How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes.

Nuclear eukaryotic genomes are transcribed by three related RNA polymerases (Pol), which transcribe distinct gene sets. Specific Pol recruitment is achieved through selective core promoter recognition by basal transcription factors (TFs). Transcription by an inappropriate Pol appears to be rare and to generate mostly unstable products. A collection of short noncoding RNA genes [for example, small nuclear RNA (snRNA) or 7SK RNA genes], which play essential roles in processes such as maturation of RNA molecules or control of Pol II transcription elongation, possess highly similar core promoters, and yet are transcribed for some by Pol II and for others by Pol III as a result of small promoter differences. Here we discuss the mechanisms of selective Pol recruitment to such promoters

HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs.

HCF-2 is a member of the host-cell-factor protein family, which arose in early vertebrate evolution as a result of gene duplication. Whereas its paralog, HCF-1, is known to act as a versatile chromatin-associated protein required for cell proliferation and differentiation, much less is known about HCF-2. Here, we show that HCF-2 is broadly present in human and mouse cells, and possesses activities distinct from HCF-1. Unlike HCF-1, which is excluded from nucleoli, HCF-2 is nucleolar-an activity conferred by one and a half C-terminal Fibronectin type 3 repeats and inhibited by the HCF-1 nuclear localization signal. Elevated HCF-2 synthesis in HEK-293 cells results in phenotypes reminiscent of HCF-1-depleted cells, including inhibition of cell proliferation and mitotic defects. Furthermore, increased HCF-2 levels in HEK-293 cells lead to inhibition of cell proliferation and metabolism gene-expression programs with parallel activation of differentiation and morphogenesis gene-expression programs. Thus, the HCF ancestor appears to have evolved into a small two-member protein family possessing contrasting nuclear versus nucleolar localization, and cell proliferation and differentiation functions

Mechanism of selective recruitment of RNA polymerases II and III to snRNA gene promoters

RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i.e., TATA-box-binding protein [TBP], TFIIB, and TFIIA for Pol II transcription and TBP and BRF2 for Pol III transcription) assemble to ensure specific Pol recruitment. TFIIB and BRF2 could each, in a mutually exclusive fashion, be recruited to SNAPc. In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters

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

Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation.

Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a closed to an open Pol III pre-initiation complex, a process dependent on the activity of the Bdp1 subunit. Here, we present a crystal structure of a Brf2-TBP-Bdp1 complex bound to DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis and in vitro biochemical assays. Our study provides a structural insight on how Bdp1 is assembled into TFIIIB complexes, reveals structural and functional similarities between Bdp1 and Pol II factors TFIIA and TFIIF, and unravels essential interactions with DNA and with the upstream factor SNAPc. Furthermore, our data support the idea of a concerted mechanism involving TFIIIB and RNA polymerase III subunits for the closed to open pre-initiation complex transition.Transcription initiation by RNA polymerase III requires TFIIIB, a complex formed by Brf1/Brf2, TBP and Bdp1. Here, the authors describe the crystal structure of a Brf2-TBP-Bdp1 complex bound to a DNA promoter and characterize the role of Bdp1 in TFIIIB assembly and pre-initiation complex formation

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