Ligand dependent gene regulation by transient ERα clustered enhancers.

Unliganded Estrogen receptor alpha (ERα) has been implicated in ligand-dependent gene regulation. Upon ligand exposure, ERα binds to several EREs relatively proximal to the pre-marked, unliganded ERα-bound sites and affects transient but robust gene expression. However, the underlying mechanisms are not fully understood. Here we demonstrate that upon ligand stimulation, persistent sites interact extensively, via chromatin looping, with the proximal transiently ERα-bound sites, forming Ligand Dependent ERα Enhancer Cluster in 3D (LDEC). The E2-target genes are regulated by these clustered enhancers but not by the H3K27Ac super-enhancers. Further, CRISPR-based deletion of TFF1 persistent site disrupts the formation of its LDEC resulting in the loss of E2-dependent expression of TFF1 and its neighboring genes within the same TAD. The LDEC overlap with nuclear ERα condensates that coalesce in a ligand and persistent site dependent manner. Furthermore, formation of clustered enhancers, as well as condensates, coincide with the active phase of signaling and their later disappearance results in the loss of gene expression even though persistent sites remain bound by ERα. Our results establish, at TFF1 and NRIP1 locus, a direct link between ERα condensates, ERα enhancer clusters, and transient, but robust, gene expression in a ligand-dependent fashion.

Lineage-specific dynamics of loss of X upregulation during inactive-X reactivation.

In mammals, X chromosome dosage is balanced between sexes through the silencing of one X chromosome in females. Recent single-cell RNA sequencing analysis demonstrated that the inactivation of the X chromosome is accompanied by the upregulation of the active X chromosome (Xa) during mouse embryogenesis. Here, we have investigated if the reactivation of inactive-X (Xi) leads to the loss of Xa upregulation in different cellular or developmental contexts. We find that while Xi reactivation and loss of Xa upregulation are tightly coupled in mouse embryonic epiblast and induced pluripotent stem cells, that is not the case in germ cells. Moreover, we demonstrate that partial reactivation of Xi in mouse extra-embryonic endoderm stem cells and human B cells does not result in the loss of Xa upregulation. Finally, we have established a mathematical model for the transcriptional coordination of two X chromosomes. Together, we conclude that the reactivation of Xi is not always synchronized with the loss of Xa upregulation.

The role of nuclear organization in trans-splicing based expression of heat shock protein 90 in Giardia lamblia.

Hsp90 gene of G. lamblia has a split nature comprising two ORFs separated by 777 kb on chromosome 5. The ORFs of the split gene on chromosome 5 undergo transcription to generate independent pre-mRNAs that join by a unique trans-splicing reaction that remains partially understood. The canonical cis-acting nucleotide elements such as 5'SS-GU, 3'SS-AG, polypyrimidine tract and branch point adenine are present in the independent pre-mRNAs and therefore trans-splicing of Hsp90 must be assisted by spliceosomes in vivo. Using an approach of RNA-protein pull down, we show that an RNA helicase selectively interacts with HspN pre-mRNA. Our experiments involving high resolution chromosome conformation capture technology as well as DNA FISH show that the trans-spliced genes of Giardia are in three-dimensional spatial proximity in the nucleus. Altogether our study provides a glimpse into the in vivo mechanisms involving protein factors as well as chromatin structure to facilitate the unique inter-molecular post-transcriptional stitching of split genes in G. lamblia.

Single-Cell Analysis Reveals Partial Reactivation of X Chromosome instead of Chromosome-wide Dampening in Naive Human Pluripotent Stem Cells.

Recently, a unique form of X chromosome dosage compensation has been demonstrated in human preimplantation embryos, which happens through the dampening of X-linked gene expression from both X chromosomes. Subsequently, X chromosome dampening has also been demonstrated in female human pluripotent stem cells (hPSCs) during the transition from primed to naive state. However, the existence of dampened X chromosomes in both embryos and hPSCs remains controversial. Specifically, in preimplantation embryos it has been shown that there is inactivation of X chromosome instead of dampening. Here, we performed allelic analysis of X-linked genes at the single-cell level in hPSCs and found that there is partial reactivation of the inactive X chromosome instead of chromosome-wide dampening upon conversion from primed to naive state. In addition, our analysis suggests that the reduced X-linked gene expression in naive hPSCs might be the consequence of erasure of active X chromosome upregulation.

A study on axillary artery and its branching pattern among the population of West Bengal, India.

Variations in the branching pattern of the axillary artery have paramount importance among anatomists, surgeons and radiologists. A study was conducted on this topic in Kolkata, among the people of West Bengal, a state of India. The upper limbs of 70 cadavers were dissected bilaterally at the Department of Anatomy, Calcutta National Medical College, Kolkata, between 2008 and 2011. Among the study population, 52 cadavers (74.3%) were male and the rest were female, with average age 62.01 years (standard deviation = 6.58) and average height 1.59 meter (standard deviation = 0.096) respectively. The mean length of the axillary artery was 10.15 cm (standard deviation = 1.056). The superior thoracic, thoracoacromial and subscapular arteries were found to be constant branches of the axillary artery while the other branches showed considerable variations. Among those constant branches a high, significant correlation was found between the distance of origin of thoracoacromial artery from the outer border of the 1st rib and the length of the axillary artery, for the right and respectively the left upper limb of male cadavers. In females it showed a moderate, albeit significant correlation only. Similarly, the length of the axillary artery established a moderate correlation with the distance of origin of the superior thoracic and of the subscapular arteries on the right side of female cadavers. No other significant correlation was obtained.

Unilateral variation in the position of internal and external carotid arteries.

During the routine dissection of the neck region of a 77 years old male cadaver in the Department of Anatomy at Bankura Sammilani Medical College, a unilateral variation in the position and course of internal and external carotid arteries was noticed on the right side of neck. The internal carotid artery was anteromedial to the external carotid artery at the site of bifurcation of the common carotid artery. Knowledge of variation in the course and relation of internal and external carotid arteries is important for surgeons to perform neck surgery and also for the radiologists to interpret carotid system imaging.

Role of scaphoid in the abduction and adduction movements of wrist joint.

Being a carpal bone scaphoid has an important role in wrist movements. Wrist joint is a synovial modified ellipsoid joint where movements like flexion, extension and adduction, abduction take place around two axes (transverse and anteroposterior). These movements at the wrist joint are associated with considerable range of movements at the midcarpal joint, as same group of muscles act on both of these joints. A study has been done amongst 120 persons at the Institute of Postgraduate Medical Education and Research, Kolkata, West Bengal during the period from 1998-2000 to detect the important movements of scaphoid bone specially during the abduction and adduction of wrist joint (which occur in association with the intercarpal joints) and also to detect whether such movements have any speciality in the population of eastern part of India. It was found in this study that the scaphoid acts as a link bone between the two rows of carpal bones and prevents the buckling of midcarpal joint specially of the capitato-lunate joint interface.