A conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation.

HOTAIRM1 is unlike most long non-coding RNAs in that its sequence is highly conserved across mammals. Such evolutionary conservation points to it having a role in key cellular processes. We previously reported that HOTAIRM1 is required to curb premature activation of downstream HOXA genes in a cell model recapitulating their sequential induction during development. We found that it regulates 3' HOXA gene expression by a mechanism involving epigenetic and three-dimensional chromatin changes. Here we show that HOTAIRM1 participates in proper progression through the early stages of neuronal differentiation. We found that it can associate with the HOXA1 transcription factor and contributes to its downstream transcriptional program. Particularly, HOTAIRM1 affects the NANOG/POU5F1/SOX2 core pluripotency network maintaining an undifferentiated cell state. HOXA1 depletion similarly perturbed expression of these pluripotent factors, suggesting that HOTAIRM1 is a modulator of this transcription factor pathway. Also, given that binding of HOTAIRM1 to HOXA1 was observed in different cell types and species, our results point to this ribonucleoprotein complex as an integral part of a conserved HOTAIRM1-HOXA1 regulatory axis modulating the transition from a pluripotent to a differentiated neuronal state.

The Talented LncRNAs: Meshing into Transcriptional Regulatory Networks in Cancer.

As a group of diseases characterized by uncontrollable cell growth, cancer is highly multifaceted in how it overrides checkpoints controlling proliferation. Amongst the regulators of these checkpoints, long non-coding RNAs (lncRNAs) can have key roles in why natural biological processes go haywire. LncRNAs represent a large class of regulatory transcripts that can localize anywhere in cells. They were found to affect gene expression on many levels from transcription to mRNA translation and even protein stability. LncRNA participation in such control mechanisms can depend on cell context, with given transcripts sometimes acting as oncogenes or tumor suppressors. Importantly, the tissue-specificity and low expression levels of lncRNAs make them attractive therapeutic targets or biomarkers. Here, we review the various cellular processes affected by lncRNAs and outline molecular strategies they use to control gene expression, particularly in cancer and in relation to transcription factors.

Positive Psychological Factors and Life Themes in Relation to Health Outcomes in Women Living with HIV.

BACKGROUND: This mixed methods study identified positive psychological factors and life themes expressed in autobiographical narratives of predominantly Black women living with HIV (WLWH) and investigated these in relation to depressive symptoms, antiretroviral therapy (ART) adherence (≥ 95% of time), and undetectable HIV viral load (VL) (< 80 copies/ml). METHOD: Ninety-eight WLWH from the Women's Interagency HIV Study Chicago site (M age = 45.3; 91% Black) narrated three autobiographical life turning points, reliably coded for positive factors and life themes. ART adherence, VL and depressive symptoms, assessed with Center for Epidemiologic Studies Depression Scale total score (TOT) including its four factors (negative affect (NA), positive affect (PA), somatic symptoms (SS), and interpersonal problems (IP)), were collected over two time points: concurrently with narratives and 6 months later. Composite scores across the two time points were used in all analyses. RESULTS: Ten positive psychological factors (gratitude, insight, compassion, meaning-making, acceptance, mindfulness, generativity, optimism, self-reliance, and benevolent God beliefs) and three positive life themes (health improvements, positive relationships, and accomplishments) were identified in narratives. Higher accomplishments, overall positive factors, insight, mindfulness, self-reliance, optimism, meaning-making, and acceptance related to lower depressive symptoms (TOT, NA, SS, or IP). Positive factors and life themes did not significantly relate to PA. Higher compassion related to higher ART adherence. Higher accomplishments related to undetectable VL independent of ART adherence. CONCLUSION: Findings that positive psychological factors and life accomplishments may relate to better health, especially to lower depression, potentially contribute to developing positive psychology interventions for Black WLWH.

Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP.

Chromatin immunoprecipitation (ChIP) is used to probe the presence of proteins and/or their posttranslational modifications on genomic DNA. This method is often used alongside chromosome conformation capture approaches to obtain a better-rounded view of the functional relationship between chromatin architecture and its landscape. Since the inception of ChIP, its protocol has been modified to improve speed, sensitivity, and specificity. Combining ChIP with deep sequencing has recently improved its throughput and made genome-wide profiling possible. However, genome-wide analysis is not always the best option, particularly when many samples are required to study a given genomic region or when quantitative data is desired. We recently developed carbon copy-ChIP (2C-ChIP), a new form of the high-throughput ChIP analysis method ideally suited for these types of studies. 2C-ChIP applies ligation-mediated amplification (LMA) followed by deep sequencing to quantitatively detect specified genomic regions in ChIP samples. Here, we describe the generation of 2C-ChIP libraries and computational processing of the resulting sequencing data.

The Costs of Silencing the Self and Divided Self in the Context of Physical Abuse, Racial/Ethnic Identity, and Medication Adherence in Women Living with HIV.

Racial/ethnic minority status and physical abuse history are risk factors for higher mortality rates and lower adherence to antiretroviral therapy (ART) in women living with HIV (WLWH) in the United States. The current study tested the hypotheses that minority status and physical abuse history might lead women to silence the self (minimize and hide thoughts and feelings in order to avoid relational conflict, loss, and/or abuse) as measured by the Silencing the Self Scale (STSS), and that STSS might mediate and moderate relationships of physical abuse and racial/ethnic minority status with ART adherence. Divided Self (DS; acting in ways inconsistent with inner thoughts and feelings), an STSS subscale, was targeted for study along with the total STSS score. Participants were 513 women from the U.S. Women's Interagency HIV Study (M age = 46; 387, 75%, Black; 66, 13%, Hispanic; 60, 12%, White). Multiple logistic regressions indicated that across all racial/ethnic groups, physical abuse history related to higher DS and lower adherence. DS significantly mediated relationships between abuse and adherence. Compared to White women, Black women demonstrated worse ART adherence, but had lower total STSS. Racial/ethnic minority women and women with a physical abuse history who had higher DS had lower adherence than other groups. Results indicate that being a racial/ethnic minority or having a history of physical abuse may increase vulnerability to the deleterious effects of DS on ART adherence, findings that can help inform interventions to decrease health disparities in WLWH.

2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.

BACKGROUND: Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. RESULTS: Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. CONCLUSIONS: 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis.

Life Lessons from Women with HIV: Mutuality, Self-Awareness, and Self-Efficacy.

Women with HIV in the United States cope with multiple traumas that influence adherence to antiretroviral therapy (ART) and well-being. Narrative themes from three life turning points and a projective story task were compared for two groups of women with HIV (HIV well-managed vs. HIV not well-managed, matched on demographics and narrative word count) to understand predictors of successful outcomes. The well-managed group (n = 10) was virally suppressed and reported ≥95% ART adherence; the not well-managed group (n = 10) had detectable viral load and reported <95% ART adherence. Women were predominantly African American with low socioeconomic status and averaged 46.51 years. A three-stage coding process (with coders blind to group status in stages 1 and 2) involved (1) line by line thematic analyses that generated 155 subthemes reflecting six content areas (interpersonal relationships; culture and community; sense of self; relationship to past, present, and future experiences; self-care; and motivators for change); (2) absence/presence of the 155 subthemes was compared for the two groups; the frequency of 37 subthemes was found to significantly differ; and (3) the 37 differentiating subthemes were conceptually integrated, revealing that the well-managed group's narratives more frequently reflected (a) mutuality (growth-fostering relationships involving reciprocal care and empathy); (b) self-awareness (recognition of personal strengths and weaknesses and multiple factors contributing to life choices and trajectories); and (c) self-efficacy (active coping, self-advocacy, and utilizing resources). Implications for treatment and interconnections among themes are discussed, emphasizing the factors that enable women to care for themselves and others.