Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here, we present a novel algorithm named CaTCH that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation, which is a single and biologically relevant parameter. By applying CaTCH to published Hi-C data sets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal boundary enrichment in CTCF and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that the likelihood that genes in a domain are coregulated during differentiation is also maximized at the scale of TADs. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the same scale. Our analysis suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the specific genomic position of regulatory sequences

PO-355 Enhancers mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer

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Radiation resistant LGAD design

In this paper, we report on the radiation resistance of 50-micron thick LGAD detectors manufactured at the Fondazione Bruno Kessler employing several different doping combinations of the gain layer. LGAD detectors with gain layer doping of Boron, Boron low-diffusion, Gallium, Carbonated Boron and Carbonated Gallium have been designed and successfully produced. These sensors have been exposed to neutron fluences up to $\phi_n \sim 3 \cdot 10^{16}\; n/cm^2$ and to proton fluences up to $\phi_p \sim 9\cdot10^{15}\; p/cm^2$ to test their radiation resistance. The experimental results show that Gallium-doped LGADs are more heavily affected by initial acceptor removal than Boron-doped LGAD, while the presence of Carbon reduces initial acceptor removal both for Gallium and Boron doping. Boron low-diffusion shows a higher radiation resistance than that of standard Boron implant, indicating a dependence of the initial acceptor removal mechanism upon the implant width. This study also demonstrates that proton irradiation is at least twice more effective in producing initial acceptor removal, making proton irradiation far more damaging than neutron irradiation.Comment: 22 pages, 17 figure

O processo de inclusão: da legislação à realidade: uma análise crítica

A presente monografia pretendeu fazer uma análise crítica do processo de construção da escola inclusiva, observando-se a compatibilização da legislação com o cotidiano escolar. Pretendeu-se verificar se a escola está atendendo à legislação no que se refere à formação do educador; se o espaço físico da mesma está suprindo às necessidades do aluno deficiente; se a escola está realizando a adaptação curricular de modo a atender aos alunos inclusivos; observar se os sistemas de apoio estão sendo ofertados; e, por fim, oferecer subsídios à comunidade escolar, no sentido de perceber a prescrição da lei e sua concomitante aplicação ao cotidiano escolar. Para tanto, a pesquisa foi realizada com 5 (cinco) professoras do ensino fundamental (1ª a 4ª séries) da rede regular de ensino público do DF(Taguatinga, Plano Piloto, Samambaia, Guará e Ceilândia). Os instrumentos utilizados foram a análise documental (leis, portarias, decretos) e a entrevista de caráter qualitativo/interpretativo abordando as categorias mencionadas, anteriormente, com a finalidade de subsidiar uma análise crítica do processo de inclusão e a compatibilização da legislação com o cotidiano escolar. Pode-se concluir, através deste estudo, que muitas modificações no âmbito da práxis ainda devem ser feitas e que a realidade escolar ainda não é condizente com a legislação. É notório o estabelecimento de medidas que visem assegurar os direitos conquistados, a melhoria da qualidade da educação, o investimento em uma ampla formação dos educadores, a remoção de barreiras físicas e atitudinais, a previsão e provisão de recursos materiais e humanos entre outras possibilidades. Nesta perspectiva potencializa- se um movimento de transformação da realidade para se conseguir reverter o percurso de exclusão de pessoas com ou sem deficiência no sistema educaciona

SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response. Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair. Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs’ biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence

Topologically associating domain boundaries are required for normal genome function

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1,2,3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.This work was supported by U.S. National Institutes of Health (NIH) grants to L.A.P. and A.V. (UM1HG009421). Research was conducted at the E.O. Lawrence Berkeley National Laboratory and performed under U.S. Department of Energy Contract DE-AC02-05CH11231, University of California (UC). Phenotyping performed by the UC Davis Mouse Biology Program (MBP) (www.mousebiology.org) was funded by an NIH administrative supplement to the KOMP2 grant, 3UM1OD023221-07S1, for phenotyping non-coding elements. Adyam Akeza was supported by the NIH Bridges to Baccalaureate Program Grant R25GM095401 via UC Berkeley. J.L.-R. is supported by the Spanish Ministerio de Ciencia e Innovacion (PID2020-113497GB-I00).Peer reviewe

Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes

Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response

Cardiovascular Risk with Non-Steroidal Anti-Inflammatory Drugs: Systematic Review of Population-Based Controlled Observational Studies

David Henry and colleagues reevaluate the evidence from observational studies on the cardiovascular risk associated with non-steroidal anti-inflammatory drugs