal interactions of genes associated with synaptic transmission and AMPA receptor genes on chromosomes 7 and 17.

neuroscience↗

bioRxiv2019

Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation

Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants in close proximity to the target gene, trans effects are due to distal genetic variants that affect diffusible elements such as transcription factors. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we used massively parallel reporter assays to directly measure cis and trans effects between human and mouse embryonic stem cells at thousands of individual regulatory elements. Our approach revealed that cis effects are widespread across regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we found that trans effects are rare but stronger in enhancers than promoters, and can be attributed to a subset of transcription factors that are differentially expressed between human and mouse. While previous studies have found extensive co-occurrence of cis and trans effects in opposite directions that stabilize gene expression throughout evolution, we find that cis-trans compensation is uncommon within individual regulatory elements. Thus, our results are consistent with a model wherein compensatory cis-trans effects at the gene level are explained by cis and trans effects that separately impact several regulatory elements rather than cis-trans effects that occur simultaneously within a single regulatory element. Together, these results indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.

genomics↗

bioRxiv2018

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity

Transcription initiates at both coding and non-coding genomic elements, including mRNA and long non-coding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each class has different expression profiles with lncRNAs and eRNAs being the most tissue-specific. How these complex differences in expression profiles and tissue-specificities are encoded in a single DNA sequence, however, remains unresolved. Here, we address this question using computational approaches and massively parallel reporter assays (MPRA) surveying hundreds of promoters and enhancers. We find that both divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than non-divergent lncRNA and mRNA core promoters, respectively. Conversely, lincRNAs and eRNAs have lower capacities to drive transcription and are more tissue-specific than divergent genes. This higher tissue-specificity is strongly associated with having less complex TF motif profiles at the core promoter. We experimentally validated these findings by testing both engineered single-nucleotide deletions and human single-nucleotide polymorphisms (SNPs) in MPRA. In both cases, we observe that single nucleotides associated with many motifs are important drivers of promoter activity. Thus, we suggest that high TF motif density serves as a robust mechanism to increase promoter activity at the expense of tissue-specificity. Moreover, we find that 22% of common SNPs in core promoter regions have significant regulatory effects. Collectively, our findings show that high TF motif density provides redundancy and increases promoter activity at the expense of tissue specificity, suggesting that specificity of expression may be regulated by simplicity of motif usage.

genomics↗

bioRxiv2017

High-throughput identification of RNA nuclear enrichment sequences

One of the biggest surprises since the sequencing of the human genome has been the discovery of thousands of long noncoding RNAs (lncRNAs)1-6. Although lncRNAs and mRNAs are similar in many ways, they differ with lncRNAs being more nuclear-enriched and in several cases exclusively nuclear7,8. Yet, the RNA-based sequences that determine nuclear localization remain poorly understood9-11. Towards the goal of systematically dissecting the lncRNA sequences that impart nuclear localization, we developed a massively parallel reporter assay (MPRA). Unlike previous MPRAs12-15 that determine motifs important for transcriptional regulation, we have modified this approach to identify sequences sufficient for RNA nuclear enrichment for 38 human lncRNAs. Using this approach, we identified 109 unique, conserved nuclear enrichment regions, originating from 29 distinct lncRNAs. We also discovered two shorter motifs within our nuclear enrichment regions. We further validated the sufficiency of several regions to impart nuclear localization by single molecule RNA fluorescence in situ hybridization (smRNA-FISH). Taken together, these results provide a first systematic insight into the sequence elements responsible for the nuclear enrichment of lncRNA molecules.

genomics↗