Transcription shapes 3D chromatin organization by interacting with loop-extruding cohesin complexes

Cohesin organizes mammalian interphase chromosomes by reeling chromatin fibers into dynamic loops (Banigan and Mirny, 2020; Davidson et al., 2019; Kim et al., 2019; Yatskevich et al., 2019). "Loop extrusion" is obstructed when cohesin encounters a properly oriented CTCF protein (Busslinger et al., 2017; de Wit et al., 2015; Fudenberg et al., 2016; Nora et al., 2017; Sanborn et al., 2015; Wutz et al., 2017), and recent work indicates that other factors, such as the replicative helicase MCM (Dequeker et al., 2020), can also act as barriers to loop extrusion. It has been proposed that transcription relocalizes (Busslinger et al., 2017; Glynn et al., 2004; Lengronne et al., 2004) or interferes with cohesin (Heinz et al., 2018; Jeppsson et al., 2020; Valton et al., 2021; S. Zhang et al., 2021), and that active transcription start sites function as cohesin loading sites (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), but how these effects, and transcription in general, shape chromatin is unknown. To determine whether transcription can modulate loop extrusion, we studied cells in which the primary extrusion barriers could be removed by CTCF depletion and cohesin's residence time and abundance on chromatin could be increased by Wapl knockout. We found evidence that transcription directly interacts with loop extrusion through a novel "moving barrier" mechanism, but not by loading cohesin at active promoters. Hi-C experiments showed intricate, cohesin-dependent genomic contact patterns near actively transcribed genes, and in CTCF-Wapl double knockout (DKO) cells (Busslinger et al., 2017), genomic contacts were enriched between sites of transcription-driven cohesin localization ("cohesin islands"). Similar patterns also emerged in polymer simulations in which transcribing RNA polymerases (RNAPs) acted as "moving barriers" by impeding, slowing, or pushing loop-extruding cohesins. The model predicts that cohesin does not load preferentially at promoters and instead accumulates at TSSs due to the barrier function of RNAPs. We tested this prediction by new ChIP-seq experiments, which revealed that the "cohesin loader" Nipbl (Ciosk et al., 2000) co-localizes with cohesin, but, unlike in previous reports (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), Nipbl did not accumulate at active promoters. We propose that RNAP acts as a new type of barrier to loop extrusion that, unlike CTCF, is not stationary in its precise genomic position, but is itself dynamically translocating and relocalizes cohesin along DNA. In this way, loop extrusion could enable translocating RNAPs to maintain contacts with distal regulatory elements, allowing transcriptional activity to shape genomic functional organization.

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modelling approaches.

A rational route to transformative decisions

According to Paul (Transformative experience, 1st edn, Oxford University Press, 2014), transformative experiences pose a challenge to decision theory since their value cannot be anticipated. Building on Pettigrew’s (in: Lambert, Schwenkler (eds) Becoming someone new: essays on transformative experience, choice, and change, Oxford University Press, pp 100–121, 2020) redescription, this paper presents a new approach to how and when transformative decisions can nevertheless be made rationally. Thanks to fundamental higher-order facts that apply to any kind of experience, an agent always at least knows the general shape of the utility space. This in combination with the knowledge about the non-transformative alternative in the choice set can enable rational decision-making despite the presence of a transformative experience. For example, this paper’s approach provides novel arguments for why gender transition (cf. McKinnon in Res Philosophica 92(2):419–440, 2015) or staying childfree (cf. Barnes in Philos Phenomenol Res 91(3):775–786, 2015) can be rational.

New records of Pseudotachidiidae from South Korea, including a key to species of the Pseudomesochrinae (Copepoda: Harpacticoida)

Two species of the marine harpacticoid family Pseudotachidiidae (Copepoda) are reported from subtidal sediments in the Southern Sea of Korea. Psammis wellsi sp. nov. (Danielsseniinae) is most closely related to P. longisetosa Sars, 1910 but differs from its European congener in the ventral ornamentation of the female genital double-somite, the dorsal ornamentation of the second abdominal somite in the male, the armature of the proximal endite of the maxillary syncoxa, the relative setal lengths and general shape of the female P5, and the relative length of the inner seta of the male P5 endopodal lobe and P6. The female of Pseudomesochra tatianae Drzycimski, 1968 is redescribed in detail, constituting the only other record of the species since its discovery at the type locality in western Norway. East Asian records of members of the four subfamilies currently recognized in the Pseudotachidiidae are summarized. Published and other records of the 23 described species in the Pseudomesochrinae are collated and their armature patterns of P1–P5 are tabulated and corrected where necessary. Pseudomesochra affinis (Sars, 1920) is removed from its synonymy with P. longifurcata T. Scott, 1902 and formally reinstated as a valid species. An updated female-based key to the 19 valid species of Pseudomesochra T. Scott, 1902 and four species of Keraia Willen & Dittmar, 2009 is presented.

The influence of scientific knowledge on mollusk and arthropod illustration

ABSTRACT Our attraction to fossils is almost as old as humans themselves, and the way fossils are represented has changed and evolved with technology and with our knowledge of these organisms. Invertebrates were the first fossils to be represented in books and illustrated according to their original form. The first worldwide illustrations of paleoinvertebrates by recognized authors, such as Christophorus Encelius and Conrad Gessner, considered only their general shape. Over time, paleoillustrations became more accurate and showed the position of organisms when they were alive and as they had appeared when found. Encyclopedic works such as those of the Sowerbys or Joachim Barrande have left an important legacy on fossil invertebrates, summarizing the knowledge of their time. Currently, new discoveries, techniques, and comparison with extant specimens are changing the way in which the same organisms are shown in life position, with previously overlooked taxonomically important elements being displayed using modern techniques. This chapter will cover the history of illustrations, unpublished nineteenth-century author illustrations, examples showing fossil reconstructions, new techniques and their influence on taxonomical work with regard to illustration, and the evolution of paleoinvertebrate illustration.

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports on the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of stereochemistry, established for RNA, that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure prediction accuracy.

STUDY OF FRUITS MORPHOLOGICAL FEATURES FOR 33 SPECIES BELONG TO CRUCIFERAE FAMILY IN IRAQ

The research was aimed to identify fruits morphological characteristics of 33 taxa belonging to the Lepidieae tribe from Brassicaceae. The characteristics of the fruit's general shape, apex shape, dimensions, colors, surface ornamentation, and beak were determined, the results indicated the importance of each of those characters in isolated species, In general, all the tribe's fruits were open capsule and short silicula. According to the dimensions of fruit, three species can be distinguished as a group with dimensions greater than 20mm, as in Brossardia, Coluteocarpus, and Didymophysa, and depending on the shape, it was possible to differentiate the species within this group, while the other species were less than 20 mm. in dimensions. They were distinguished by the general shapes, as the fruits of the Aethionema species were distinguished by their winged shaped, whereas the fruits of the genus Biscutella are bi-lobed, and the fruits have an inverted semi-triangular shape in the Capsella and peltate with prominent veins in the genus Horwoodia, or maybe peltate and longitudinally splintered with dark veins in Iberis, while the genus Sameraria fruit is circular to semi-circular characterized by intermediate appendages, while the individuals of the genus Isatis have linear-oblong fruits, and the species of both genus Lipidium and Hymenolobus were distinguished by their small and elliptic fruits and could be differentiated according to other fruits features. So could be conclude the importance of the characteristic of the general shape of the fruit firstly in species isolation then size, ornamentation, and some other traits.

THE ECONOMIC DIRECTIONS FOR RATIONALIZING THE SYSTEM OF PUBLIC FINANCE IN POLAND AS A RESULT OF THE EFFECTS OF THE COVID-19 EPIDEMIC

Public finance management has a very global nature. Here decisions are made that determine everything related to collecting and allocating public means. However, we need to realize that this level is also highly entangled politically, with political transformations accompanying changes of governments and cooperating party coalitions. This accounts for the fact that some general recommendations are formed, specifying the ways of managing public means. This is manifested in various slogans, such as “cheap state”, which stands for reduction of expenditure on administrative purposes. In this context some discussions take place in the government or in the parliament on seeking possibilities of limiting expenditure. Another direction of political disputes turns to public income. This is expressed, for example, in aiming at lowering tax bur-den. Thus public attention is drawn to two sides of the finance economy, namely on processes of gathering and allocating public means. In this system we often oversee a fundamental issue – instructions to manage public finance. As already stated, this cannot have a general shape, as there is no uniformity in the area of public finance even though the general assumption is the same for all areas.