Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module

Integrator (INT) is a transcriptional regulatory complex associated with RNA polymerase II that is required for the 3′-end processing of both UsnRNAs and enhancer RNAs. Integrator subunits 9 (INTS9) and INTS11 constitute the catalytic core of INT and are paralogues of the cleavage and polyadenylation specificity factors CPSF100 and CPSF73. While CPSF73/100 are known to associate with a third protein called Symplekin, there is no paralog of Symplekin within INT raising the question of how INTS9/11 associate with the other INT subunits. Here, we have identified that INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually. Although INTS4 has no significant homology with Symplekin, it possesses N-terminal HEAT repeats similar to Symplekin but also contains a β-sheet rich C-terminal region, both of which are important to bind INTS9/11. We assess three functions of INT including UsnRNA 3′-end processing, maintenance of Cajal body structural integrity, and formation of histone locus bodies to conclude that INTS4/9/11 are the most critical of the INT subunits for UsnRNA biogenesis. Altogether, these results indicate that INTS4/9/11 compose a heterotrimeric complex that likely represents the Integrator ‘cleavage module’ responsible for its endonucleolytic activity.

Cajal bodies are linked to genome conformation

The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

Nuclear bodies can nucleate at sites of active transcription and are beneficial for efficient gene expression. Here, the authors show that Cajal bodies, a prominent type of nuclear body, contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

SRSF1 splicing factor and nuclear-localized MALAT1 RNA influence the assembly of nuclear speckles. Depletion of SRSF1 compromises the association of splicing factors to nuclear speckles and influences the levels of other SR proteins. SRSF1 regulates RNA polymerase II–mediated transcription.

The mammalian cell nucleus is compartmentalized into nonmembranous subnuclear domains that regulate key nuclear functions. Nuclear speckles are subnuclear domains that contain pre-mRNA processing factors and noncoding RNAs. Many of the nuclear speckle constituents work in concert to coordinate multiple steps of gene expression, including transcription, pre-mRNA processing and mRNA transport. The mechanism that regulates the formation and maintenance of nuclear speckles in the interphase nucleus is poorly understood. In the present study, we provide evidence for the involvement of nuclear speckle resident proteins and RNA components in the organization of nuclear speckles. SR-family splicing factors and their binding partner, long noncoding metastasis-associated lung adenocarcinoma transcript 1 RNA, can nucleate the assembly of nuclear speckles in the interphase nucleus. Depletion of SRSF1 in human cells compromises the association of splicing factors to nuclear speckles and influences the levels and activity of other SR proteins. Furthermore, on a stably integrated reporter gene locus, we demonstrate the role of SRSF1 in RNA polymerase II–mediated transcription. Our results suggest that SR proteins mediate the assembly of nuclear speckles and regulate gene expression by influencing both transcriptional and posttranscriptional activities within the cell nucleus.

Activation of beta-catenin signaling pathways by classical G-protein-coupled receptors: mechanisms and consequences in cycling and non-cycling cells

Wnt signaling pathways are some of the most intensely studies in all of biology. Recently, a number of classical heterotrimeric G protein coupled receptors (GPCRs) have been shown to activate the canonical Wnt pathway, culminating in the stabilization of beta-catenin and induction of transcription of genes regulated by the Tcf/Lef family of transactivators. However, mechanisms by which these GPCRs accomplish this differ in key ways, and in some circumstances, the phenotypes produced are novel. Herein, we will examine mechanisms by which classical GPCRs interact with the canonical Wnt pathway, culminating in its activation, and describe the consequences of this activation, focusing on the heart. In the heart, the contractile cells, or cardiomyocytes, are terminally differentiated and virtually exclusively grow by increasing cell size (hypertrophy) rather than cell number, and we will describe how GPCR-mediated activation of the canonical pathway can drive this process.

[Clinical and molecular genetic investigation of Waardenburg syndrome type 1]

Hypoacusis is a common sensory defect in humans which creates problems in communication. Heredity is essential in etiology of hypoacusis and deafness. Genes PAX3 and MITF were studied in patients with Vaardenburg syndrome in 14 unrelated families. Five mutation defects in the gene PAX3 were found. This provided the final diagnosis of the syndrome in these families.

Two novel low-density lipoprotein receptor gene mutations (E397X and 347delGCC) in St. Petersburg familial hypercholesterolemia

Familial hypercholesterolemia (FH), a monogenic disease known to be caused by low-density lipoprotein receptor (LDLR) gene mutations, results in the development of premature atherosclerosis and coronary artery disease in affected individuals. The spectrum of LDLR gene mutations in Russia is poorly known. Using polymerase chain reaction (PCR)-single-strand conformational polymorphism (SSCP) analysis, followed by DNA sequencing, we have screened selected exons of the LDLR gene in 80 unrelated St. Petersburg FH patients for the presence of mutations. Two new LDLR gene mutations, 347delGCC and E397X, were characterized among individuals with familial hypercholesterolemia in St. Petersburg. The carriers of both mutations possessed highly elevated blood serum cholesterol. Cosegregation of E397X mutation and LDLR gene RFLP haplotypes with hyperlipidemia was demonstrated by family study. Both mutations seem to be specific to Slavic patients.

Two novel slavic point mutations in the low-density lipoprotein receptor gene in patients with familial hypercholesterolemia from St. Petersburg, Russia

Using PCR-single-strand conformation polymorphism analysis, followed by sequencing of the abnormal samples, two novel point mutations in the 5' end of the fourth exon of the low-density lipoprotein receptor gene were found in two Russian families with familial hypercholesterolemia. These missense mutations consist of C127W and C139G transitions and result in a loss of one of three disulfide bonds in the fourth cysteine-rich repeat of the ligand-binding domain of the low-density lipoprotein receptor. Hypercholesterolemia segregated with the identified mutations.

[Absence of DNA polymorphisms on the region of the APOV gene coding the proposed low density lipoprotein-binding domain of the ApoB-100 protein]

To reveal the molecular basis of hereditary diathesis to hypercholesterolemia, single-strand conformation polymorphism (SSCP) analysis and subsequent sequencing were used to study structural organization of the APOB gene for apolipoprotein B-100 (ApoB-100). The gene region encoding a putative low density lipoprotein (LDL) receptor binding domain was analyzed in patients with myocardial infarction (MI). Differences in structure of the gene between patients with MI and healthy people were not detected.

Nonisotopic identification of two point mutations in the CYP21 gene responsible for nonclassic 21-hydroxylase deficiency

A simple nonradioactive method was developed for identification of the Pro-30-Leu and Val-281-Leu mutant alleles in the CYP21B gene. Not only does this approach improve mutation analysis for patients with the late onset form of 21-hydroxylase deficiency, but it also decreases problems with interference by the CYP21A pseudogene sequence.

[Amplification of DNA for 15-30 minutes in single-use pipette tips]

Amplification of 200-1000-bp DNA fragments was performed in 15-30 min using a rapid thermal cycler based on the commercial instrument TC-1000-1 (IRLEN, St. Petersburg, Russia). Plastic pipette tips were used as thin walled, high surface to volume-ratio tubes, to increase the rate of heating (cooling) of 20 microliters samples, which allowed the time required for DNA amplification to be considerably reduced (5-10 times).

A rapid and simple DNA fingerprinting method using RFLP and SSCP analysis of the hypervariable noncoding region of human mitochondrial DNA

A simple method for identification of individuals and maternity testing has been developed. This technique includes PCR amplification of the 199-bp hypervariable portion of the noncoding region of human mtDNA, digestion with RsaI and subsequent SSCP analysis of restriction fragments with DNA silver staining. Using this approach we have analysed the DNA fingerprint patterns of the family members. The fingerprints of maternally related individuals appeared to be identical in three generations, while maternally unrelated members of the family showed differences in their fingerprints, either in SSCP or both RFLP and SSCP patterns. Sequencing data have confirmed the results obtained. Further DNA fingerprinting analysis of 19 unrelated mother-child pairs by means of the method described revealed complete identity of the fingerprint patterns within the pairs. The probability of a random fingerprint match for two maternally unrelated individuals was estimated as 8%.

Approach to identification of a point mutation in apo B100 gene by means of a PCR-mediated site-directed mutagenesis

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