Mediator and cohesin connect gene expression and chromatin architecture

Transcription factors control cell-specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. Here we report that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with cohesin, which can form rings that connect two DNA segments. The cohesin-loading factor Nipbl is associated with mediator–cohesin complexes, providing a means to load cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by mediator and cohesin. Mediator and cohesin co-occupy different promoters in different cells, thus generating cell-type-specific DNA loops linked to the gene expression program of each cell.National Institutes of Health (U.S.) (Fellowship)Canadian Institutes of Health Research (Research Fellowship)National Institutes of Health (U.S.) (Grant R01 HG002668

Modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps

TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved "topological regions" that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with xeroderma pigmentosum and trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit. For more information about how to reproduce this modeling, see https://salilab.org/tfiih or the README file

Dementia and mild cognitive impairment in patients with Parkinson's disease Demência e transtorno cognitivo leve em pacientes com doença de Parkinson

The objective of this research was to assess the occurrence of cognitive impairment in 32 individuals (average age: 67.2 years old) with Parkinson' disease (PD). Procedures: clinical-neurological assessment; modified Hoehn and Yahr staging scale (HYS); standard neuropsychological battery of CERAD (Consortium to Establish a Registry for Alzheimer' Disease); Pfeffer questionnaire; and Clinical Dementia Rating. A comparison was made with a control group (CG), consisting of 26 individuals with similar age and educational level but without cognitive impairment. The PD patients showed an inferior performance in the CERAD battery when compared to the CG. Three PD sub-groups were characterised according to cognition: no cognitive impairment - 15 cases; mild cognitive impairment - 10; dementia - 7 cases. There was a significant association between motor disability (HYS) and the occurrence of dementia. Dementia and mild cognitive impairment frequently occur in PD patients and should be investigated in a routine way.<br>O objetivo desta pesquisa foi avaliar a ocorrência de déficits cognitivos em 32 indivíduos (idade média: 67,2 anos) com doença de Parkinson (DP). Procedimentos: avaliação clínico-neurológica, escala de Hoehn and Yahr modificada (EHY), bateria neurospicológica do CERAD (Consortium to Establish a Registry for Alzheimer' Disease), questionário de Pfeffer e escore clínico da demência (Clinical Dementia Rating). Foi feita comparação com grupo controle (GC) de 26 indivíduos sem declínio cognitivo, com idade e nível educacional similares. Os pacientes com DP tiveram desempenho inferior na bateria CERAD, quando comparados ao do GC. Foram caracterizados 3 subgrupos com PD segundo a cognição: sem déficits cognitivos - 15 casos; transtorno cognitivo leve - 10; demência - 7 casos. Houve associação entre comprometimento motor e ocorrência de demência. Demência e transtorno cognitivo leve são freqüentes em pacientes com DP e devem ser investigados de modo rotineiro

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference