CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions.

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution

Functional assays for the assessment of the pathogenicity of variants of GOSR2, an ER-to-Golgi SNARE involved in progressive myoclonus epilepsies.

Progressive myoclonus epilepsies (PMEs) are inherited disorders characterized by myoclonus, generalized tonic-clonic seizures, and ataxia. One of the genes that is associated with PME is the ER-to-Golgi Qb-SNARE GOSR2, which forms a SNARE complex with syntaxin-5, Bet1 and Sec22b. Most PME patients are homo-zygous for a p.Gly144Trp mutation and develop similar clinical presentations. Recently, a patient who was compound heterozygous for p.Gly144Trp and a previously unseen p.Lys164del mutation was identified. Because this patient presented with a milder disease phenotype, we hypothesized that the p.Lys164del mutation may be less severe compared to p.Gly144Trp. To characterize the effect of the p.Gly144Trp and p.Lys164del mutations, both of which are present in the SNARE motif of GOSR2, we examined the corresponding mutations in the yeast ortholog Bos1. Yeasts expressing the orthologous mutants in Bos1 showed impaired growth, suggesting a partial loss of function, which was more severe for the Bos1 p.Gly176Trp mutation. Using anisotropy and gel filtration, we report that Bos1 p.Gly176Trp and p.Arg196del are capable of complex formation, but with partly reduced activity. Molecular dynamics (MD) simulations showed that the hydrophobic core, which triggers SNARE complex formation, is compromised due to the glycine-to-tryptophan substitution in both GOSR2 and Bos1. In contrast, the deletion of residue p.Lys164 (or p.Arg196del in Bos1) interferes with the formation of hydrogen bonds between GOSR2 and syntaxin-5. Despite these perturbations, all SNARE complexes stayed intact during longer simulations. Thus, our data suggest that the milder course of disease in compound heterozygous PME is due to less severe impairment of the SNARE function

Lessons from non-canonical splicing

Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies

Ubiquitin-ligase AIP4 controls differential ubiquitination and stability of isoforms of the scaffold protein ITSN1.

At present, the role of ubiquitination of cargoes internalized from the plasma membrane is better understood than the consequences of ubiquitination of proteins comprising the endocytic machinery. Here, we show that the E3 ubiquitin ligase AIP4/ITCH contributes to the differential ubiquitination of isoforms of the endocytic scaffold protein intersectin1 (ITSN1). The major isoform ITSN1-s is monoubiquitinated, whereas the minor one, ITSN1-22a undergoes a combination of mono- and oligoubiquitination. The monoubiquitination is required for ITSN1-s stability, whereas the oligoubiquitination of ITSN1-22a causes its proteasomal degradation. This explains the observed low abundance of the minor isoform in cells. Thus, different modes of ubiquitination regulated by AIP4 have opposite effects on ITSN1 isoform stability

Novel isoform of adaptor protein ITSN1 forms homodimers via its C-terminus

Aim. Previously we have identified a novel isoform of endocytic adaptor protein ITSN1 designated as ITSN122a. Western blot revealed two immunoreactive bands of 120 and 250 kDa that corresponded to ITSN1-22a. The goal of this study was to investigate the possibility of dimer formation by the novel isoform. Methods. Dimerization ability of ITSN1-22a was tested by immunoprecipitation and subsequent Western blot analysis. To specify the region responsible for dimerization, site-directed mutagenesis and truncation analysis were carried out. Inhibition of endocytosis by potassium depletion and EGF stimulation of HEK293 were performed. Results. We have found that ITSN1-22a forms dimers in HEK293 cells. The dimerization of ITSN1-22a was mediated by C-terminal domain. We showed that cysteines C1016 and C1019 were involved in homodimerization. Inhibition of clathrin-mediated endocytosis and mitogen stimulation did not affect ITSN1-22a dimer formation. Conclusions. ITSN1-22a is the only one known ITSN1 isoform, which is capable to form homodimers via disulphide bonds. This could be important for the formation of protein complexes containing ITSN1 molecules

Differential recognition of ITSN2/Ese2 by the SH2 domains of Fyn, Abl1, PLCg1 and PI3KR1 in mouse tissues

Phosphorylation of endocytic adaptor ITSN2 that enabled its interaction with the SH2 domains of signaling proteins was recently reported. The aim of this study was to determine whether tissue-specific ITSN2 phosphorylation and subsequent recognition by phosphotyrosine-binding domains could occur in mouse tissues. Methods. In silico prediction of interaction motifs, expression of recombinant proteins in bacterial system, GST pull-down analysis, immunoblotting. Results. Analysis of phosphoproteomic data demonstrated tyrosine phosphorylation of mouse ITSN2 homologue, Ese2 protein. Scansite service was used to predict binding motifs for the SH2 domains of Fyn, Abl1, PLCg1 and PI3KR1 within Ese2. Comparison of ITSN2 and Ese2 sequences showed conservation of predicted interaction motifs between human and mouse. GST-fused SH2 domains of Fyn, Abl1, PLCg1 and PI3KR1 were obtained and used as phosphorylation «sensors» of tyrosine-based motifs within Ese2 molecule. Binding of Ese2 to the SH2 domains of Fyn and PLCg1 was observed in brain, lung and heart whereas SH2 domains of Abl1 and PI3KR1 interacted with Ese2 in lung and heart only. Conclusions. Differential Ese2/ SH2 interactions in tissues suggest that tissue-specific tyrosine phosphorylation might regulate specific binding of the Ese2 adaptor to the signaling molecules.Нещодавно виявлено фосфорилювання адаптора ендоцитозу ITSN2, що забезпечує впізнавання цього білка SH2-доменами білків, залучених до передачі мітогенного сигналу. Метою цієї роботи було перевірити, чи має взаємодія ITSN2 з SH2-вмісними біл- ками тканиноспецифічний характер. Методи. Передбачення мотивів взаємодії in silico, експресія білків у бактерійній системі та культурі клітин ссавців, преципітація з використанням білків, злитих з GST. Результати. Дані фосфопротеомних досліджень свідчать про фосфорилювання тирозинових залишків гомолога ITSN2 миші, білка Ese2. За допомогою сервісу Scansite у складі Ese2 передбачено мотиви взаємодії з доменами SH2 білків Fyn, Abl1, PLCg1 і PI3KR1. Порівняння послідовностей інтерсектинів людини та миші показало консервативність передбачених мотивів. Отримано злиті з GST домени SH2 білків Fyn, Abl1, PLCg1 і PI3KR1, які використано для преципітації білка Ese2 з лізатів мозку, легень і серця миші. Зв’язування Ese2 з доменами SH2 білків Fyn і PLCg1 спостерігали в усіх досліджуваних тканинах, тоді як домени SH2 білків Abl1 і PI3KR1 упізнавали Ese2 лише в легенях та серці. Висновки. Диференційне впізнавання Ese2/SH2 у тканинах дозволяє припустити, що тканиноспецифічне фосфорилювання регулює специфічне зв’язування адапторного білка Ese2 із сигнальними молекулами.Недавно показано фосфорилирование адаптора эндоцитоза ITSN2, опосредующее узнавание этого белка SH2-доменами белков, вовлеченных в передачу митогенного сигнала. Целью этой работы было проверить, имеет ли взаимодействие ITSN2 с SH2- содержащими белками тканеспецифический характер. Методы. Предсказание мотивов взаимодействия in silico, экспрессия белков в бактериальной системе и культуре клеток млекопитающих, преципитация с использованием белков, слитых с GST. Результаты. Данные фосфопротеомных исследований свидетельствуют о фосфорилировании тирозиновых остатков гомолога ITSN2 мыши, белка Ese2. При помощи сервиса Scansite в составе Ese2 предсказано мотивы взаимодействия с доменами SH2 белков Fyn, Abl1, PLCg1 и PI3KR1. Сравнение последовательностей интерсектинов человека и мыши показало консервативность предсказанных мотивов. Получены слитые с GST домены SH2 белков Fyn, Abl1, PLCg1 и PI3KR1, использованных для преципитации белка Ese2 из лизатов головного мозга, легких и сердца мыши. Связывание Ese2 с доменами SH2 белков Fyn и PLCg1 наблюдали во всех исследованных тканях, тогда как домены SH2 белков Abl1 и PI3KR1 узнавали Ese2 только в тканях легких и сердца. Выводы. Дифференциальное узнавание Ese2/SH2 в тканях позволяет предположить, что тканеспецифическое фосфорилирование опосредует специфическое связывание адаптерного белка Ese2 с сиг- нальными молекулами

CDK4 Regulates Lysosomal Function and mTORC1 Activation to Promote Cancer Cell Survival.

Cyclin-dependent kinase 4 (CDK4) is well-known for its role in regulating the cell cycle, however, its role in cancer metabolism, especially mTOR signaling, is undefined. In this study, we established a connection between CDK4 and lysosomes, an emerging metabolic organelle crucial for mTORC1 activation. On the one hand, CDK4 phosphorylated the tumor suppressor folliculin (FLCN), regulating mTORC1 recruitment to the lysosomal surface in response to amino acids. On the other hand, CDK4 directly regulated lysosomal function and was essential for lysosomal degradation, ultimately regulating mTORC1 activity. Pharmacologic inhibition or genetic inactivation of CDK4, other than retaining FLCN at the lysosomal surface, led to the accumulation of undigested material inside lysosomes, which impaired the autophagic flux and induced cancer cell senescence in vitro and in xenograft models. Importantly, the use of CDK4 inhibitors in therapy is known to cause senescence but not cell death. To overcome this phenomenon and based on our findings, we increased the autophagic flux in cancer cells by using an AMPK activator in combination with a CDK4 inhibitor. The cotreatment induced autophagy (AMPK activation) and impaired lysosomal function (CDK4 inhibition), resulting in cell death and tumor regression. Altogether, we uncovered a previously unknown role for CDK4 in lysosomal biology and propose a novel therapeutic strategy to target cancer cells. SIGNIFICANCE: These findings uncover a novel function of CDK4 in lysosomal biology, which promotes cancer progression by activating mTORC1; targeting this function offers a new therapeutic strategy for cancer treatment

A conformational switch driven by phosphorylation regulates the activity of the evolutionarily conserved SNARE Ykt6.

Ykt6 is a soluble N-ethylmaleimide sensitive factor activating protein receptor (SNARE) critically involved in diverse vesicular fusion pathways. While most SNAREs rely on transmembrane domains for their activity, Ykt6 dynamically cycles between the cytosol and membrane-bound compartments where it is active. The mechanism that regulates these transitions and allows Ykt6 to achieve specificity toward vesicular pathways is unknown. Using a Parkinson's disease (PD) model, we found that Ykt6 is phosphorylated at an evolutionarily conserved site which is regulated by Ca <sup>2+</sup> signaling. Through a multidisciplinary approach, we show that phosphorylation triggers a conformational change that allows Ykt6 to switch from a closed cytosolic to an open membrane-bound form. In the phosphorylated open form, the spectrum of protein interactions changes, leading to defects in both the secretory and autophagy pathways, enhancing toxicity in PD models. Our studies reveal a mechanism by which Ykt6 conformation and activity are regulated with potential implications for PD