Biology subjects

Makalowska, I.

Publications and source records attributed to Makalowska, I..

4 recordsLinked to original sources

bioRxiv2024

Application of a new data management system to the study ofthe gut microbiome of children who are small for theirgestational age

Microbiome studies aim to answer the following questions: which organisms are in the sample and what is their impact on the patient or the environment? To answer these questions, investigators have to perform comparative analyses on their classified sequences based on the collected metadata, such as treatment, condition of the patient, or the environment. The integrity of sequences, classifications, and metadata is paramount for the success of such studies. Still, the area of data management for the preliminary study results appears to be neglected. Here, we present the development of a central data management system with an accessible web interface for the study of the gut microbiome in children who are small for their gestational age. We have called this system MetagenomicsDB. The web interface allows users, regardless of their bioinformatics expertise, to operate the system. The interface contains links to external resources in order to facilitate literature search, statistical analyses, and assessments of the potential pathogenicity of taxa. Preliminary study results are automatically quality-controlled and subsequently imported into a relational database. After exploration and optional filtering by the user, data are exported in a format directly suitable for follow-up analyses. Compared to a more conventional approach of storing the data in plain files, the automated quality control and database storage offered by MetagenomicsDB provides an enhanced quality assurance of the produced study results. This is especially true in a collaborative setting. Also, the automation of the data transfer from the format of the input data to the format needed for downstream analyses makes basic statistical and bioinformatic analyses accessible. The web interface not only allows us to perform our internal analyses, but will also facilitate transparent sharing of the complete study results at publication time with reviewers and the general public. We demonstrated the viability of this approach by making a subset of our preliminary study results already publicly accessible: https://www.bioinformatics.uni-muenster.de/tools/metagenomicsDB In the context of our study, our system provided more flexibility to conduct study- specific analyses and to integrate specific external resources than existing and necessarily more generic solutions. Our system is not yet ready to be widely applicable out-of-the-box for any microbiome study. However, we expect that due to the modular concept, the tests, and the extensive description of the underlying rationale, large parts of our implementation can be adapted for future projects in a fraction of the time needed to develop a new data management system from scratch. Thus, we report our endeavors in order to motivate the application of data management systems at the scale of single studies in microbiome research.

bioinformatics↗

bioRxiv2023

5' extended protein-coding INO80E transcript regulates expression of two head-to-head overlapping genes: INO80E and HIRIP3

The INO80E gene encodes the protein involved in the chromatin remodeling processes as a part of the multi-subunit INO80-chromatin remodeling complex. The INO80E gene is located on chromosome 16 and overlaps head-to-head with the HIRIP3 gene encoding protein, which binds H2B and H3 core histones and HIRA protein and regulates the chromatin and histone metabolism. Antisense transcription of head-to-head overlapping PC genes may have several consequences and none of them have been comprehensively investigated and explained. Here, we determined that INO80E-201, which overlaps the HIRIP3 gene transcripts, forms an R-loop at its 5 end. We also demonstrated that overlapping transcripts of INO80E and HIRIP3 form an RNA:RNA duplex that has the stabilizing effect on the involved mRNAs. Our results confirmed that this stabilization could be mediated by the ELAVL1 protein. We additionally introduced de novo methylation using the CRISPR/Cas system into the promoter sequence of INO80E gene. As a result of the introduced changes, reduced expression of HIRIP3 and INO80E gene transcripts was observed. It was determined that methylated cytosines were located in the binding sites for four transcription factors including RARG, which was further confirmed to be important in the transcription of both studied genes. Our results strongly suggest that the formation of an RNA:RNA duplex is necessary for stable simultaneous expression of both genes. Lack of this dsRNA structure results in a loss of a wider DNA opening and in consequence transcriptional interference. We also concluded that forming R-loops probably plays only a supplementary role and is not required for proper expression of HIRIP3 and INO80E gene transcripts.

molecular biology↗

bioRxiv2023

Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells

U7 snRNA is part of U7 snRNP, a complex required for the 3end processing of replication-dependent histone pre-mRNAs in the S phase of the cell cycle. During this maturation event, the 5 region of U7 snRNA hybridizes with the highly complementary sequence present in the 3UTR of histone pre-mRNAs, called histone downstream element, HDE. This base-pair interaction triggers subsequent reactions that eventually result in cleavage and release of mature histone transcripts. Intriguingly, U7 snRNP is constitutively expressed throughout the cell cycle and in nondividing cells, suggesting another function of U7 snRNA/snRNP in cells. Here, we show that several human endogenous retroviruses (HERVs) are significantly upregulated in HEK293T cells with U7 snRNA knockdown. They predominantly belong to the LTR12 class. Interestingly, some of them are located within long intergenic noncoding RNAs (lincRNAs), which in turn are upregulated in U7 snRNA knockdown cells as well. Significantly, both these HERV1/LTR12s and lincRNAs contain two or more sequence motifs that perfectly match the 5 end of U7 snRNA, which we called HDE-like motifs. We confirmed that mutations within the HDE-like motifs abrogate U7 snRNA regulatory function and stimulate the expression of selected lincRNAs. Furthermore, we demonstrate that U7 snRNA inhibits HERV1/LTR12 and lincRNA expression at the transcription level. We propose a mechanism in which U7 snRNA hampers binding/activity of NF-Y transcription factor to CCAAT motifs that are frequently found in LTRs as well as in a close proximity to HDE-like motifs. The expression of many HERV1/LTR12s and lincRNAs regulated by U7 snRNA seems to be tissue specific, therefore, we suggest that U7 snRNA plays a protective role in keeping deleterious genetic elements in silence in selected types of cells.

molecular biology↗

bioRxiv2018

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression

FUS is a multifunctional protein involved in many steps of RNA metabolism, including transcription, splicing, miRNA processing and replication-dependent histone gene expression. In this paper, we show for the first time that FUS binds and negatively regulates the levels of a subset of snoRNAs in cells. Scanning of available human small RNA databases revealed the existence of smaller RNA fragments that can be processed from FUS-dependent snoRNAs. Therefore, we suggest that FUS mediates the biogenesis of snoRNA-derived small RNAs, called sdRNAs. Further in silico approaches enabled us to predict putative targets of selected FUS-dependent sdRNAs. Our results indicate that sdRNAs may bind to different regions of target mRNAs as well as to noncoding transcripts and influence the posttranscriptional level or translation of these targets. SIGNIFICANCE STATEMENTRNA metabolism is orchestrated by a complex network of RNA-protein interactions and involves various classes of RNA molecules. Small nucleolar RNAs (snoRNAs) are commonly considered essential components of the ribosome biogenesis pathway. However, recent studies have revealed that snoRNAs can also be fragmented into small entities called snoRNA-derived RNAs (sdRNAs), which have been linked to multiple cancer types and thus may serve as next-generation prognostic or diagnostic biomarkers. In this paper, a multifunctional protein, FUS, was shown to be involved in the biogenesis of snoRNA-derived fragments. Furthermore, we combined bioinformatic analyses with complementary experimental approaches to elucidate the role of FUS-dependent sdRNAs in gene expression regulation. Our findings reveal the considerable regulatory potential of this new class of small noncoding RNAs.

molecular biology↗