DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

To elucidate how genomic sequences build transcriptional control networks, we need to understand the connection between DNA sequence and transcription factor binding and function. Binding predictions based solely on consensus predictions are limited, because a single factor can use degenerate sequence motifs and because related transcription factors often prefer identical sequences. The ETS family transcription factor, ETS1, exemplifies these challenges. Unexpected, redundant occupancy of ETS1 and other ETS proteins is observed at promoters of housekeeping genes in T cells due to common sequence preferences and the presence of strong consensus motifs. However, ETS1 exhibits a specific function in T cell activation; thus, unique transcriptional targets are predicted. To uncover the sequence motifs that mediate specific functions of ETS1, a genome-wide approach, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), identified both promoter and enhancer binding events in Jurkat T cells. A comparison with DNase I sensitivity both validated the dataset and also improved accuracy. Redundant occupancy of ETS1 with the ETS protein GABPA occurred primarily in promoters of housekeeping genes, whereas ETS1 specific occupancy occurred in the enhancers of T cell–specific genes. Two routes to ETS1 specificity were identified: an intrinsic preference of ETS1 for a variant of the ETS family consensus sequence and the presence of a composite sequence that can support cooperative binding with a RUNX transcription factor. Genome-wide occupancy of RUNX factors corroborated the importance of this partnership. Furthermore, genome-wide occupancy of co-activator CBP indicated tight co-localization with ETS1 at specific enhancers, but not redundant promoters. The distinct sequences associated with redundant versus specific ETS1 occupancy were predictive of promoter or enhancer location and the ontology of nearby genes. These findings demonstrate that diversity of DNA binding motifs may enable variable transcription factor function at different genomic sites

Use of Intravascular Imaging During Chronic Total Occlusion Percutaneous Coronary Intervention: Insights From a Contemporary Multicenter Registry

Background: Intravascular imaging can facilitate chronic total occlusion (CTO) percutaneous coronary intervention. Methods and Results: We examined the frequency of use and outcomes of intravascular imaging among 619 CTO percutaneous coronary interventions performed between 2012 and 2015 at 7 US centers. Mean age was 65.4±10 years and 85% of the patients were men. Intravascular imaging was used in 38%: intravascular ultrasound in 36%, optical coherence tomography in 3%, and both in 1.45%. Intravascular imaging was used for stent sizing (26.3%), stent optimization (38.0%), and CTO crossing (35.7%, antegrade in 27.9%, and retrograde in 7.8%). Intravascular imaging to facilitate crossing was used more frequently in lesions with proximal cap ambiguity (49% versus 26%, P<0.0001) and with retrograde as compared with antegrade‐only cases (67% versus 31%, P<0.0001). Despite higher complexity (Japanese CTO score: 2.86±1.19 versus 2.43±1.19, P=0.001), cases in which imaging was used for crossing had similar technical and procedural success (92.8% versus 89.6%, P=0.302 and 90.1% versus 88.3%, P=0.588, respectively) and similar incidence of major cardiac adverse events (2.7% versus 3.2%, P=0.772). Use of intravascular imaging was associated with longer procedure (192 minutes [interquartile range 130, 255] versus 131 minutes [90, 192], P<0.0001) and fluoroscopy (71 minutes [44, 93] versus 39 minutes [25, 69], P<0.0001) time. Conclusions: Intravascular imaging is frequently performed during CTO percutaneous coronary intervention both for crossing and for stent selection/optimization. Despite its use in more complex lesion subsets, intravascular imaging was associated with similar rates of technical and procedural success for CTO percutaneous coronary intervention. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT02061436

At the Speed of Sound: Gene Discovery in the Auditory System

As auditory genes and deafness-associated mutations are discovered at a rapid rate, exciting opportunities have arisen to uncover the molecular mechanisms underlying hearing and hearing impairment. Single genes have been identified to be pathogenic for dominant or recessive forms of nonsyndromic hearing loss, syndromic hearing loss, and, in some cases, even multiple forms of hearing loss. Modifier loci and genes have been found, and investigations into their role in the hearing process will yield valuable insight into the fundamental processes of the auditory system

Gene Discovery in the Auditory System: Characterization of Additional Cochlear-Expressed Sequences

To identify genes involved in hearing, 8494 expressed sequence tags (ESTs) were generated from a human fetal cochlear cDNA library in two distinct sequencing projects. Analysis of the first set of 4304 ESTs revealed clones representing 517 known human genes, 41 mammalian genes not previously detected in human tissues, 487 ESTs from other human tissues, and 541 cochlear-specific ESTs (http://hearing.bwh.harvard.edu ). We now report results of a DNA sequence similarity (BLAST) analysis of an additional 4190 cochlear ESTs and a comparison to the first set. Among the 4190 new cochlear ESTs, 959 known human genes were identified; 594 were found only among the new ESTs and 365 were found among ESTs from both sequencing projects. COL1A2 was the most abundant transcript among both sets of ESTs, followed in order by COL3A1, SPARC, EEF1A1, and TPTI. An additional 22 human homologs of known nonhuman mammalian genes and 1595 clusters of ESTs, of which 333 are cochlear-specific, were identified among the new cochlear ESTs. Map positions were determined for 373 of the new cochlear ESTs and revealed 318 additional loci. Forty-nine of the mapped ESTs are located within the genetic interval of 23 deafness loci. Reanalysis of unassigned ESTs from the prior study revealed 338 additional known human genes. The total number of known human genes identified from 8494 cochlear ESTs is 1449 and is represented by 4040 ESTs. Among the known human genes are 14 deafness-associated genes, including GJB2 (connexin 26) and KVLQT1. The total number of nonhuman mammalian genes identified is 43 and is represented by 58 ESTs. The total number of ESTs without sequence similarity to known genes is 4055. Of these, 778 also do not have sequence similarity to any other ESTs, are categorized into 700 clusters, and may represent genes uniquely or preferentially expressed in the cochlea. Identification of additional known genes, ESTs, and cochlear-specific ESTs provides new candidate genes for both syndromic and nonsyndromic deafness disorders

Changes in rat n-3 and n-6 fatty acid composition during pregnancy are associated with progesterone concentrations and hepatic FADS2 expression

The mechanisms responsible for changes to long-chain polyunsaturated fatty acid (LC PUFA) status during pregnancy have not been fully elucidated. Tissue samples were collected from virgin and pregnant (day 12 and 20) female rats. LC PUFA status, sex hormone concentrations and hepatic mRNA expression of FADS1, FADS2 and elongase were assessed. Day 20 gestation females had higher plasma and liver docosahexaenoic acid and lower arachidonic acid content than virgin females (P&lt;0.05). There was higher FADS2 mRNA expression during pregnancy (P=0.051). Progesterone and oestradiol concentrations positively correlated with hepatic FADS2 mRNA expression (P=0.043, P=0.004). Progesterone concentration positively correlated with hepatic n-6 docosapentaenoic acid content (P=0.006), and inversely correlated with intermediates in LC PUFA synthesis including n-3 docosapentaenoic acid, ?-linolenic acid and 20:2n-6 (P&lt;0.05). Changes in progesterone and oestradiol during pregnancy may promote the synthesis of LC PUFA via increased FADS2 expression

Expression studies of osteoglycin/mimecan (OGN) in the cochlea and auditory phenotype of Ogn-deficient mice

Genes involved in the hearing process have been identified through both positional cloning efforts following genetic linkage studies of families with heritable deafness and by candidate gene approaches based on known functional properties or inner ear expression. The latter method of gene discovery may employ a tissue- or organ-specific approach. Through characterization of a human fetal cochlear cDNA library, we have identified transcripts that are preferentially and/or highly expressed in the cochlea. High expression in the cochlea may be suggestive of a fundamental role for a transcript in the auditory system. Herein we report the identification and characterization of a transcript from the cochlear cDNA library with abundant cochlear expression and unknown function that was subsequently determined to represent osteoglycin (OGN). Ogn-deficient mice, when analyzed by auditory brainstem response and distortion product otoacoustic emissions, have normal hearing thresholds

Characterization of an abundant COL9A1 transcript in the cochlea with a novel 3' UTR:Expression studies and detection of miRNA target sequence

EST N66408 represents one of several large unique clusters expressed in the Morton human fetal cochlear cDNA library. N66408 is 575 bp in size and initial BLAST analysis of this sequence showed no homology to any known genes or expressed sequence tags (ESTs) from other organs or tissues. Sequence of the original cochlear clone from which N66408 was derived revealed that the corresponding cDNA was about 700 bp in size, including 125 bp at its 5′ end with homology to the 3′ end of COL9A1 in addition to 575 bp of novel sequence. RT-PCR analysis using primers specific to COL9A1 isoforms 1 and 2 detected expression of both isoforms in human fetal cochlea. Tissue in situ hybridization using the novel 3′ UTR sequence as probe showed abundant expression in spiral limbus and spiral ligament, and a moderate level of expression in the organ of Corti. dbEST analysis of ESTs specific to the 3′ UTR of COL9A1 showed 19 ESTs derived from various tissues; three polyadenylation sites were identified and the majority of these ESTs were derived from overlapping polyadenylation signals at the second site (position 749–758). Comparison of the 3′ UTR of human COL9A1 with its orthologs as well as with dbEST uncovered a highly conserved region around the overlapping polyadenylation signals at position 749–758 in mammals. A search of the microRNA database revealed a highly conserved target sequence for miR-9 immediately preceding the overlapping polyadenylation signals in the novel 3′ UTR of COL9A1, suggesting its role in posttranscriptional regulation of COL9A1