Biology subjects

Nowacki, M.

Publications and source records attributed to Nowacki, M..

5 recordsLinked to original sources

bioRxiv2026

Cholesterol transport cycle of human ABCA2

Cholesterol is a key component of cellular membranes and is critical for brain function, particularly axon myelination. Among the 48 human ATP-binding cassette (ABC) transporters, ABCA2 exhibits the highest expression in the brain and is involved in cholesterol metabolism, primarily in oligodendrocytes. Notably, ABCA2 has been associated with myelin sheath integrity and maintenance, as well as Alzheimer's disease. Here, we report cryo-EM structures of human ABCA2 that reveal critical endogenous lipid-binding sites unique to ABCA2. Our five distinct conformations include a previously uncharacterized intermediate between the closed and apo states of ABCA subfamily transporters. Most importantly, we elucidated the cholesterol transport mechanism of ABCA2, which involves novel interdependent rotations of the exocytoplasmic domains (ECDs) and regulatory domains (RDs). Our structural findings provide a new perspective on ABCA transporter function and highlight the role of ABCA2 in facilitating efficient cholesterol recycling and transport in the brain.

molecular biology↗

bioRxiv2026

N6-methyldeoxyadenosine is a transgenerational epigenetic mark protecting DNA from deletion

DNA N6-adenine methylation (6mA) is emerging as an important DNA modification present in all eukaryotic kingdoms, where its roles mostly involve transcriptional regulation and chromatin modification. Here, we demonstrate a distinct role for 6mA in Paramecium tetraurelia. We find that it is a trans-generational epigenetic mark which distinguishes host DNA from invasive elements, protecting the former. During development, Paramecium deletes around 25% of its germline genome, removing TEs, repetitive sequences and transposon-derived elements, to form a functional somatic genome. We show that 6mA is present in the Paramecium germline nucleus, where it is preferentially located on host DNA and excluded from TEs. Ectopic addition of 6mA to germline DNA causes failure to excise TE-derived sequences, leading to lethality. 6mA presence on a synthetic TE-derived element is sufficient to block its excision during development. These effects are inherited via sexual reproduction, demonstrating their trans-generational capacity.

cell biology↗

bioRxiv2025

Germline-limited transposon remnants foster somatic genome diversification

Transposable elements are mobile DNA sequences that propagate within genomes, often with deleterious effects on host fitness. Some organisms excise transposons from their somatic genomes via programmed DNA elimination yet paradoxically retain them in their germline. The evolutionary rationale for this selective retention remains poorly understood. To address this, we first set out to develop a germline enrichment method in Paramecium tetraurelia, since the somatic DNA is several hundred times more abundant than the transposon-rich germline. Our approach improved the germline assembly significantly by reducing the number of contigs from the previously published 26186 to just 179, close to the expected chromosomal count. Contrary to the view that the germline serves merely for transgenerational genome propagation, long-read sequencing of poly(A)+ RNA uncovered abundant coding transcripts derived from germline-limited DNA. Furthermore, we detected numerous modified somatic transcripts caused by incorporation of ultrashort transposon remnants from germline sequences. Notably, these insertions show a size bias that preserves open reading frames, consistent with translation mediated quality control. Together, our results suggest that the germ-soma nuclear dimorphism serves as an intrinsic system for the emergence of genome innovations and transcriptome diversification through the retention of germline-limited sequences.

cell biology↗

bioRxiv2023

ISWI1 complex proteins facilitate developmental genome editing in Paramecium

Chromatin remodeling is required for essential cellular processes, including DNA replication, DNA repair, and transcription regulation. The ciliate germline and soma are partitioned into two distinct nuclei within the same cell. During a massive editing process that forms a somatic genome, ciliates eliminate thousands of DNA sequences from a germline genome copy in the form of internal eliminated sequences (IESs). Recently we showed that the chromatin remodeler ISWI1 is required for somatic genome development in the ciliate Paramecium tetraurelia. Here we describe two paralogous proteins, ICOP1 and ICOP2, essential for DNA elimination. ICOP1 and ICOP2 are highly divergent from known proteins; the only domain detected showed distant homology to the WSD motif. We show that both ICOP1 and ICOP2 interact with the chromatin remodeler ISWI1. Upon ICOP knockdown, changes in alternative IES excision boundaries and nucleosome densities are similar to those observed for ISWI1 knockdown. We thus propose that a complex comprising ISWI1 and either or both ICOP1 and ICOP2 are needed for chromatin remodeling and accurate DNA elimination in Paramecium.

molecular biology↗

bioRxiv2022

RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA.

Small RNAs are known to mediate silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. Post-zygotic development of the Paramecium somatic genome requires elimination of thousands of transposon remnants (IESs) and transposable elements that are scattered throughout the germline genome (Garnier et al. 2004). The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries (Bouhouche et al. 2011; Furrer et al. 2017). Previous research suggests that small RNAs induce heterochromatin formation within IESs, which, in turn, is required for DNA elimination (Liu et al. 2007). Here we show that IES recognition and precise excision is facilitated by recruitment of a homolog of a chromatin remodeler ISWI, which depletes target genomic regions of nucleosomes, making the chromatin accessible for DNA cleavage. ISWI knockdown in Paramecium leads to pronounced inhibition of DNA elimination. Furthermore, nucleosome profiling indicates that ISWI is required for IES elimination in nucleosome-dense genomic regions, while other IESs do not require small RNAs or ISWI for excision. ISWI silencing notably also reduces DNA elimination precision, resulting in aberrant excision at alternative IES boundaries. In summary, we demonstrate that chromatin remodeling that increases DNA accessibility together with small RNAs are necessary for efficient and precise DNA elimination in Paramecium.

molecular biology↗