A computational study of nucleosomal binding and alternative isoforms of human transcription factors

Eukaryotic transcription factors (TFs) are proteins that bind short DNA motifs and regulate gene transcription. Because genomic DNA is organised into nucleosomes via binding histone octamers, TFs compete with histones for binding DNA. Also, the functions of a TF are mainly defined by its domains; therefore, a TF gene can vary the characteristics of its protein product through the expression of alternative isoforms with different domains. However, the mechanisms of TF-nucleosome interactions and the functional importance of alternative TF isoforms are not fully understood. Here, I address these two problems computationally via the integrative analysis of publicly available in vivo human sequencing data. First, I evaluated a novel, gyre-spanning, mode of TF-nucleosome binding proposed recently by another lab based on in vitro evidence. Analysing the nucleosome occupancy and TF binding in the human genome, I found no evidence of such binding and concluded that it must be extremely rare, if at all present. Secondly, I studied the alternative isoforms of human TFs genome-wide. I found that independently of the gene length and the number of exons, TF genes more efficiently sample the set of possible alternative isoforms than non-TF genes, suggesting the particular importance of alternative isoforms for TFs. Also, I found that TF isoforms without a DNA-binding domain (DBD) are produced by almost a third of all human TFs, tend to be tissue-specific and likely reverse the transcription regulation effect of DBD-containing isoforms. Moreover, I demonstrated that the switches of the highest-expressed TF isoforms across human adult tissues may represent a widespread functional mechanism. Finally, I collected a compendium of human TFs with experimentally characterised alternative isoforms which will hopefully serve as a resource for future studies. In summary, my analysis further developed the fundamental knowledge about the TF-nucleosome interactions and the alternative isoforms of TFs in humans.Open Acces

Reduction of SPARC protects mice against NLRP3 inflammasome activation and obesity

The comprehensive assessment of long-term effects of reducing intake of energy (CALERIE-II; NCT00427193) clinical trial established that caloric restriction (CR) in humans lowers inflammation. The identity and mechanism of endogenous CR-mimetics that can be deployed to control obesity-associated inflammation and diseases are not well understood. Our studies have found that 2 years of 14% sustained CR in humans inhibits the expression of the matricellular protein, secreted protein acidic and rich in cysteine (SPARC), in adipose tissue. In mice, adipose tissue remodeling caused by weight loss through CR and low-protein diet feeding decreased, while high-fat diet-induced (HFD-induced) obesity increased SPARC expression in adipose tissue. Inducible SPARC downregulation in adult mice mimicked CR\u27s effects on lowering adiposity by regulating energy expenditure. Deletion of SPARC in adipocytes was sufficient to protect mice against HFD-induced adiposity, chronic inflammation, and metabolic dysfunction. Mechanistically, SPARC activates the NLRP3 inflammasome at the priming step and downregulation of SPARC lowers macrophage inflammation in adipose tissue, while excess SPARC activated macrophages via JNK signaling. Collectively, reduction of adipocyte-derived SPARC confers CR-like metabolic and antiinflammatory benefits in obesity by serving as an immunometabolic checkpoint of inflammation

Analytical “Bake-Off” of Whole Genome Sequencing Quality for the Genome Russia Project Using a Small Cohort for Autoimmune Hepatitis

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence

Genome-wide sequence analyses of ethnic populations across Russia

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country

Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs

RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin

Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis

<div><p>A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (<i>FTCD</i>), plus multiple occurrences of known <i>HLA-DRB1</i> alleles associated with AIH <i>(HLA-DRB1-03</i>:<i>01</i>:<i>01</i>, <i>13</i>:<i>01</i>:<i>01 and 7</i>:<i>01</i>:<i>01</i>). We also list putative SNVs in other genes as suggestive in AIH influence.</p></div

Sample description.

<p>Sample description.</p

Genotype comparison.

<p>(A) Concordance of WGS genotypes with microarray genotypes. The concordance was estimated based on the trio data as the ratio of microarray SNPs with identical genotypes in WGS results. (B) Comparison of the three WGS datasets between each other in terms of precision, sensitivity and F-measure for pairwise comparisons. Color legend is given on the top right. (C) Concordance of genotypes in the three WGS datasets for all variants, SNPs and indels. Color legend is given on the top right.</p

<i>HLA-DRB1</i> and <i>FTCD</i> genotypes.

<p><i>HLA-DRB1</i> and <i>FTCD</i> genotypes.</p